diff --git a/tools/phylophlan/.shed.yml b/tools/phylophlan/.shed.yml
new file mode 100644
index 0000000000..3177886007
--- /dev/null
+++ b/tools/phylophlan/.shed.yml
@@ -0,0 +1,10 @@
+name: phylophan
+owner: bgruening
+description: Tool for high-resolution phylogenetic analysis and taxonomic classification of microbial genomes and MAGs.
+homepage_url: https://github.com/biobakery/phylophlan
+long_description: PhyloPhlAn is a comprehensive and scalable pipeline for phylogenetic profiling of microbial genomes and metagenomes. It supports accurate species- and strain-level classification, including for metagenome-assembled genomes (MAGs), and can reconstruct large-scale phylogenies using clade-specific informative markers.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/phylophlan
+categories:
+  - Metagenomics
+  - Sequence Analysis
+  - Phylogenetics
\ No newline at end of file
diff --git a/tools/phylophlan/macros.xml b/tools/phylophlan/macros.xml
new file mode 100644
index 0000000000..8c8a67645d
--- /dev/null
+++ b/tools/phylophlan/macros.xml
@@ -0,0 +1,102 @@
+<macros>
+    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    
+    <!-- Requirements -->
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">phylophlan</requirement>
+            <yield/>
+            <!-- phylophlan uses python disutils which was removed in python 3.12 -->
+            <requirement type="package" version="3.11">python</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_phylophlan">
+        <expand macro="requirements">
+            <requirement type="package" version="2.1.11">diamond</requirement>
+            <requirement type="package" version="2.16.0">blast</requirement>
+            <requirement type="package" version="12.0">usearch</requirement>
+            <requirement type="package" version="5.3">muscle</requirement>
+            <requirement type="package" version="7.526">mafft</requirement>
+            <requirement type="package" version="2.1.10">fasttree</requirement>
+            <requirement type="package" version="8.2.12">raxml</requirement>
+            <requirement type="package" version="2.4.0">iqtree</requirement>
+            <requirement type="package" version="5.7.8">astral-tree</requirement>
+        </expand>
+    </xml>
+    <xml name="requirements_assign_sgbs">
+        <expand macro="requirements">
+            <requirement type="package" version="2.3">mash</requirement>
+        </expand>
+    </xml>
+    
+    <!-- PhyloPhlAn input blocks -->
+    <xml name="config_select_software">
+        <conditional name="db">
+            <param name="type" type="select" argument="-d / -t" label="Database marker type">
+                <option value="n">Nucleotides</option>
+                <option value="a">Amino acids</option>
+            </param>
+            <when value="n">
+                <param argument="--db_dna" type="select" label="Nucleotide database">
+                    <option value="makeblastdb">makeblastdb</option>
+                </param>
+                <param argument="--map_dna" type="select" label="Map genomes using">
+                    <option value="blastn">blastn</option>
+                    <option value="tblastn">tblastn</option>
+                    <option value="diamond">diamond</option>
+                </param>
+            </when>
+            <when value="a">
+                <param argument="--db_aa" type="select" label="Amino acid database">
+                    <option value="diamond">diamond</option>
+                    <option value="usearch">usearch</option>
+                </param>
+                <param argument="--map_aa" type="select" label="Map proteomes using">
+                    <option value="diamond">diamond</option>
+                    <option value="usearch">usearch</option>
+                </param>
+                <param argument="--map_dna" type="select" optional="true" label="Map genomes using">
+                    <option value="diamond">diamond</option>
+                    <option value="blastn">blastn</option>
+                    <option value="tblastn">tblastn</option>
+                </param>
+            </when>
+        </conditional>
+        <param argument="--msa" type="select" label="Multiple-sequence alignment">
+            <option value="mafft">mafft</option>
+            <option value="muscle">muscle</option>
+            <!-- <option value="opal">opal</option> -->
+            <!-- <option value="upp">upp</option> -->
+        </param>
+        <yield/>
+    </xml>
+    <xml name="config_supertree_maas">
+        <!-- WARNING! PhyloPhlAn sends the second column of the file to raxml via the command line. -->
+        <conditional name="maas">
+            <param name="source" type="select" label="Substitution models"
+                   help="A mapping file that specifies the RAxML substitution model to use for each specific marker for gene tree reconstruction. &lt;br&gt;This file must be present for every Supertree analysis, but is only used if raxml is selected for --gene_trees1/2. Otherwise you can ignore the parameter. &lt;br&gt;The included file lists the substitution models for each of the 400 universal markers of the PhyloPhlAn database.">
+                <option value="default">Included PhyloPhlAn models file</option>
+                <option value="history">From History</option>
+            </param>
+            <when value="default"/>
+            <when value="history">
+                <param name="models" type="data" format="tabular" label="Substitution models"
+                       help="The file should be a mapping from amino acid markers to their respective (raxml) substitution model. It should be a two-columns file separated by TAB, where the first column specifies the name of the marker and the second the name of the substitution model to use. e.g. &lt;br&gt;p0000	PROTCATLG&lt;br&gt;...&lt;br&gt;p0004	PROTCATLG&lt;br&gt;p0005	PROTCATCPREVF"/>
+            </when>
+        </conditional>
+    </xml>
+    
+    <!-- Misc -->
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">PhyloPhlAn</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41467-020-16366-7</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/tools/phylophlan/phylophlan.xml b/tools/phylophlan/phylophlan.xml
new file mode 100644
index 0000000000..893dbe29a1
--- /dev/null
+++ b/tools/phylophlan/phylophlan.xml
@@ -0,0 +1,583 @@
+<tool id="phylophlan" name="PhyloPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>
+        microbial genome characterization and phylogenetic analysis
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements_phylophlan"/>
+    <required_files>
+        <include path="validate_mapping_file.py"/>
+        <include path="test-data/phylophlan.tsv"/>
+    </required_files>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        
+        #if "nt" in $config.analysis.value
+            #set $db_type = "n"
+        #else if "aa" in $config.analysis.value
+            #set $db_type = "a"
+        #else
+            #set $db_type = $config.db.type
+        #end if
+        
+        mkdir -p 'input/' &&
+        #for $i in $input
+            #set $identifier = re.sub('[^\w\-\._]', '_', str($i.element_identifier))
+            ln -s '$i' 'input/${identifier}' &&
+        #end for
+        
+        mkdir -p 'database/' &&
+        #if $database.file_ext == "fasta"
+            ln -s '$database' 'database/database.f${db_type}a' &&
+        #else
+            gzip -d -c '$database' > 'database/database.f${db_type}a' &&
+        #end if
+        
+        phylophlan_write_config_file
+            -o config.cfg
+            -d $db_type
+            #if $trimming.trim != "None"
+                --trim trimal
+            #end if
+            
+            #if $config.analysis == "supermatrix_nt"
+                --db_dna makeblastdb
+                --map_dna blastn
+                --msa mafft
+                --tree1 fasttree
+                --tree2 raxml
+            #else if $config.analysis == "supertree_nt"
+                --db_dna makeblastdb
+                --map_dna blastn
+                --msa mafft
+                --gene_tree1 fasttree
+                --gene_tree2 raxml
+                --tree1 astral
+            #else if $config.analysis == "supermatrix_aa"
+                --db_aa diamond
+                --map_dna diamond
+                --map_aa diamond
+                --msa mafft
+                --tree1 fasttree
+                --tree2 raxml
+            #else if $config.analysis == "supertree_aa"
+                --db_aa diamond
+                --map_dna diamond
+                --map_aa diamond
+                --msa mafft
+                --gene_tree1 fasttree
+                --gene_tree2 raxml
+                --tree1 astral
+            #else
+                #if $config.db.type == "n"
+                    --db_dna $config.db.db_dna
+                    --map_dna $config.db.map_dna
+                #else if $config.db.type == "a"
+                    --db_aa $config.db.db_aa
+                    --map_aa $config.db.map_aa
+                    #if $config.db.map_dna
+                        --map_dna $config.db.map_dna
+                    #end if
+                #end if
+                --msa $config.msa
+                
+                #if $config.analysis == "custom_supertree"
+                    --gene_tree1 $config.gene_tree.gene_tree1
+                    #if $config.gene_tree.gene_tree2
+                        --gene_tree2 $config.gene_tree.gene_tree2
+                    #end if
+                    --tree1 $config.tree.tree1
+                #else
+                    --tree1 $config.tree.tree1
+                    #if $config.tree.tree2
+                        --tree2 $config.tree.tree2
+                    #end if
+                #end if
+            #end if
+            
+            $force_nucleotides
+            --overwrite &&
+
+        ## fixing astral binary path
+        sed -i "\%program_name.*astral%s%=.*%= `which astral`%" config.cfg &&
+        
+        #if "supertree" in $config.analysis.value
+            #if $config.maas.source == "history"
+                #set $maas_file = $config.maas.models
+            #else
+                #set $maas_file = $__tool_directory__ + '/test-data/phylophlan.tsv'
+            #end if
+            python '$__tool_directory__/validate_mapping_file.py' '$maas_file' &&
+        #end if
+        
+        phylophlan
+            -i input
+            -o output
+            -d database
+            -f config.cfg
+            
+            --diversity $diversity
+            $accuracy
+            
+            #if "supertree" in $config.analysis.value
+                --maas '$maas_file'
+            #end if
+            
+            --min_num_proteins $quality.min_num_proteins
+            --min_len_protein $quality.min_len_protein
+            #if $quality.min_num_markers
+                --min_num_markers $quality.min_num_markers
+            #end if
+            #if $quality.min_num_entries
+                --min_num_entries $quality.min_num_entries
+            #end if
+            
+            $quality.remove_only_gaps_entries
+            #if not $quality.remove_only_gaps_entries
+                $quality.remove_fragmentary_entries
+                #if $quality.fragmentary_threshold
+                    --fragmentary_threshold $quality.fragmentary_threshold
+                #end if
+            #end if
+            
+            #if $trimming.trim != "None"
+                --trim $trimming.trim
+                #if $trimming.trim.value in {'gap_perc', 'greedy'}
+                    --gap_perc_threshold $trimming.gap_perc_threshold
+                #end if
+                #if $trimming.trim.value in {'not_variant', 'greedy'}
+                    --not_variant_threshold $trimming.not_variant_threshold
+                #end if
+            #end if
+            
+            #if $sample.subsample != "default"
+                --subsample $sample.subsample
+            #end if
+            #if $sample.scoring_function
+                --scoring_function $sample.scoring_function
+            #end if
+            #if $sample.submat
+                --submat $sample.submat
+            #end if
+            
+            --unknown_fraction $quality.unknown_fraction
+            $quality.convert_N2gap
+            $force_nucleotides
+            $sort
+            $mrate.mutation_rates
+            
+            -t $db_type
+            --nproc \${GALAXY_SLOTS:-4}
+            --verbose
+    ]]></command>
+    <inputs>
+        <!-- Todo: Handle input/database files with unexpected filenames/designations -->
+        <param name="input" type="data_collection" collection_type="list" format="fasta,fasta.gz" label="Input genomes and/or proteomes"
+               help="In order for PhyloPhlAn to detect the input files in the collection, the fasta files MUST have the extensions '.fna' for nucleotide sequences and '.faa' for amino acid sequences. (Or '.fna.gz' and '.faa.gz' respectively.)"/>
+        <param name="database" type="data" format="fasta,fasta.gz" label="Reference database of markers"/>
+        <conditional name="config">
+            <param name="analysis" type="select" label="Configure which external software to use for the analysis">
+                    <option value="supermatrix_nt">Nucleotide supermatrix (blast, mafft, fasttree, raxml)</option>
+                    <option value="supertree_nt">Nucleotide supertree (blast, mafft, fasttree, raxml, astral)</option>
+                    <option value="supermatrix_aa">Amino acid supermatrix (diamond, mafft, fasttree, raxml)</option>
+                    <option value="supertree_aa">Amino acid supertree (diamond, mafft, fasttree, raxml, astral)</option>
+                    <option value="custom_supermatrix">Custom supermatrix (or concatenation) pipeline</option>
+                    <option value="custom_supertree">Custom supertree (or gene trees) pipeline</option>
+            </param>
+            <when value="supermatrix_nt"/>
+            <when value="supertree_nt">
+                <expand macro="config_supertree_maas"/>
+            </when>
+            <when value="supermatrix_aa"/>
+            <when value="supertree_aa">
+                <expand macro="config_supertree_maas"/>
+            </when>
+            <when value="custom_supermatrix">
+                <expand macro="config_select_software">
+                    <section name="tree" expanded="true" title="Phylogeny">
+                        <param argument="--tree1" type="select" label="Build phylogeny">
+                            <option value="fasttree">fasttree</option>
+                            <option value="raxml">raxml</option>
+                            <option value="iqtree">iqtree</option>
+                            <!-- <option value="astral">astral</option>
+                                Astal crashed when I tried it. Does it only work in the supertree pipeline? -->
+                            <!-- <option value="astrid">astrid</option> -->
+                        </param>
+                        <param argument="--tree2" type="select" optional="true" label="Refine phylogeny">
+                            <option value="raxml">raxml</option>
+                        </param>
+                    </section>
+                </expand>
+            </when>
+            <when value="custom_supertree">
+                <expand macro="config_supertree_maas"/>
+                    <!-- PhyloPhlAn always requires a substitution model to be provided, but only uses it when
+                         'gene_tree1' is raxml. I have no idea what this means for wrapping. -->
+                <expand macro="config_select_software">
+                    <section name="gene_tree" expanded="true" title="Single-gene trees (Supertree)">
+                        <param argument="--gene_tree1" type="select" label="Build phylogenies">
+                            <option value="fasttree">fasttree</option>
+                            <option value="raxml">raxml</option>
+                            <option value="iqtree">iqtree</option>
+                        </param>
+                        <param argument="--gene_tree2" type="select" optional="true" label="Refine phylogenies">
+                            <option value="raxml">raxml</option>
+                        </param>
+                    </section>
+                    <section name="tree" title="Phylogeny">
+                        <param argument="--tree1" type="select" label="Build phylogeny">
+                            <!-- The documentation says only astral is allowed for the gene tree pipeline,
+                                 but phylophlan_write_config also allows astrid.
+                                 A comment clarifies that the tool must support a "consensus approach".
+                                 I did not find out if astrid supports this,
+                                 but I found several performance comparisons with astral, so I left it in. -->
+                            <option value="astral">astral</option>
+                            <!-- <option value="astrid">astrid</option> -->
+                        </param>
+                        <!-- When phylophlan_write_config writes a config for the gene tree pipeline it ignores the 'tree2'
+                             parameter as it does not expect there to be a tool that refine a consensus phylogeny (yet). -->
+                    </section>
+                </expand>
+            </when>
+        </conditional>
+        <param argument="--diversity" type="select" label="Diversity" help="Set parameters to default values in accordance with the expected diversity of the phylogeny to be build.">
+            <option value="low">low (for species- and strain-level phylogenies)</option>
+            <option value="medium">medium (for genus- and family-level phylogenies)</option>
+            <option value="high">high (for tree-of-life and higher-ranked taxonomic phylogenies)</option>
+        </param>
+        <param name="accuracy" type="boolean" truevalue="--fast" falsevalue="--accurate" argument="--fast"
+               label="Reduce the number of considered phylogenetic positions (faster, but less accurate)"
+               help="Affected parameters depend on the --diversity level."/>
+        <section name="quality" title="Input quality thresholds" help="Discard input genomes/proteomes and phylogenetic markers with insufficient quality.">
+            <!-- If PhyloPhlAn uses a consistent default value, I display it, otherwise the filed is optional.
+                 Should the default change it must be changed here as well. -->
+            <param argument="--min_num_proteins" type="integer" value="1" label="Minimum proteins per proteome"/>
+            <param argument="--min_len_protein" type="integer" value="50" label="Minimum protein length"/>
+            <param argument="--min_num_markers" type="integer" value="1" label="Minimum mapped markers"
+                   help="Discard input genomes or proteomes that map to less markers."/> <!-- default changes for special -d databases -->
+            <param argument="--min_num_entries" type="integer" value="4" label="Minimum found entries."
+                   help="Discard markers that are found in less inputs than this."/>
+            <param argument="--remove_fragmentary_entries" type="boolean" truevalue="--remove_fragmentary_entries" falsevalue=""
+                   label="Remove fragmentary entries"/>
+            <param argument="--fragmentary_threshold" type="float" optional="true" label="Fragmentary threshold"
+                   help="The fraction of gaps in the MSA to be considered fragmentary."/>
+            <param argument="--remove_only_gaps_entries" type="boolean" truevalue="--remove_only_gaps_entries" falsevalue=""
+                   label="Remove gap-only entries"
+                   help="Remove entries composed only of gaps (&#34;-&#34;)&lt;br&gt;Equivalent to &#34;--remove_fragmentary_entries --fragmentary_threshold 1&#34;."/>
+            <param argument="--unknown_fraction" type="float" value="0.3" max="1.0" label="Maximum unknown fraction"
+                   help="The fraction of unknowns ('X' and '-') allowed in each column of the MSA of the markers."/>
+            <param argument="--convert_N2gap" type="boolean" truevalue="--convert_N2gap" falsevalue=""
+                   label="Convert Ns in nucleotides MSAs to gaps ('-') after MSAs"/>
+        </section>
+        <conditional name="trimming">
+            <param argument="--trim" type="select" label="Trimming strategy">
+                <option value="None">Default</option>
+                <option value="gap_trim">Use trimAl (gap_trim)</option>
+                <option value="gap_perc">Gap percentage</option>
+                <option value="not_variant">Not a variant</option>
+                <option value="greedy">All (greedy)</option>
+            </param>
+            <when value="None"/>
+            <when value="gap_trim"/>
+            <when value="gap_perc">
+                <param argument="--gap_perc_threshold" type="float" optional="true" label="Gap threshold"
+                       help="Remove columns with a percentage of gaps above the threshold."/>
+            </when>
+            <when value="not_variant">
+                <param argument="--not_variant_threshold" type="float" optional="true" label="Variant threshold"
+                       help="Remove columns where at least one amino acid appears more often than the threshold frequency."/>
+            </when>
+            <when value="greedy">
+                <param argument="--gap_perc_threshold" type="float" optional="true" label="Gap threshold"
+                       help="Remove columns with a percentage of gaps above the threshold."/>
+                <param argument="--not_variant_threshold" type="float" optional="true" label="Variant threshold"
+                       help="Remove columns where at least one amino acid appears more often than the threshold frequency."/>
+            </when>
+        </conditional>
+            <section name="sample" title="Subsampling"
+                     help="Retain only a certain amount of phylogenetically relevant marker positions.">
+            <param argument="--subsample" type="select" label="How many positions per marker should be retained?">
+                <option value="default">Default</option>
+                <option value="full">All</option>
+                <option value="onethousand">Retain up-to 1000 positions</option>
+                <option value="sevenhundred">Retain up-to 700 positions</option>
+                <option value="fivehundred">Retain up-to 500 positions</option>
+                <option value="threehundred">Retain up-to 300 positions</option>
+                <option value="onehundred">Retain up-to 100 positions</option>
+                <option value="fifty">Retain up-to 50 positions</option>
+                <option value="twentyfive">Retain up-to 25 positions</option>
+                <option value="tenpercent">Retain 10%</option>
+                <option value="twentyfivepercent">Retain 25%</option>
+                <option value="fiftypercent">Retain 50%</option>
+                <!-- <option value="phylophlan"></option> -->
+            </param>
+            <param argument="--scoring_function" type="select" optional="true" label="Scoring function"
+                   help="Used to rank MSA positions to decide which to retain.">
+                <!-- Todo: explain functions -->
+                <option value="muscle"></option>
+                <option value="trident"></option>
+            </param>
+            <param argument="--submat" type="select" label="Substitution matrix"
+                   help="The scoring functions use a substitution matrix to evaluate the expected substitution rates of amino acids.">
+                <!-- technically optional, but always defaults to pfasum60 -->
+                <option value="pfasum60"></option>
+                <option value="vtml200"></option>
+                <option value="vtml240"></option>
+                <option value="miqs"></option>
+            </param>
+        </section>
+        <param argument="--force_nucleotides" type="boolean" truevalue="--force_nucleotides" falsevalue=""
+               label="Force nucleotides"
+               help="Force PhyloPhlAn to use nucleotide sequences for the phylogenetic analysis, even in the case of a database of amino acids."/>
+        <param argument="--sort" type="boolean" truevalue="--sort" falsevalue=""
+               label="Sort markers"
+               help="Force PhylophlAn to consider markers in a specific order when concatenating sequences."/>
+               <!-- Sort is only used for super-matrix approach (concatenation) -->
+        <section name="mrate" title="Mutation rates">
+            <param argument="--mutation_rates" type="boolean" truevalue="--mutation_rates" falsevalue=""
+                   label="Calculate mutation rates"
+                   help="If specified will produced a mutation rates table for each of the aligned markers and a
+                            summary table for the concatenated MSA. This operation can take a long time to finish"/>
+            <param name="discard_individual_tables" type="boolean" checked="true" label="Discard individual mutation rate tables."
+                   help="Only add the summary table to the galaxy history. The individual mutation rates are still calculated. If unchecked, they will be accumulated in a collection."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt">
+            <!-- Parse shorter designations for known files and assign a primary output. -->
+            <!-- RAxML -->
+            <discover_datasets pattern="(?P&lt;designation&gt;.+(bestTree|result))\.input_refined\.tre" format="newick" visible="true" directory="output" assign_primary_output="true"/>
+            <discover_datasets pattern="input_(?P&lt;designation&gt;resolved\.tre)" format="newick" visible="true" directory="output" assign_primary_output="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+(info|log))\.input_refined\.tre" format="txt" visible="true" directory="output"/>
+            <!-- fasttree -->
+            <discover_datasets pattern="(?P&lt;designation&gt;input\.tre)$" format="newick" visible="true" directory="output" assign_primary_output="true"/>
+            <!-- iqtree -->
+            <discover_datasets pattern="(?P&lt;designation&gt;input\.tre\.(bionj|treefile))" format="newick" visible="true" directory="output" assign_primary_output="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;input\.tre\.iqtree)" format="txt" visible="true" directory="output"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;input\.tre\.mldist)" format="mldist" visible="true" directory="output"/>
+            <!-- misc -->
+            <discover_datasets pattern="input_(?P&lt;designation&gt;.+\.aln)" format="fasta" visible="true" directory="output"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;mutation_rates)\.tsv" format="tabular" visible="true" directory="output"/>
+            <!-- astral -->
+            <discover_datasets pattern="(?P&lt;designation&gt;gene_trees\.tre)" format="newick" visible="true" directory="output/tmp"/>
+        </data>
+        <collection name="mrates_collection" type="list" label="mutation rates">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv\.bz2" format="tabular" visible="false" directory="output/mutation_rates"/>
+            <filter>mrate['mutation_rates'] and not mrate['discard_individual_tables']</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input">
+                <collection type="list">
+                    <element name="GCA_003236755_trunc.fna" ftype="fasta" value="GCA_003236755_trunc.fna"/>
+                    <element name="GCA_003236765_trunc.fna" ftype="fasta" value="GCA_003236765_trunc.fna"/>
+                    <element name="GCA_003236795_trunc.fna" ftype="fasta" value="GCA_003236795_trunc.fna"/>
+                    <element name="GCA_003236805_trunc.fna" ftype="fasta" value="GCA_003236805_trunc.fna"/>
+                </collection>
+            </param>
+            <param name="database" ftype="fasta" value="database_trunc.faa"/>
+            <conditional name="config">
+                <param name="analysis" value="supermatrix_aa"/>
+            </conditional>
+            <param name="diversity" value="low"/>
+            <param name="accuracy" value="false"/>
+            <section name="quality">
+                <param name="min_num_entries" value="1"/>
+                <param name="remove_fragmentary_entries" value="true"/>
+                <param name="fragmentary_threshold" value="0.67"/>
+            </section>
+            <conditional name="trimming">
+                <param name="trim" value="gap_trim"/>
+            </conditional>
+            <param name="force_nucleotides" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="\(.?(?:GCA_003236(?:805|755|765|795)_trunc:.+)+\):\d+\.\d+;"/>
+                </assert_contents>
+                <discovered_dataset designation="concatenated.aln"> <!-- ftype="txt" value="input_concatenated.aln" compare="contains" -->
+                    <assert_contents>
+                        <has_line_matching n="4" expression=">GCA_003236(?:805|755|765|795)_trunc"/>
+                        <has_n_lines n="736" delta="1"/>
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input">
+                <collection type="list">
+                    <element name="GCA_000007905_truncated.fna" ftype="fasta" value="GCA_000007905_truncated.fna"/>
+                    <element name="GCA_000008525_truncated.fna" ftype="fasta" value="GCA_000008525_truncated.fna"/>
+                    <element name="GCA_000012345_truncated.fna" ftype="fasta" value="GCA_000012345_truncated.fna"/>
+                    <element name="GCA_000012965_truncated.fna" ftype="fasta" value="GCA_000012965_truncated.fna"/>
+                    <element name="GCA_000014865_truncated.fna" ftype="fasta" value="GCA_000014865_truncated.fna"/>
+                    <element name="GCA_000020825_truncated.fna" ftype="fasta" value="GCA_000020825_truncated.fna"/>
+                </collection>
+            </param>
+            <param name="database" ftype="fasta" value="phylophlan_markers_filtered.faa.gz"/>
+            <conditional name="config">
+                <param name="analysis" value="custom_supermatrix"/>
+                <conditional name="db">
+                    <param name="type" value="a"/>
+                    <param name="db_aa" value="diamond"/>
+                    <param name="map_dna" value="diamond"/>
+                    <param name="map_aa" value="diamond"/>
+                </conditional>
+                <param name="msa" value="mafft"/>
+                <section name="tree">
+                    <param name="tree1" value="iqtree"/>
+                </section>
+            </conditional>
+            <param name="diversity" value="high"/>
+            <param name="accuracy" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="\(.?(?:GCA_0000(?:0790|0852|1234|1296|1486|2082)5_truncated:.+)+\);"/>
+                </assert_contents>
+                <discovered_dataset designation="concatenated.aln">
+                    <assert_contents>
+                        <has_line_matching n="6" expression=">GCA_0000(?:0790|0852|1234|1296|1486|2082)5_truncated"/>
+                        <has_n_lines n="18" delta="1"/>
+                    </assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="input.tre.treefile">
+                    <assert_contents>
+                        <has_text_matching expression="\(.?(?:GCA_0000(?:0790|0852|1234|1296|1486|2082)5_truncated:.+)+\);"/>
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input">
+                <collection type="list">
+                    <element name="GCA_000007905_truncated.fna" ftype="fasta" value="GCA_000007905_truncated.fna"/>
+                    <element name="GCA_000008525_truncated.fna" ftype="fasta" value="GCA_000008525_truncated.fna"/>
+                    <element name="GCA_000012345_truncated.fna" ftype="fasta" value="GCA_000012345_truncated.fna"/>
+                    <element name="GCA_000012965_truncated.fna" ftype="fasta" value="GCA_000012965_truncated.fna"/>
+                    <element name="GCA_000014865_truncated.fna" ftype="fasta" value="GCA_000014865_truncated.fna"/>
+                    <element name="GCA_000020825_truncated.fna" ftype="fasta" value="GCA_000020825_truncated.fna"/>
+                </collection>
+            </param>
+            <param name="database" ftype="fasta" value="phylophlan_markers_filtered.faa.gz"/>
+            <conditional name="config">
+                <param name="analysis" value="custom_supertree"/>
+                <conditional name="maas">
+                    <param name="source" value="default"/> <!-- phylophlan.tsv -->
+                </conditional>
+                <conditional name="db">
+                    <param name="type" value="a"/>
+                    <param name="db_aa" value="diamond"/>
+                    <param name="map_dna" value="diamond"/>
+                    <param name="map_aa" value="diamond"/>
+                </conditional>
+                <param name="msa" value="mafft"/>
+                <section name="gene_tree">
+                    <param name="gene_tree1" value="fasttree"/>
+                </section>
+                <section name="tree">
+                    <param name="tree1" value="astral"/>
+                </section>
+            </conditional>
+            <param name="diversity" value="high"/>
+            <param name="accuracy" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="\(.?(?:GCA_0000(?:0790|0852|1234|1296|1486|2082)5_truncated.+){6}\);"/>
+                </assert_contents>
+                <discovered_dataset designation="gene_trees.tre">
+                    <assert_contents>
+                        <has_text_matching expression="\(.?(?:GCA_0000(?:0790|0852|1234|1296|1486|2082)5_truncated:.+)+\);"/>
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
+It is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution.
+
+When using PhyloPhlAn 3, the user can customize each step of the pipeline to build the tree (marker genes identification,
+multiple sequence alignment, concatenation or gene trees inference, and phylogeny reconstruction).
+
+Required Inputs
+===============
+
+- **Input input genomes and/or proteomes**: A collection of (compressed) FASTA files.
+  Genome and proteome inputs can be mixed and are distinguished by the .fna and .faa extension, respectively.
+- **Reference database of markers**: A multi-fasta file containing the marker sequences.
+- **Substitution models** (for the supertree pipeline): A mapping from amino acid markers to their respective (raxml) substitution model.
+
+When both markers and inputs are nucleotides, the phylogenetic analysis will be done on nucleotides.
+Otherwise, it will proceed in translated sequence space (amino acids). If the inputs are all genomes,
+the user can decide to specify the --force_nucletides parameter to perform the phylogenetic analysis on nucleotides.
+
+Main Parameters
+===============
+
+- **Software Configuration**: Tune the pipeline according to the input and the type of markers in the database:
+
+  - Choose one of four predefined configurations for different database types and analysis pipelines.
+  - OR assemble a custom pipeline from available external software (make sure to select the appropriate database type).
+- **Diversity** (--diversity) and **Accuracy** (--accurate or --fast): Set default values for several parameters at once
+  (trimming, subsampling, fragmentary removal, etc.) in accordance with the expected diversity of the phylogeny to be built.
+  [See https://github.com/biobakery/phylophlan/wiki#accurate-or-fast-1]
+- **Input quality thresholds**: Specify minimum requirements to include inputs and markers in the analysis and how to deal with gaps in the MSA.
+- **Trimming strategy** (--trim): Which strategies to use for trimming.
+- **Subsampling** (--subsample): allows retaining only a certain amount of phylogenetically relevant positions.
+- **Force nucleotides** (--force_nucleotides): Perform the phylogenetic analysis on nucleotides (Ignore proteomes in the input collection).
+- **Sort markers** (--sort): sort the markers and consider them in a specific order (used only for the supermatrix pipeline).
+- **Mutation rates**: Calculate a mutation rates table for the concatenated MSA.
+
+Generated Outputs
+=================
+
+The specific outputs depend on the type of analysis and the specific software configuration.
+
+**Supermatrix (fasttree / raxml)**
+  - concatenated.aln: Final alignment.
+  - input.tre: Initial Approximately-Maximum-Likelihood Trees of the phylogeny.
+  - resolved.tre: Phylogeny with polytomies resolved.
+  - RAxML_log, RAxML_info: Information on the refinement and optimization history.
+  - RAxML_result, RAxML_bestTree: Refined phylogeny.
+
+**Supermatrix (iqtree)**
+  - concatenated.aln: Final alignment.
+  - input.tre.bionj, input.tre.treefile: Reconstructed phylogeny.
+  - input.tre.mldist: Pairwise maximum likelihood distances as a matrix.
+  - input.tre.iqtree: Information on the analysis.
+
+**Supertree**
+  - gene_trees.tre: Gene trees before constructing the phylogeny.
+  - input.tre: Final unrooted species tree.
+
+**Mutation rates**
+  - mutation_rates: Summary mutation rates table.
+
+Notes
+=====
+
+This version of the tool is missing some of the functionality of the original PhyloPhlAn pipeline, such as
+
+- the external tools Opal and UPP as well as support for custom tool configurations and passed parameters.
+- using aligned markers from StrainPhlAn.
+- special functionality with the databases included with PhyloPhlAn.
+
+Please don't hesitate to contact the tool maintainer should you need these options.
+
+To add additional reference databases contact your Galaxy administrator.
+
+Additional Resources
+====================
+
+PhyloPhlAn GitHub: https://github.com/biobakery/phylophlan
+
+For further analysis you might consider the other tools of the PhyloPhlAn tool suite:
+
+- phylophlan_assign_sgbs: Reports the closest species-level genome bins.
+- phylophlan_strain_finder: Perform analysis on trees built with phylophlan.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/phylophlan/phylophlan_assign_sgbs.xml b/tools/phylophlan/phylophlan_assign_sgbs.xml
new file mode 100644
index 0000000000..7adad0b9db
--- /dev/null
+++ b/tools/phylophlan/phylophlan_assign_sgbs.xml
@@ -0,0 +1,125 @@
+<tool id="phylophlan_assign_sgbs" name="PhyloPhlAn: Assign SGBs and taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>
+         to metagenome-assembled genomes.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements_assign_sgbs"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        
+        mkdir -p 'input/' &&
+        #for $i in $input
+            #set $identifier = re.sub('[^\w\-\._]', '_', str($i.element_identifier))
+            ln -s '$i' 'input/${identifier}' &&
+        #end for
+        
+        #if $analysis.type != "matrix"
+            mkdir -p 'database/' &&
+            #if $reference.source == "history"
+                #set $sanitized_name = re.sub('[^\w\-\._]', '', str($reference.database.element_identifier))
+                #if $reference.database.element_identifier != $sanitized_name or $sanitized_name[-4:] != ".tar"
+                    exit 1 &&
+                #end if
+                #set $database_name = $sanitized_name[:-4]
+                ln -s '$reference.database' 'database/${sanitized_name}' &&
+                cd database &&
+                tar -xf '${sanitized_name}' &&
+                md5sum '${sanitized_name}' > '${database_name}.md5' &&
+                cd .. &&
+            #end if
+        #end if
+        
+        phylophlan_assign_sgbs
+            -i input
+            -o output
+            --database_folder database
+            #if $analysis.type == "closest"
+                -d '$database_name'
+                #if $analysis.assign_all
+                    -n all
+                #else
+                    -n $analysis.n
+                #end if
+            #else if $analysis.type == "taxonomy"
+                -d '$database_name'
+                --add_ggb_fgb
+            #else if $analysis.type == "matrix"
+                --only_input
+            #end if
+            
+            --overwrite
+            --nproc \${GALAXY_SLOTS:-4}
+            --verbose
+    ]]></command>
+    <inputs>
+        <param name="input" type="data_collection" collection_type="list" format="fasta" label="Input Dataset"/>
+        <conditional name="reference">
+            <param name="source" type="select" label="Select a reference database">
+                <!-- <option value="cached">Locally cached</option> -->
+                <option value="history">From history</option>
+            </param>
+            <!-- <when value="cached">
+                <param name="database" type="select" label="Cached database">
+                    <options from_data_table="TODO">
+                        <validator type="no_options" message="No database is available"/>
+                    </options>
+                </param>
+            </when> -->
+            <when value="history">
+                <param name="database" type="data" format="tar" label="Reference database"/>
+            </when>
+        </conditional>
+        <conditional name="analysis">
+            <param name="type" type="select" label="Output type">
+                <option value="closest">Closest n SGBs</option>
+                <option value="taxonomy">Single closest SGB, GGB, FGB and reference genome</option>
+                <option value="matrix">Pairwise mash distances of the inputs</option>
+            </param>
+            <when value="closest">
+                <param argument="-n" type="integer" value="1" label="How many SGBs to assign to each input genome"/>
+                <param name="assign_all" type="boolean" label="Assign all SGBs instead" argument="-n all"/>
+            </when>
+            <when value="taxonomy"/> <!-- Todo -->
+            <when value="matrix"/> <!-- Todo -->
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="output.tsv"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input">
+                <collection type="list">
+                    <element name="CM_ethiopia__CM_A06_M0_18__bin.34.fna" ftype="fasta" value="CM_ethiopia__CM_A06_M0_18__bin.34.fna"/>
+                </collection>
+            </param>
+            <conditional name="reference">
+                <param name="source" value="history"/>
+                <param name="database" value="ethiopia_tutorial.tar"/>
+            </conditional>
+            <conditional name="analysis">
+                <param name="type" value="closest"/>
+            </conditional>
+            <output name="output" file="output.tsv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+The phylophlan_assign_sgbs.py script assigns the SGB and taxonomy to a given set of input genomes. Outputs can be of
+three types: (1) for each input genomes returns the list of the closest -n/--how_many SGBs sorted by average Mash
+distance; (2) for each input genomes returns the closest SGB, GGB, FGB, and reference genomes; (3) returns a all vs.
+all matrix with all the pairwise mash distances
+
+options:
+  --database_list       List of all the available databases that can be specified with the -d/--database option
+                        (default: False)
+  --database_update     Update the databases file (default: False)
+  -e INPUT_EXTENSION, --input_extension INPUT_EXTENSION
+                        Specify the extension of the input file(s) specified via -i/--input. If not specified will try
+                        to infer it from the input files (default: None)
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/phylophlan/phylophlan_draw_metagenomic.xml b/tools/phylophlan/phylophlan_draw_metagenomic.xml
new file mode 100644
index 0000000000..fd40947d05
--- /dev/null
+++ b/tools/phylophlan/phylophlan_draw_metagenomic.xml
@@ -0,0 +1,55 @@
+<tool id="phylophlan_draw_metagenomic" name="PhyloPhlAn: Visualize metagenomic SGBs as Heatmaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        phylophlan_draw_metagenomic
+            -i '$input1'
+            ## -o '$output1'
+            --map '$input_mapping'
+            --top $number
+            -f $out_format
+            --dpi $dpi
+            --verbose
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="tabular" argument="-i"/>
+        <param name="input_mapping" type="data" format="tabular" argument="--map" help='A mapping file that maps each bin to its metagenome'/>
+        <param name="number" type="integer" value="20" argument="--top" label="number of SGBs to display in the figure"/>
+        <param name="out_format" type="select" argument="-f" label="output image format">
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="png">png</option>
+        </param>
+        <param argument="--dpi" type="integer" value="200" label="dpi of output"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="data">
+            <discover_datasets pattern="output_heatmap_(?P&lt;designation&gt;.*)\.pdf" format="pdf" visible="true" assign_primary_output="true" />
+            <discover_datasets pattern="output_heatmap_(?P&lt;designation&gt;.*)\.svg" format="svg" visible="true" assign_primary_output="true" />
+            <discover_datasets pattern="output_heatmap_(?P&lt;designation&gt;.*)\.png" format="png" visible="true" assign_primary_output="true" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="output_metagenomic.tsv"/>
+            <param name="input_mapping" value="bin2meta.tsv"/>
+            <param name="number" value="20"/>
+            <param name="out_format" value="png"/>
+            <output name="output1" file="output_heatmap_counts.png" compare="image_diff">
+                <discovered_dataset designation="pres_abs" ftype="png" value="output_heatmap_pres_abs.png" compare="image_diff"/>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+The phylophlan_draw_metagenomic.py script takes as input the output table
+generated form the phylophlan_metagenomic.py script and produces two heatmap
+figures: (1) presence/absence heatmap of the SGBs and the metagenomic samples
+of the recontructed input genomes; and (2) heatmap showing the amount of kSGB,
+uSGB, and unassinged for each metagenome.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/phylophlan/test-data/CM_ethiopia__CM_A06_M0_18__bin.34.fna b/tools/phylophlan/test-data/CM_ethiopia__CM_A06_M0_18__bin.34.fna
new file mode 100644
index 0000000000..043c31360c
--- /dev/null
+++ b/tools/phylophlan/test-data/CM_ethiopia__CM_A06_M0_18__bin.34.fna
@@ -0,0 +1,99 @@
+>NODE_56_length_69222_cov_8.30568
+ATTTCTACACAACCTCAATATAGCTATTCTCAACAAGCTATAGATTTTATTTACGATGAA
+ATTAGGAAAAACCCAGATACAATTTTAGAGGATTTAAAAGAAAAAGTAAAAAAGTCAACC
+CCAGGAGCAAAGGATTCTAAGTGAAAAACACCTACTCCCATTCGGGAACCCAGCTTTATC
+CATCACAAGTTGACTAACTTTAGTATATGAAAAAAATGTTAAAAAGTCAAAAGTTTTTTA
+AATTAGTGAAAACAAAAAGGAGGCTCACCATATGAAATTACTGATCAAACAAAGAGTTTT
+TTCATGGACCGATTCTTATGACATATATGATGAATCCGGTAATGCAAAGTATTTTGTGAA
+AGCAGAATTCCTTACATTAGGACACCGGCTGCATATATATGATCAGGCGGGAAATGAACT
+GGGACTGATCAAAGAAAAGGTATTTTCCCTGCTTCCGGTGTTTGAGATCGAGCAGCATGG
+ACAGCTGAAGGGGAGAATCCAGAAACAATTTACATTTTTTAAGCCAAAGTATGAGATTGA
+TTATAATGGCTGGCGTGTGGAAGGTGATTTTCTGGGATGGGAATATGACGTGTATCATGG
+ATGCAGTTCGATCGTACATATTTCAAAGGAACTACTGCACTGGGGGGATACTTATGCGAT
+CAATATCAGTGATCCGTCCGATGAATTGGATGCTCTTATGCTGGTGATCGCAATCGACGC
+AGCAAACTGCTCAGATGGAAATTAGAAAGAAAGGTGTAATTATGGCAGGATATTTAATTA
+AGGATACAACAAAAGAAGAAAGAGAACAGATCGTAGCAGAGTCGCTTGGAAATATTGAGG
+CGAACTGTGATGGCTGTATGCGCGGACTTGCAGACATGTATCAGGATTACATCGATGGCA
+AAAAGGAATTGCGTGAGATCAACATGGAATTCAATACAAGATTTGTAAAAAGCGGTGATG
+ATATGCCGGGCAGACACAGCTGTGCGATGTATGGAGAATAATAAGATGAACATATTATTA
+ACACAGATTATGGAACCGCAGGCTGCAGCATTCACACATGGAGGGAAATTTCATGCGGAT
+GATGTATTCTCTGCGGCTTTATTGCGCTATTTGAACCCCGATATCACCATTGAGCGCGGA
+AACCGTGTGCCGGAAGAATATAAGGGAATCGTATTTGACATTGGAAGAGGCAGATATGAC
+CATCATCAGAGGGACAGCCGCATCCGGGAAAACGGAGTGCCATATGCGGCATTTGGGCTG
+CTCTGGGAGGAACTTGGAGTTGAGATACTTGGAGAAGATCTTACATTGAGGTTCGATGAA
+GATTTTGTGCAGCCGCTGGATCTCAATGACAATACCGGAGAGAAGAATGAGCTTGCGACA
+CTGATCGGACAGTTTAATCCGGTGTGGGACGATCACCGGGGAAGTGATGAGGGCTTCTTC
+CGTGCCGTTTCGGTCGCAGAGATGATCCTTAAAAATAAATTTGACCGGTATCTTGGAAAA
+GCCAGAGCAGACCAGCAGACGGAAGCGATTCTCGCAGAGCATGACAAAGCGGTTCATTCC
+GGCGATGCTGCGCCGGAGGATGCACGAATCTTAGTGCTTCCGGACTTTGTTCCATGTCAG
+AAACGGCTTGAGGAAACGGATATTGCATTTATCGTTTTTCCATCGAACCGTGGTGGATAT
+TGTATACAACCTTTGAAAAAGAAGCAGTCGATGAATTATAAATGCAGTTTCCCAGAGGAA
+TGGCTGGGACTGGAAAACGAGGAACTTGCGGCAGCAAGCGGACTGCAGAGTGCCACATTT
+TGCCATAAGGGCGGTTTCCTGATGTCTGTGGGAGATCTCGAGGATGCTGTGAAAGCCTGC
+AGGATCAGTCTTTTACAATATAAAGACCAGCCGGTGATCGTGAGACTTGGTGAAGATTCC
+GGAGCCGACGGGTTGTTGCTTCAGATTCCGGGAATGGAACATGCACAGGTGGTCTGGATG
+CCGCTTTTTTCAGCTCCGGAGCTTGAAATGCAGGGAAATTATGGCGAAATAGCCATGGAG
+AAGCCACAGTGGAAACAACTGGTCAAAGAGTATGTCAGAGAAATACTGCATTTTCATCCG
+GAAGCAGTATTTGTGAATGGAGAACTTCTGGAGGTTTATCCGGTTGTGCATGCACTCCGT
+AAAAAACATGTTCCGGTTCTGACGGTTTCAAAACAGAATGGAAGATCTGTGATCGTAAGG
+ATCCCGGCCGGTTCATAAAGTGCGGTTCACAAAGCAGATGCAGAAAATTCTTTTTTTTCA
+TAGGAAGAAATGCTAGAATTAAAGATTGTATCAGGATAAACGGAGGTTTATGATGGACAT
+TCTATTTGCAGGAAACACTAATTTTTTCTCTCCGGAATTTTATGAGGAGTTTGCAGTGGA
+GGATCGCTGCGCCGTAATTGGCAATGCAAAGCCCCGGAAGCAGATAAACAGGAAAGGCAT
+CAGATTTTTTCCGGAGACGAAGGACGCAGAGACGGAAAGGATATTCCAGAGCTATGATTT
+TGAGACGGTTCTGTTTCTTTCCAGGACGCTGGACTGTGAAAAAAAGGTTTTTGATGAGCT
+GGAGAACCTGGAGTATATTCTCTATCAGTGCAGAAAGAGAAATGTACCGGAGTTTATCTA
+CATTACAGAAAACCGTCATGTGAATGAGATTAAGGACGGTGAAGTAAGCAGAAAGATCCT
+TCTGGAAGCGTGCGACAAGCTGTGCAGGCATGCGGCAGAAAAGGACCATATCCGTGTTCT
+TGTCCTGCGCGTACCATATTTATATGGAGCAATGGGGGACAAGTGTGCTTCACAGGATCG
+CAGAGTGCTGGAAAAATGGATACAGGATACCGTAACAGAAAAGAGGCTTGAACTTCAGGG
+GGAACGGGATACGGAGATTGATTTTCTGCATACGGATGATCTGAAGGAGCTATTGAAAAG
+GATATTGGATGATCCGTGGAAAGAACCTTATTTTTCGGTCAGCGTGGGTGGAAAAAATAA
+CTGCACAATGGGGGAAGTTGAGGACTTTCTGAAGGCTGCAGAACCACAGCTTACAGTGCA
+TTACAGCGGAAAAACAGAGTATGTTCCGGCTGCAGGGGAGAACCAGTGGGCGAGAAGGGA
+GTATGGATTTATCCCCAAGGCAGATGTCTGGCAGGATGCTGCCCGTCAACTGGAACTGGA
+AAAGAAACAGCATGAAAAGTCAGCCGGGAAACGAAACCAATGGACGGGAAGATGGCTTCG
+TACCGGGATCGAACAGGCTGCCCTTTTTGCAGGAGCGGAATTTTTAAATGCGGTAACACA
+AAACAATGTTCTGGTCAATTTTCTTGATTTCAGATTTATTTATATTGCAATTATGGCGTG
+CGTGAATGGACTGGGTGCGGGTGTGTTTGCAGCACTGCTTGCCAGCGCAGGATATATTGT
+ATCGAAAGCAGGGGCAGTGAACTGGCAGGTTTTATTCTTCAATGTCGAGAACTGGCTGCC
+GTTCGCAAGTTATCTGCTGCTTGGATGTGTGATCGGATACACGATGGACCGTTCGGAAGA
+TGAACTGCAGAACAGTAGAGAGGAATATCAGATCCTGGATGAAAAATACAGCTTTCTCCA
+TGGACTATATATGGAAGTCCTTGAGGGAAAAGAGCGGTTTAACAGCCAGATTATCGGCTA
+CAGGGACAGCTTTGGACGGATGTATGCTGTCGTGAAAAAATTAAATACGACGCTGCCGGA
+ACAGGTATTTTATGAGGCTGTAGATGTGCTGGAGGAGATTTTGGACAATCCATATGTCGC
+AATCTATAATATACGCCCGAACAGCGTCTATGCGAGGTTAAATGTCTGCTCTAAACGGTG
+TATGGGGAATGTAAAAAAATCCTTGAAAATGACAGATTATCCGAAATTGTCAGAGTGTCT
+GTCTGCAAATGAGACATTCGTGAATATCGATGCGTTGGAGGATTATCCGGCATATGCGAC
+ACCGGTATTCAGAAATGACGTACTTGTGGGAATGATTCTTCTGATGCAGGCAGATTATCA
+GCAGATGAATATGGAGTTTTCCAATAAGTTCCGTATCATGACGGACATGATCCGTGATTC
+CCTGATCCGTGCCATGGATTTTTATGAGCAGAATGAGAATGCCGTGAAGAATACAAGGAT
+TCTTGAGAATGACAGGTTTGAAGAAATCCTGAAGGTGAAACAGGCAATGCGTAAGAAACA
+GTACTTAAATTACCGTATGCTTCATATTTTTCTGGATGGATCAGGTCTGGAGGAGATTAA
+TGAAAAGCTCTCCGGTCTGGTACGTGAAAATGATGTGCTAGGCCTTGGAGGAGATGGCGG
+GCTGTATCTGCTTTTGTCACAGACAAATGAGACGGATTTAAAGATCGTGGAAACCAGGCT
+GAAAACAAATCACATTCGGTACAAAGAGGTTATGGAATGAGAATTGCGATGATTTTTCTG
+TTGATCCATATTGCCGTCTGCATCGCAGTCGGGTATTTGTATAAGACGAAAAAACTAAAA
+ACGAGGAACCCGGTTCTTCTGGTCGTGATCTGCATTCCGGTGTGGGGGATAGGGATGCTT
+CTTGTGGAGGAGACCGCAGAACGGAGACATACTATGGGCAGAAGACCGGTCCGGATGTAT
+GAGACCATAGAAAAGAACGATCTGAATTACCGGACGATTCAGACAGGGACGCATGAGGAT
+ATTGTTCCGCTGGAGGAAGCAATGACCGTCAATGATACATCCGTAAGCCGCCGGCTTATG
+CTTGAAATTCTGCATAAAAATCCCGATGAATATATAGATCTTCTGAAGAAAGCGACTTCA
+TCAGATGATGTGGAACTGACACATTATGCGACGACAACAATGCTGGAGATCCAGAGCCGA
+TATGAGTGGAGGATCGAACAGAGTCTGGAAAGGCTGGAAGAGCAGCCGGAGAATCTGAAT
+ACGTTACGGAGAACAAAGAATTTACTGGAGAAATATCTTGAGAGCGGACTGATCTCCGGT
+GCGATTGCAGGACAATACAGAAAACGGCTGCAGGAGGTGCTGGAAACACTGCAGCGTCTA
+CAGCCGCAGACACACCGCTATGTATATGAAAGCCTGGAAAACAGGATTCTGGAGGGCAGC
+CTAAAAGGTGTAGAGAAGGAACTGCAAAAACTCCTGGAGCAATTCCCACAGGATGAGAAC
+GTGTACCGCTTGTCTGCACAATACTATTATATCCAGAAGGATGGCCAGAAACTCCGGGAA
+CTTTTCAGGCTTATGGAGCAGAGGCAGGTATACCTTGATAATGAAAGCCGGAAGTGGTAT
+GACTTCTGGACGCAAAAAGGATGAATAAATGAGAAGAAAAGCATTTGGAAAAATTATGGT
+GCCGGTTCTGGCACTGTTTCTGCTCAGTCTGCTTATTTTCCGGGAGAGGGCGGGAATCGA
+CTATGATCATACGGGTGACGGCAATAACGGATGGAATACAGCCTGCTATACGGATGCGGT
+AAGCCAGACACCATCCTGCCTGATTTTATCTTCTTCCGAAGCGGTCAGTACCCAGTACAC
+GGATATGATGCAGAAGGTCTTATCTGGCATGAAAATTGCATATGATATATGTGATGTGGA
+ACAGGGCTTTGATGCAGATATACTGGACAGATATGATACCGTCGTAGTGACCTTCCAGGA
+GTGGAGTGTGCTTGGGGATGAGATTTTTCCGGTATTTTCCTGGGTGGAATCCGGGGGATG
+CCTTCTGGATGCACTGACACCATCGGTGGATGGCTATTTTCAGGCAGTTTCGATGAAATT
+CGGAATTGAAATGATCGGATCTTCCTATCCTGCAGTATATGGGATAAGGTTTTTCAATGA
+CTGTATGCTCGGAGCATCGCAGGATGATGTATTCTGGTACGACAGAACCAAAGAAGAGGG
\ No newline at end of file
diff --git a/tools/phylophlan/test-data/GCA_000007905_truncated.fna b/tools/phylophlan/test-data/GCA_000007905_truncated.fna
new file mode 100644
index 0000000000..b057070083
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000007905_truncated.fna
@@ -0,0 +1,36 @@
+>AE017125.1 Helicobacter hepaticus ATCC 51449, complete genome
+AGCAAATTAAATACCAAAAGGCATTTTATGGAATCCAAAGCACAAGAAAAGCAAGAGCAAAAAAAAGGCTATAATCCACA
+AGATATAGAATCTAGATTCTATGCTATATGTGAGAAACGAGGCTATTTTGAAATTGAGGGGAATAAATCTCTCTGGCAAG
+GTTGTGCGCCAAAATGCTTTAGCATTATGATGCCCCCACCTAATGTTACAGGAGTGCTTCACATAGGACACGCACTTACT
+TTTACTCTCCAAGATATTATCACAAGATTTAAACGAATGGAGGGCTTTAAAACACTCTATCAACCCGGTTTAGACCACGC
+AGGGATTGCTACTCAAAATGTCGTATTAAAACAGCTTTTAGCACAAGGTATAACTAAAGAATCTTTAGGAAGAGAAGCAT
+TTATAGCTAAAGTATGGGAATGGAAAGAGCAAAGTGGGGGGGAGATTCTCAATCAAATGCGTCATCTTGGCATCACACCT
+GCGTGGTCGCGTTTGCGTTTTACGATGGATAAAGGATTACAAAAAGCTGTAAAAAAAGCCTTTGTGCAATGGTATAATCA
+AGGGCTTATCGTGCAAGATAATTATATGGTAAATTGGTGCGTGAATGATGGTGCGCTTTCAGATATTGAGGTAGAGTATG
+AGCAAAATCACGGCAAGCTTTATTATTTGCGCTATCCTATTAAAGATTCTGCTCAATCCCTCATCGTAGCTACCACGCGT
+CCGGAAACATTTTTTGGCGATACTGGCGTAATGGTCAATCCAAATGATGAACGATATAAGCATCTCATTGGTAAAAGCGT
+GATTCTCCCATTATTGGGGAGAGAAATACCTATTATAGCAGATTCTCACGTTGATATGAGCTTTGGAAGTGGCTGTGTAA
+AAGTAACACCTGCCCACGATATGAATGACTACGAAGTAGGTAAAAGGCACAATCTCCCATTTATTACGATTTTTGACGAA
+AAGGGTATATTCAATAAAAATGCAGGAATCTTTCAGGGACAAGAACGTTTAGAATCTCGCCCTCTTATTGTCCAAAAATT
+ACAAGAAAATGGCTTTGTAGAAAAAATAGAAGATTATACAAATCAAGTTGGTAAATGTTATCGCTGCGGTAACATTGTAG
+AACCTTATATCTCCAAACAATGGTTTGTCAAAAAAGAAACAGCACATAATGCCATTCAACGTGTCAATAATGGCGAATTA
+CATTTTTACCCTGCACAATGGCTTAATAATTATAATGCGTGGATGAGAGAACTCAAAGATTGGTGTATTTCACGGCAGCT
+TTGGTGGGGACATAGAATCCCTGTATGGTATTGTGAATGCGGCAATAAAGTCGCTTCAGAATCTGATAATCCTATCTGCC
+CTCAATGTCAATCCACTATCACAAAGCAAGATGAAGATGTGCTTGATACTTGGTTTAGTTCTGGATTATGGGCTTTTAGC
+ACTTTGGGCTGGGGTAATGAGGATACAAATACTCAACCTCCCCTTTATCACGCAAATGATTTGGCAGAATTTTATCCTAA
+TTCATTGCTTATTACGGGTTTTGATATTTTATTCTTTTGGGTGGCACGTATGATTTTAAGTGGAGAATCCTTACTTGATT
+CACTGCCTTTTAAAGATGTTTATCTTCACGCACTTGTGCGCGATGAAAATGGGCAAAAAATGAGCAAAAGCAAAGGCAAT
+ATCATTGACCCTATGGAAATTATATCCTCTTATGGGGCAGACACACTCCGCTTCACTCTAGCAATTTTATGCGCACAAGG
+GCGCGATGTGAAACTCTCTACTCAATCTCTTGAAATTTCTAAAAATTTCACAAATAAGCTTTATAATGCTACAAATTTCC
+TTAATATGTATTTGGAACAACTCGGCGGTAAAGAGGCTTTAAAAAAAGGTTTTGGCGATATTAACCATATACACATAAAT
+ACACCACTTGGACAATATATGTTAGTAAGATTCTATACTGCTACAAACGAAGTAAGAGCAGCACTTGAGAACTATCGTTT
+TAATGATGGGGCAAGTATTCTTTATCGCTTCTTATGGGGAGAATTTTGCGATTGGGGTATTGAACTTGCAAAAGCAAGTA
+AAGATTCTATTTATGAGCTAGGAGCAATCTTTAAAGCTGCGCTTATACTGCTTCACCCTTATATGCCCTTTATCACAGAT
+GCGCTTTGGCATACGCTCAATGCAAGCGATATACAAACTTCCGATTCTATTATGATTCACTCTTATCCCAAAGCTATGGA
+AAAAAATGAGCAACACTCGCAGCTAGAGCGGACTTTTGAGGTTATTCAAGATGTCATTACTTCTATCCGCCGATTAAAAG
+CAATGCTTGAGCTTGGCTCTACAAATATTGAGTGTATTTTTGTCAAACTCAATGCACCATTTGAACACTCACTCCTTGAG
+CAGTTTGTTTGCAAGCTTGCTAAAGTCAAAACTCTTTGTATCACACAGCAAAAGCCTAAAGATTGCGTAGGGGATGTAAG
+CAAATATTGTGAATGCTACATACAACTTGGAGAGATTGATTTACAAGCTATTGGCACTCGTTTGCACAATCAACGTCAAA
+AACTTGAAAAAGAAATTACCAAACTTCAAGCTATGCTTGGAAATGAAAATTTTATAAAAAATGCCCCAAAGGCTGTAATG
+GAACAAAATCAAAGTGCATTACACAATGCGCAAGAAAAATTGGATAAAATTAACGCTGAACTTATCGCACTTGGATTGCA
+ATCTTAAAAATACAAAGGAGAACAAATGAAAAAAATACTCTTGCTCGTGCTGTGCTTTTATCTTAGTGGCTGTGGAGATT
diff --git a/tools/phylophlan/test-data/GCA_000008525_truncated.fna b/tools/phylophlan/test-data/GCA_000008525_truncated.fna
new file mode 100644
index 0000000000..5b0b8c088c
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000008525_truncated.fna
@@ -0,0 +1,34 @@
+>AE000511.1 Helicobacter pylori 26695, complete genome
+TATTATGGTTGTTCTAACAAGTCCAATTCTTGCTTAATTTTACTTTCTTTTTCTAAAAGCGTTTTTAAACTCTCTTTAGC
+TTTTTCTAGCACGCTTTTAGGCGCGTTTTTGACAAAATTTTCATTGTGCAAATTGAGTTTTAATTTTTCTTTTTCCAATT
+TTTCCAACTGCTTTTTCAAACGCGCAACAAGCGGGCTTAAATCAAGATTTTCTAAATTCGCATAAGTCTGGCAAAATTCC
+CCCACATCGCTCACGCTTTTTAAAGGCTTAGAACTAATCACGCTGACTTTTTCCAACCTCGCTAATTTTTGGGCGTAAGT
+TTGCAAACGCTCTGTGTTTTCTATGGCTTCTCTTAATCCCACGCTCGCTTCTTTTAGAACAATCGGTGGGGTTTCTAGCA
+TGATTTTTAAACGCCTTAAAGACACAATGCAATCTTTAATCACTTCAAATTCATGCTCTAATTTTTCATCTTGCGCCAAA
+TCTTTAGGGTAAGGCATGACCATGATAGATTCAGTGTTTTCTAGTTCCGTATTGCTGAGCTTGTGGTATAAAGACTCGCT
+GATAAAGGGCATGAAAGGGTGCAAGAGTTTTAAAGCCTCTTTTAACACGCTCCCTAATTCGTCTATCGCTTCATTTTCCA
+CTTTAGAAAATTCAATGAACCAGTCGCAAAATTCCCCCCACAAAAAGCGGTATAACAAAGTCGTGGCGTCATTAAAACGA
+TAATTATCTAAAGCGTTACGCGCCTCTTTAGTCGCTGAATTCAAGCGCGATTTCGCATAACGCCCCAAAGGCGTTTGGTA
+TTCATTCAAACGCTCTTTATCTTTGAAAGATTCTTGTTTGAGCTTCAAGTAACTCGCCGCATTAAAAAGCTTGTTGGCGA
+AATTCTTGTTATTTTCTAAATGCGTAGTGGAAAGCTTAATGTCCCTACCCGTAGCGCACAAATTGGCTAAAGTGAAACGC
+AAGCTATCCGCGCCGTATTTTTCTATCATCTCTAAAGGATCGATCACATTACCCTTAGATTTGCTCATTTTTTCACCCTT
+TTCATCTCTCACTAAGGCGTGCAAGTAAATATCTTTAAAGGGCAATTCGCCTAAAAGCGATTCGCTGCAAAAAAGCATCC
+TAGCCACCCAAAAAAAGAGGATGTCAAACCCAGTAATGAGCGTTGTGTTAGGGTAGAAATCTTTCAAATCGCTTTCATTA
+AACAAACCGCTTTTTTCTTGCCCCCACCCTAGAGTGGAAAACGCCCATAGCCCTGAACTAAACCATGTGTCTAGCACATC
+CTTATCTTGCTCTAGTGTTTCGCTCTTACAAGTAGGGCAACTTAAGGGGGTGTCTAAGCTTACGAACTGGTGGTTATTCT
+CGCAAGTGAATACCGGTATTTGATGCCCCCAAAACAATTGCCTGCTGATACACCAAGGGCGTAATTCCCTCATCCAAGCG
+TTGTAATTATTGATCCAATTAGAAGGGTAGAATCGCGCCAAACCTTGTTGGATTTTTTCAATAGAACTTTGAGCGATTTC
+AGGCTTGACAAACCATTGCTTAGACACATAAGGTTCTACCACATTATGACAACGATAGCAATGCCCCACTTGATGCGTGT
+GTTCTTCTATTTTTTCCAATAGGGCGTTTTCTTTTAATCTTTCTACGACCTTATCTCTAGCTTCTAATCGTTCTAAATTT
+TCAAACTCCCCGCAATGCGCGTTTAAAATCCCCTTTTCATCAAAGATTTTAATCGTTTCCAAATGGTGGCGTTTGCCCAC
+TTCATAATCGTTAAAATCATGCCCAGGGGTTACTTTCACACACCCTGTGCCAAACTCCATTTCAACATGTTCATCAGCGA
+TAATAGGGATTGTGCGATGGATTAAAGGCAAGATCGCTTTTTGCCCCACCAAATGCTTGTATCTCTCATCGTTAGGATTG
+ACCATAAGCGCGCTATCGCCAAACAAGGTTTCAGGGCGTGTGGTAGCCACCACTAAATAATCTTTTTGATTTTCTAAATA
+ATATCTAATATAATACAACGCCCCCTTACGCTCTTCATACTCCACTTCAATATCGCTCAACGCCCCATCTTTAGTGCACC
+AATTCACCATGTAATTATCTTGAATAATGAGACCTTTTTCATACCATTTCAAAAACGCCAATTTGACCGCTCTTTGCAAG
+CCCTTATCCATCGTGAAACGAGTCCTAGAAAAGGCCGCGCTCACGCCTAAACGCTTCATTTGCTCTAAAATCGCTCCCCC
+GCTCTTTTCTTTCCATTCCCACACTTTTTTAATGAACTCTTCACGCCCTAAATCTTCTTTTTTAATCCCTTGACTTAAAA
+GCTGCTTTTCCACGACATTTTGCGTTGCAATGCCAGCGTGATCCAACCCGGGCTGATACAAAGTCTTATACCCATCCATG
+CGTTTGTAACGCGCTAAAATATCTTGCAAGCTTAAAGTCAGGGCATGCCCTATGTGCAACACACCGGTCACATTAGGAGG
+GGGCATCATCAAGCAAAATCGTTTGTTTTTTTCTTGGATCGCTTCATTGCCATCAATTTCAAAATACCCCCTATGAGAGC
+AAATTTCATAAATCTTTTTTTCTATCTCTTCTGGTTGGTAGGTGGTGGGTTCTTGTTTCATTATCATTATTATCCTAAAA
diff --git a/tools/phylophlan/test-data/GCA_000012345_truncated.fna b/tools/phylophlan/test-data/GCA_000012345_truncated.fna
new file mode 100644
index 0000000000..ab94cfc6cd
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000012345_truncated.fna
@@ -0,0 +1,35 @@
+>CP000084.1 Candidatus Pelagibacter ubique HTCC1062, complete genome
+ATAAACTTATTATCACCTATGAGTAACGATAAATATATACATACAGACGTTGAAGATAAGATTTATTCTTATTGGGAAAA
+AAACAATTTATTTAAACCCACTAAAAATAAGAAACAATTTTCAGTGGTTATACCTCCGCCCAATGTAACTGGTAGCCTTC
+ATATGGGTCATGCTTTGAATAATTCAATTCAAGATCTTTTGGTTAGATACCACCGTATGAATAATTATGAAACCTTATGG
+CAACCTGGAACAGATCATGCAGGTATTGCCACACAGGCCTTAGTTGAGAAAAAATTAACCGCTGATGGTATTGATAAAAA
+TGAAATTGGAAGAGAAAAGTTCATAGAAAAGGTTTGGGAATGGAAGGAAGAACATGGTGATATCATTTTAAATCAACTAA
+AAAAACTAGGTTGCTCTTGTGATTGGTCAAGAAATGCTTTTACAATGGATGAAAACCTTTCAAAATCAGTTTTAAAAGTT
+TTTGTAGAGCTTCACAAAAAAGGTTTAATTTATAAAGATAAAAAACTAGTAAACTGGGATACGGTTTTAAAAACAGCAAT
+ATCTGATTTAGAAGTGGATCAAAGAGAAGTTAATTCTAAGATTTACTATATTCAATATCCTATAGAAGCTTCTAGTGATT
+TTATAACTATAGCAACAACAAGACCTGAAACCATGTTGGGTGATACAGCGATAGCTGTAAATCCAAAGGATGATCGATTT
+AAACATTTAGTTGGTAAGTTTGTAACAGTACCAATTGTTGGAAAAAAAATAAAAATTATTGAAGATGAATATGCTGATCC
+TGAGATGGGAACGGGTGCTTTAAAGATAACACCAGCACATGATTTTAATGACTATGAAGTGGGACAAAGAAATAATTTAG
+AAATCATAAATATTTTTACTGAAGGTGGCAAAGTAAACGAAAACGCTCCTAAAGAATATATTGGACTTGATAGATTTGAA
+GCTAGAAAAAGAATTATAAAAGAACTTAAAGAAAAAGAGTTTTTTGTTAAGGAAGAGAACATAAAGAATAAAGTTCCTTA
+TGGGGATAGGTCTAATTCAATAATTGAGCCTTTTTTAACAGAACAATGGTTTGTCGATGCAAAAAAATTATCAATTAAAG
+CTAAAGATATAGTTAACTCTAAAAAAACTAATTTTTTTCCTGCTAATTGGTCAAAAACTTATTTTCAATGGATGAACAAT
+ATTGAGCCATGGTGTATCTCAAGACAGCTTTGGTGGGGACATCAAATACCTGCTTGGTATGGACCAGATAAAAAAATCTT
+CGTTGCAATAAATGAAGAAGAAGCAAAATTGGATGCAAAAAAATTCTATAATAAAGATGTAGATTTAATTCGTGACCCAG
+ATGTATTGGATACTTGGTTTTCATCAGGTCTATGGCCTTTTGCTACATTGGGTTGGCCTGACAATAAAGAATATGTAGAT
+AAATTTTACCCGACATCAGTACTGGTTACAGGGTTTGACATTATATTTTTTTGGGTAGCACGCATGATCATGTTTGGAAT
+GGAGTTTCTAGACAAAGAGCCTTTTAAAGATGTTTACGTTCACGCCCTTGTTAAAGACGAGAAGGGACAAAAAATGTCTA
+AATCTAAAGGAAACGTAATTAATCCCTTAGACCTAATTGAAAAATATAGTGCAGATGCTTTAAGGTTTACTCTACTGTCA
+ATGGCGTCACCCGGAACAGATGTAAAACTTTCTGAAGATAGAGTTAAGGGTTATAGAAATTTTTTAAATAAATTATGGAA
+TGCAAACAATTTTTTAATTACCAATAATTGTGATTTTTCTAAAATTGATGAAAAACCAATTTTATCAATTAATATTAACA
+AATGGATCTATGCTGAACTTATAGAAACTAAAAATAAAATTGAAAAAAATCTAAAAGATTACAGGTTTGATGAAGCTGCA
+AAAAATGCCTATCAATTTACTTGGCACTCTTATTGTGATTGGTATTTAGAGCTATCTAAAACAATCCTATTTTCAGAAGA
+TGAAAAGGCAAAAGATGAAGTAAGACAGGTATCAGCTTACGTATTTAAACAGATATTAATATTATTACATCCATTTATTC
+CATTTGTGACTGAAGAAATTTGGCTAAATAATAAATTTGATAACACAGGTAAAGACTTTTTAATGTTAGCTAATTGGCCT
+TCTGGAGAGTTTGAAAGAGATACATCCATTAATCAAGTTGAAAAAATTATCAGTATAGTTTCTGAATTAAGATCATTTAA
+AAATGAATTAAGTGTAAGCCCTGGGTCATTTATAGATATTTCAATAGAGACAGTTAGTAAAAAAGAACAATCATTTTTTA
+CTGAAAATGAAATTATTCTAAAAAAACTTGGTCGTATCAAAAATTTATATAATAAAGATCTGGATAAACCAACTGCTACA
+TTGATGGTTTCTGGAGATTTATTCAAAGTGTATTTTGATGAAGATGTCGATTTAGAATTAATTAAAAAAAACTTAACTAC
+AAGGCAAAATAAATACCAAGAAGAAATGAATAAAATATCACAAAGATTAGCTAATAAAGGCTTTGTTGATAGAGCACCAA
+AAGATATTGTTGATCAGGAAAAAACTAATTATAATAATTTAAAAAATGATGTTGAGAGAATATCGATAACTATAAAGGGT
+TTATAATGGCAAAATTTAATAAAAAAAAATTACCAAGCAGACATACTTCATTAGGTGCTGATAGAGCTCCACATAGATCA
diff --git a/tools/phylophlan/test-data/GCA_000012965_truncated.fna b/tools/phylophlan/test-data/GCA_000012965_truncated.fna
new file mode 100644
index 0000000000..c724ed0942
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000012965_truncated.fna
@@ -0,0 +1,35 @@
+>CP000153.1 Sulfurimonas denitrificans DSM 1251, complete genome
+TCTTAGCATTGTAAAGATTCTAATTGCTCTTTAACTTTGCTCTGCTTATCTGACGCATCCGCCAAAAGCTCTCTGTTTTT
+TACTAAAACATCCTCAGGAGCATTAGCAACGAAACGCTCATTATTTAACATTGAAGAGAGTTTGTCTATCTCTTTTTGTA
+GCTTTTCATCTTGCTTTGTAAGCTTTGAGATAATCGGAGTTAAATCAATACTCTGAGTCGGTATAAAAGTTTCACACATT
+TGGCTAATATCACTAACTGAGTCTGGGATTTTTTCATTTGTAAATTCAACTACATCAACCTTAGCAAGTCTAGCTATAAA
+AGGTCTCATCATCTCTTTTTCATCTTCACTTATGTTGTCTATCTTAACATAAGCTTTTTCTATCTTTTGGTTTGCCAAAT
+CAACCAAAACTTTAGCACGTCTAATAGAGATAATAGCATCCATGATTATCTCAAATCTCGCTTCATCTTTTGTGCGAACT
+TTTGTTTTGTAAGGGTACTTCATAATCATAATCGACTCTGAAGCTTCAAGTGTAGTACCGCTTAGCTCATGGTAGAGATA
+CTCTGTGATAAATGGCATAAATGGATGAAGAAGTTTCATCGACTCTTTAAAGATAGCTCCAAGCTCTACAATTGAGCCTT
+TGTCTGCTTTGCTTAGCTCGATTCCCCAGTCACAAAACTCATTCCATAAAAAGCGGTAAAGTACAGTTGCAGCGTCGTTA
+AATCTGTACTCATCCATACATGAGCGAACCTCTTGTGTTGCTACATTTAGGCGAGATAACATGTAACGTCCAAGTGGGCT
+CTCAACACAAAACCCTTTTAAATCAGGGAAAGTATCAACGTTCATCTGTAAGAATTTTGCGGCATTGTAGAGTTTATTTG
+TAAAGTTACGGTTTTGCTCGAGTTTGTCCGTACTCATTCTTATATCACGCCCTTGAGCAGCACTTATCGCAAGAGTAAAA
+CGAAGTATGTCGGCACTGTATTTTTCTACCATGTCAAGCGGGTCGATTACATTGCCTTTTGATTTAGACATCTTTTGTCC
+ATGCTCATCACGAACAAGTGCATGAAGGTAGATATGGTTAAATGGAAGTTCGCCTACAAAACTCTCACCCATCATCATCA
+TTCTAGCTACCCAGAAAAAGAGGATGTCAAAACCAGTTATTAGAAGCGAATTTGGATAAAAATCTTTCATATCCTGTGAA
+CTAAAGAGTTTGTCCATAGAAGCGTCGCCATTCCCCCAGCCTAAAGTTGAAAACGGCCAAAGAGCAGAGCTAAACCAAGT
+ATCTAGAACATCAGGGTCTTGAGAGATATTTTTTGAAGCACACTTTGGACATGTATGCTCTTCATCTTTGAGTGAAGCCC
+ATTCGTTGTCGCAATCCCCACAGTAAAATACAGGAATTTGATGTCCCCACCAAAGCTGACGAGAGATACACCAATCACGC
+AAATCACCCATCCAAGAGTTGTATGAGTTTATCCAGTGAGGAGGAAAAAATTTAGCTTCTCCGTTGTTTGTTTTCTCGAT
+AGATTTACGAGCAACTTCACTTCTTACAAACCACTGTTTTGAGATATAAGGCTCAACAATGTTTTTACATCTGTAACAGT
+GCCCTACTTGATGTTTATGCTCTTCAATTTTTACTACAAAACCTTCTTCATAAAGTCTTTTCATAATAATGTCACGAGCT
+TCTAAACGCTCTAAACCTTTGAATTCTCCAGCGTACTCATTTAAGATACCCTTTTCATCAAAAACAGTGATAAACTCTAA
+GTCATGACGCTTACCAACTTCATAGTCATTTTGGTCATGTGCAGGTGTAACTTTTACAACCCCCGTTCCAAAATCCATAG
+CTACATGTGAATCGGCGATGATAGAAACTTCTCTCTGAAGTAGTGGAAGTTTGATTTTTTTACCGATTAGATGCTTATAA
+CGCTCATCATCAGGATGAACCATAACCGCTGTATCGCCAAAGTATGTCTCAGGTCTTGTTGTTGCAACTTCAACAAATCC
+GCTTCCATCAGCAAAAGGGTACTTTATGTGGTAAAACTTTCCGTCATGGTCTTCATGTTCAACTTCTATATCGCTAAGTG
+CGCCATCATGTGTACACCAGTTTACCATGTAGTTTCCGCGAACTATCAGACCTTGATTGTAGAGATGAACAAAAGCCTCT
+TTTACAGATTTTTGAAGCCCGTCATCCATAGTAAAACGCTCACGCTTCCATGCAGGGCTAACTCCCATTTTGCGAAGTTG
+GCTTGTCATAATGCCAGCAGATTCTGCTTTCCACTCCCAAGCTCTCTTTAAAAACGCTTCTCTGCCAATCTCCTCTTTAG
+TCGTTCCCTCAGCAAGAAGTTGTTTCTCAACTACATTTTGAGTTGCGATTCCTGCATGGTCGGTTCCAGGTTGCCATAGA
+GTTTTATAACCGTCCATTCTCTTGTAACGGGTAATAATATCTTGAAGTGTAAATGTGAGTGCATGACCTATGTGAAGACG
+TCCAGTTACATTTGGAGGAGGCATCATGATAGAGAAGTTTTTTCCCTCTTCTTGAATACTCTTGTTAGAATCTACTTCAA
+AGTAGCCTCTCTCTTCCCAAATTTTGTAAAACTTATCTTCAGTAAGTTGTGGTTCGTAGCTGTTTGACATATTTATTACC
+TTGATTTTTGTAGTTTAAAAGTTTGAGATTATATCTAAAAAGATGTGAGGCTCTACTTATAATAAGTTCTATATTGCCTG
diff --git a/tools/phylophlan/test-data/GCA_000014865_truncated.fna b/tools/phylophlan/test-data/GCA_000014865_truncated.fna
new file mode 100644
index 0000000000..5aa9c8a23a
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000014865_truncated.fna
@@ -0,0 +1,37 @@
+>CP000471.1 Magnetococcus marinus MC-1, complete genome
+GTCGAACTAGGTATCACCTACAGGGCCTATGCCCTTGCCAGAGAAGAGAAGATCCCATGCAGGAAACATCGTTGCCAAAA
+TCCTATGACCCCACCGGTGTGGAACAGCGCTGGTATCAAACCTGGGAAGAGCAGGGGTGTTTTAAACCCAGTGGTCTAAG
+TGCGGCCAACGCCTACTGCATCATGATCCCCCCCCCCAATGTGACCGGCAGCCTGCATATGGGGCACGCTTTTCAAGATA
+CCATCATGGATGCCCTGATCCGCTACAACCGCATGCAGGGGCATAATACCCTGTGGCAGTGTGGGACCGATCATGCCGGC
+ATCGCCACCCAAATGGTGGTGGAACGGCAACTCGAAGCCGAGGGTAAAAGCCGCCACGATCTTGGCCGCGATGCCTTTAT
+TGAACGGGTTTGGGAGTGGAAAGCCAGCAGTGGTAACACCATTACCAAACAGCTCCGCCGAATGGGGGCTTCCTGCGATT
+GGAGCCGTGAACGCTTTACCATGGATGACGGACTCTCCGAGGCGGTCAAAGAGGTGTTTGTTCGCCTCTATGAAGAAGAT
+TTAATCTACCGTGGTAAGCGCTTGGTCAACTGGGACCCGGTGTTGCACACGGCGGTTTCGGATCTGGAAGTAATCAGCGA
+GGAAGAGCAGGGCCACATGTGGCACATGCGCTACCCCATGGTCGAGGGCGATGGCTTTTTGGTGGTGGCAACCACTCGAC
+CAGAAACCATGCTGGGGGATAGCGCCGTGGCGGTGCATCCCGAAGACGCGCGCTACCAGCATCTGATCGGCAAGCAGGTG
+GTGTTGCCCTTGACGGGTCGCACCATTCCTGTGATCGGGGATGACTATGTTGATCCTGAGTTTGGTTCTGGCTGTGTCAA
+GATCACACCAGCCCACGATTTTAATGACTATGAGGTAGGCAAACGGCACAATCTGCCCCAAATGAGCATCTTTACCGTGG
+ATGCCTGCATCAATGAGGATGCCCCAGCCCGCTACCGGGGAATGGATCGCTACGAGGCGCGTAAACGCATTGTGGAGGAT
+CTGCAAGAGGCAGGTTTGCTGGAAAAAATAGTCGACCACAAACTCATGGTGCCCCGTGGTGACCGTACCAAGGCAGTCAT
+TGAGCCGTTGTTGACCGATCAATGGTTTGTGACCACCGCCCCCTTGGCCGCTGAGGCGATTAAGGTGGTGGAAGAGGGGC
+GCATTAAATTTGTACCGGAAAACTGGTCCAAAACCTATTTTGAATGGATGCGGAATATTCAAGATTGGTGCATCAGTCGC
+CAGATATGGTGGGGCCACCGCATTCCCGCTTGGTATGGTCCCGATGGTCAGGTGTTTGTCTGCCGCACCCAAGAGGAAGC
+GTCCCAAAAAGCCAGCCAGCACTACGGTAAGCCGGTGGCGCTAACCCAAGATAATGATGTGCTGGATACCTGGTTCTCAT
+CGGCACTATGGACCTTTTCGACCCTGGGTTGGCCAGAAAAAAGCCAAGAATTGGCCTCTTTTCACCCCACAAACGTGCTG
+GTTACAGGTTTTGACATTATCTTTTTTTGGGTAGCCCGCATGATTATGATGGGGCTGAAATTTACCGATGAAGTGCCCTT
+TCATACCGTCTATGTGCATGGTCTGGTGCGCGATGGCGAGGGGCATAAAATGAGCAAATCCAAGGGTAATGTCTTGGACC
+CGTTGGATCTGATCGACGGTATTAGCTTGGAGGATCTGGTGGCCAAGCGTACGCGGGATATGATGCAGCCCCATCTGGCC
+AAAAAGATTGAAAAACAGACCCGTAAAGAGTTCCCCGATGGCATCGCCGCCGCAGGTACGGATGCCTTGCGCTTTACCTT
+GGCATCGTTGGCGACCCAGGGGCGGGATATCAAGTTTGACCTGGGACGGATGGAGGGCTACCGTAATTTTTGCAATAAGT
+TATGGAATGCCTCGCGCTTTGTGCTCATGAATGCAGAGGGCCAGGATTGCGGGCTGGAACGGGTGGATCTGCCCCTATCG
+GTGACCGATCAGTGGATTGTGAGCAAATTTCAGCGCACCGCCCGGGATGTTACACAGGATATTGAAAATTATCGCTTTAG
+CGATGCGGCCAATACGCTCTATCAATTTTTGTGGGGCAGTTATTGCGACTGGTACTTAGAGATGGTGAAAACCACGCTCT
+ATGATGAGAACGCCGCAGAGGCGGCCAAAGCGGCGGTACGGCACACCATGGTTGGGGTGTTGGAGGCCTCCTTGCGGCTG
+CTCCATCCGTTGATGCCCTTTATTACCGAAGAGTTGTGGCAAAAGCTGGCCCCTCTGGCGGGCAAGCCCGCAGGTAGCAT
+TATGCTGGCCCCTTGGCCCGAGGCCGATGAAGGCCGTATTTTAGACCAAATTGAGAGCGAAATTGACTGGGTGCAGCGCT
+TTACCAGCACCATTCGTGGTATCCGTAGTGAAATGGATATCCCTCCCAGCAAAAAGATCCAGGTCTTGGTGCGTGGTGAC
+GACAGTGCGGTGGCCCGTCTGCGGCGCCATGTGAGTACCGTTACCGCCCTGGCCAAATTGGAGGGGTGGGCGGTGTTGCA
+GGATGAGGCTCCGCAAGGCTGCGCCACGGGGGTGTTGGAGGATATGCAGCTGTATATCCCCATGAAGGGCCTCATTGATG
+TGGCCGCCGAGAGCGCCCGTTTGCAAAAAAGCTTGGATAAGCTGGATGCCGATTGGCAGCAAGTCACAAGAAAACTGAGC
+AACGAAAATTTTATTGCCAAGGCCAATCCCGAAGTGGTTGCCAAAGAGCGGGATAAAGCCAATGAACTGATGGAAAAAAA
+GCGTGCCGTGCAGGAGGCTCTAACACGCATTCAGGCCATGGCATAGGGCGTGCTGTTTAAAGCAATTGCCCAGGGGCTAG
diff --git a/tools/phylophlan/test-data/GCA_000020825_truncated.fna b/tools/phylophlan/test-data/GCA_000020825_truncated.fna
new file mode 100644
index 0000000000..52a6218a65
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_000020825_truncated.fna
@@ -0,0 +1,37 @@
+>CP001132.1 Acidithiobacillus ferrooxidans ATCC 53993, complete genome
+GTCCTGCACGAAGGCCTGGACCAGATCAACGCCTCGGAAATCGAGAAAGATACCCTACCATGACTGACACTCTGGATCGC
+CCCTTTGCCCCCGCCGAGATCGAAACCCAATGCTACGCACGCTGGGAAACCCACGGCCTGTTCCAGCCGAAAGGCAGTGG
+AACCCCCTATTGCATCATGCTTCCGCCACCCAATGTCACCGGCACCCTGCATATGGGTCACGCCTTTCAGGATACCCTCA
+TGGATATCCTCACCCGCGTCCACCGGATGCGCGGCGAGCGCACCCTCTGGCAGCCGGGGACCGATCATGCCGGTATCGCC
+ACCCAGATGCTGGTGGAACGGCAACTGGTACAGGAAGGCGGCGATCGCCATCAGATGGGCCGCGGTGCCTTTCTGGAACG
+GGTCTGGCAGTGGCGTCGGGAATCCGGTGGCCATATCACCCGGCAGATGCGACGGCTGGGAGCATCCTGTGACTGGTCAC
+GCGAGCGTTTTACGCTGGACAGCGGGCTCTCCCATGCGGTCACCGAAGTCTTCGTCCGCCTCCATGACGAAGGGTTGATC
+TACCGCGGCAAACGGCTGGTCAACTGGGATCCGGTCCTGCGTACCGCAGTCTCCGATCTGGAGGTCATCAGCGAAGCGGA
+GCAAGGCTCGCTCTGGCACATCCGTTATCCCCTCAGCGATGGCACCGGCTTCCTCGTGGTCGCCACCACCCGTCCGGAAA
+CCCTGCTGGGCGACGTGGCGGTGGCGGTTCACCCCGACGATCCGCGCTACGCCGCCCTCGTCGGCAAGACCCTGCGCCTA
+CCGGTCATGAACCGTGAGATTCCCATCATCGCGGACGATTATGTCGATCCGGAATTCGGCTCCGGCTGCGTCAAAATCAC
+CCCGGCCCACGATTTCAACGACTATCAGGTGGGGCAACGGCACAACCTGGCCCTGCTCAACGTCTTTACCCCCGACGCGC
+ATATCCGGGACAGTATCGAGGTCTTCGGCGACGACGTCGTCGCCGGGGAGATTCCCGAGGCCCTACGCGGACTGGACCGT
+TATGCCGCCCGCCAGCAGATTCTCATCCTGCTGGCGGCGGAAAACCTGCTGGAACGCACCGACGAACACCAACTCATGGT
+GCCCCGCGGCGACCGCTCCCATGCCGTCATCGAGCCCTACCTAACGGACCAATGGTATGTGCGGGTCGCCCCCCTGGCGG
+AACCGGCCATCCGCGCGGTGGAAGAAGGCCGCATCCGCTTCGTGCCGGAAAACTGGAGCAAAACCTACTTCGACTGGATG
+CAGCGTATCGAGGACTGGTGCATCTCTCGCCAGCTCTGGTGGGGGCACCAGATTCCCGCCTGGTACGGCCCCGACGGCAA
+AATCTTTGTCGCTCGTCGTGAAGAGGAAGCGCAGTCGGAAGCCGTCCGCCATTACGGCATGCCGGTGGTCCTGGAACGCG
+ACCCGGACGTACTCGACACCTGGTTCAGTTCGGCGTTGTGGCCCTTCACCACTCTGGGCTGGCCGGAAAAAACATCGGAC
+CTTGCCCAGTTCTACCCCACCAGCGTGCTGGTCACCGGCTTCGACATCATTTTTTTCTGGGTGGCGCGAATGATCATGAT
+GGGTCTGCGCTTCATGGACGATGTGCCATTCCATGAAGTCTATGTCCACGGTCTGGTGCGCGATGCCGAGGGCCAGAAGA
+TGAGCAAGTCCAAGGGCAATGTCCTCGACCCCATCGACCTCATAGACGGCATCAGTCTGGAAGACCTCGTCGCCAAGCGT
+ACCCGGGGCCTCATGCAGCCGCAGATGGCGGCCAAAATCGAAAAGGCCACCCGTAAGGAGTTCGCTGACGGCATTCCCGC
+CTTCGGCACCGATGCCCTGCGCTTCACCTTCGCGGCACTGGCCACCCAGGGCCGGGACATCAAGTTTGACCTCAAGCGGG
+TGGAGGGGAATCGCAATTTCTGCAACAAGCTTTGGAACGCCTCGCGTTTCGCCCTGATGCAGACACCAACTCCGGCCGCT
+CTGGAAGGCGAGCGCGAGCTGCTGGCGCCGGAACGCTGGATCATCGGTCGCCTGCAACACTGCGAGGCGGCCGTCAACAG
+CGCCATCGACCAGTATCGCTTTGCCGACGCCGCCCATGCACTCTTCCAGTTTTTCTGGAATGACTACTGCGACTGGTATA
+TCGAACTGAGCAAACCGGTGCTGCGCGAGGGCGGCCCGTTCACCTCGGCACAACAGTGCGGCACCCGCAATACCCTGCTG
+CGGGTGCTGGAGGCCGGCCTGCGTCTGATGCACCCGGTGATGCCCTTCCTCACCGAGGAACTCTGGCAGCGGGTCGCACC
+GATGATCGGCAAGGCGGGGGACAGCATTGCCCTCGCCCCCTACCCGGTGGCCGATCTCGCCCGTGTGGACACCGATGCCG
+ATGCCGATACGGAATGGCTGATTGCCGTCATCCGCGCCATCCGCTCGGTGCGCGGCGAGATGGATATCCCACCGGGGAAA
+CCTCTGCCCCTGCTCCTGCAAGCCGGCGATACCCATGACCGGGAAAGGGTGGAACGCTACCGGTCCTGGCTCTTCGCCCT
+CAGCCGCCTCGCCAGTCTGGAATGGCTGGACGCCGAAGAGGAAGCGCCGCCCGCCGCCTTGCAACTGGTCGGCGATCTGC
+GCGTCCTCGTCCCTCTCGCGGGGGTGATCAACGTCGCTGCCGAACAGATCCGCCTCGCCAAGGAACAGCAACGCCTGGAA
+CAGGATCGCGCCAAAACCGTCGCCAAACTCGGGCAGGAAAGCTTTCGCAGCCGGGCGCCCGCAGAGGTGGTCGCCAAAGA
+AGAGGAACGCCTGCGGGAGGTGGATGCCGCATTACTGCAACTGGGGGAGCAGGCACGGCGGTTAGCCTTGTTGTGATCAA
diff --git a/tools/phylophlan/test-data/GCA_003236755_trunc.fna b/tools/phylophlan/test-data/GCA_003236755_trunc.fna
new file mode 100644
index 0000000000..d8a87550cd
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_003236755_trunc.fna
@@ -0,0 +1,116 @@
+>PZRR01000001.1 Staphylococcus aureus strain CM179 PROKKA_contig000001, whole genome shotgun sequence
+TCTCGTCCGTTCGCTCGACTTGCATGTATTAGGCACGCCGCCAGCGTTCATCCTGAGCCAGGATCAAACTCTCCATAAAA
+ATTATGATGTTTGATTAGCTCATAAATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTGGAATTAACGTTGACATA
+TTGTCATTCAGTTTTCAATGTTCATTAATGTTCAATCTCTTTTATTGTACTTCATTAAATTATTGAAGTCAATAACTTTT
+TGAACGATTACTTTATTTATTTTATATTGTTTTTATAGTTATTTCAATGGTAAGTTTTACACTTTTGAAATTCTTCTTTA
+AAAACATCATCGCCGTTTTTGACGACTTTATTATCTTATCAACTTTATAATTTAAAGTCAATAACTTTTTTGAAAAATAT
+TCGTGTTTGCAAGTCGCTTCTTTTTTCAATGCGTTGATTGCTTAACACAAGAACTTATTTTACCAGCATTTTAAAACAAT
+TCAATATAAAAACGTACAAAATAAAAGTAATTTTGTACGTTTAGCATATATTATACCTATTTATTTGTCGCAGCTATAAC
+TTTTTGTGCAATCGAGCTATAAATTTTACCTAATCTGTCTTCAGCTTGATAAATTGAAGGTGCAAAGTCTTTTGGATTCC
+AAGACGGTTGCTCTAAAGGTAATTCCCCAAGTAATTGAGTATTAAGTTCATCAGCTAACTTAGTACCGCCACCTTTACCA
+AAAACATATTCTTTATTACCCGTCTCTTTACTTTCAAAATAACTCATGTTTTCAATTACTCCAAGAATAGAATGGTCCGT
+ATGTTTTGCCATCGCACCTGCGCGAGCTGCAACAAATGCTGCTGTAGGATGAGGTGTCGTTACAATAATTTCCTTACTTG
+AAGGTAACATCGTATGAACATCTAAAGCTACATCCCCTGTTCCAGGTGGAAGATCGAGTATTAAATATTCAATGTCTCCC
+CATTTAACTTCTGTAAAGAAATTCGTCAACATTTTACCTAACATTGGCCCTCTCCATATAACTGGCGCATTTTCTTCCAC
+AAAAAAGGCCATTGATATAACTTTAACGCCATGACGTTCAACTGGAATTACTTCCTTCCCTTTAATTCCAGGCTTTTCAT
+CAATACCCATCATATCTGGTACACTAAATCCATATATATCGGCATCTACTAATCCGACTTTTTTACCTTCACGGGCTAAG
+GCAACGGCTAAATTTACTGCAACAGTAGATTTACCGACGCCACCTTTACCTGAAGCAATAGCAATAAATTCAACTGGATT
+ATTTTGAGATAATAAGCCTTCTATCGTTTTAGGTTTATTTTCTTCTTTTGGTTTAAATTGATTTACTTTTTCTTCTGGTA
+ACGTTTCAAATCGTATACCCACAGTTTTTGCACCATTTTCTTTTAAAACATTAACAACTGCCATCTGTAAATCTAATTGC
+GGTGCGCCACCTAATTGTGCCATTGCCACTTTAACACTTACATGTTCTTTTTCTTCCTTAATAGAAACTTCTACAATACC
+TTCTGTTTCTTTTAAAGGTACATCTATAATAGGATCTTTAATTTCTCCTATTAGTTCTTTAACTTGATCTACCGTTAACA
+AAGCAAATCCCCCTTAATCAATTTAAAATATCTACATCATAGCAAATAACAATTTTTGCTTAGTCTATCAATAAAAGTAT
+AAAACTTTTCATTAAATAAAAAAAGAAGTTAGCCTATTATTTTCAATAGACCAACTACTATAATTATTTTAAAATTCCCT
+TCTATTACTTTCTATTACTTTAGGTTCTCTTATAAAAAGCGCTATCACATAAGCTGCCATAACAAGCACAGCTACAAAAG
+CAAATGAGATATCCACCCCTATAGCAATTGATTGCTGTTTAATTTCAGTTGCAGTTAAATGCGATGGCGATGTAGATGAG
+AATATTTTTGCGCCAAAACTCATCAAAGTAACCATTAATGCTGTTCCTAATGAGCCAGCCATTACACGACCAAAGTTCAT
+AATAGCCGTGCCATGTGAGATTTCTTCATTTCTCAAAGAATTAATTCCTGTAGTATTTATCGGCATCATGAGTAAAGAAA
+CTGAAAACATTCTAATTGCATATACGACTATTAAATACGTATAAGATGTGTCTGTATGCAAGAAACACAACATAATAGTA
+GTAATTGTTAAAATCGTAAAACCAGTATAAATCAGTGGTCTAGGACCATACTTATCATAAAATTTACCTGTAAAAACCGA
+CATAATACCATTTATGATTGCACCTGGCATGATAACAAGTCCAGACAATAATGCAGATAGAGCTAAGCTATTTTGAACAT
+AGAGCGGTATTAATAACGCTGGACCAACCATTGACATCATTATGATCATTGAGCTAATCGTACATAATGCAAATGTTCTA
+TTTTTAAAAACACTTAAATTTAAAAGTGCATTGCTTATATTGAATTGTCTACGAATAAATAAGTAGATGATAATAGAACT
+AATTATCATGGCACCAATGACTACCGGGCTAGTAAATCCTAGGTCGCCTGCACTACTGAATGCATATAACATTAATCCAA
+ATCCAATCGTTGAATACATTACAGAGCGCTTATCTAATTTAGTATATTTCACTTCATTATAGCTTGAAATTGAAATTAAA
+CCGAAGATGAATGCGACTAAAGCAATTCCTACAATTATAATAAATGGTACTCGCCAACTCGCTTGATCAATGATTAATCC
+AGTAACAGTAGGCCCGATTGCTGGTGCAAATTGAATAACTAAACCAGCTAATCCCATTGCAAATCCTCTATGTTCTTTAC
+TGAATAACGTAAACAATGTGAATTGCATTAAAGGCATGAGTACGCCTGCCCCCATAGCTTGGATGACACGCGCTACCATT
+AATACGCCAAAATTGGGTGCCATGGCTGCAACAATTGATCCTACTAAAAATGTCCCCATCGCTGCTAAGTATAAAGGTCT
+AGTTTTAATCCTGTCCATTAAGTATGCTGTTAGAGGTATCATGACGCCATTAACAAGCATAAACCCAGTAACTAGCCATT
+GCGATGTACTTTCATTAATATTTAATTCTCTCATTATACTAGGTAACGCTGTATTTAATAATGTTTGATTTAAAATAGCT
+ACAAACGCACTAATCAACATAACAGCAACTATGAAGTTTCGTCTCCGGGTTGTTAATTCAACTTTAGCCACCACAATTCC
+TCCTTTGTAACAAATTTACGTTTATTAGCATATATACTTAAAATATATTTCAGATTAAAGTACCAACTATTTATATCAAT
+GGTTATTATTAACCGTGATTAATTGAAGCAAAACAACTCATTTTCTACTATATGAATAAAAAGAAGTTGGAACACATCAT
+TGCCCCCAACTTCAAACCTCTATTTTCTATTGTTTAGATTTTTACTTTCAGGGTAAAACTGCAGCTTACAAACATATAAA
+AAGCCTATAATAACCATGATGACCCAAAAATCAATATTGATATACACATAGTTCAGATGAATAATAAAATAAAATAACGT
+TGTTGCAACCATATAAGAGATTAAATGAAAAGTTGCACCTCTAAAATAAGCATTTTCAGGTAACATTTTTCTAAAATAAT
+CCATCAAATTTTCAACTGCAAATACGATAAAGTAGCCAAATATAATATAACTACCATAATATAGCAAATTGTCGTACATA
+CTTCTGTTATATGTGAAGTCACCTAACCTAAAATAAATAAGAATTCTACTTAATCCATATAGTCCGAACCCTAAAAACGT
+TAAGAATATCGCACCAGAAAGCACAAAGATAAAGAGAACAATAATTGTTGTTAATAAATTATAAAACTTATGTTTAAGAT
+AATTCATAACTATTGTCCTCCTTACCAATAATAATTTATATTGCTTGTAATTTTAAGATAGTTGATTACACTTCAAACTT
+AGTAAAATGATTATTTGTTACTTTATTTACACTACATCAATTTTAATCATAATTCTATTCTTTTGTTTGTGACGCCGCTT
+CTCTATAAAATATGAGCCATACAACGATGAGCCCTACACTTATCAAGGATACAACGCCTAAAATATTATGCAAGTTTGCA
+CCAAACAATCCTGATTTTAATGCATAAAGGTATCCCATAATCGTCGAACCTATTGATGCGCCAAGGTTTTTTGTTAATCC
+ATAAAACGACATCATTTTCTTCATTTGTATTGGACTTGTTTCCTCTTGGACAATTACACTATCTTTTGTATAAATATATC
+CAAAGCTTAGTCCACTTAAAATTAAGACACATGCTATAAGAATTGGTAATTTTATACCAAACGCAATGATTATACTACTT
+AATAATAATAATGTAAAAGACGACAAATAGATAACTTTTCTTGATAACTTCGCTTCAATATGGTGCAAATTAAAATTCAA
+TGTAATCCACGCTACAGAAAGTGGAAAAATAACTAATCCACTTTGCAATGGCGATAACCCCAGTTGTTCTTGAAGATACA
+CAGGAATATATAAATTAAAGCCCATTAAACAAACAGCTGTAAGAAGATCTGTAATAAAGACCAAAGTAATCATTCGATTA
+AATTCTGCTACTGGTAAGAATGGGGATGAAACTTTTTTCTCAACATTAAATAATCGAAGTGCAACTAATATTGCTAAGAC
+AAAACCTATGATATTTAAATATAAATGTTGTTGGTTTAACAATGCAAACATAATTAAACCAATGAAAATATAAAACAGGG
+TGATACCTTTAGTATCGAATTTTGATTTAGCCACAGTTTTTTCTTCTGGAAAATGAAATGTCCAGACAACCAATATTATT
+GCAATAATCGCAATCGGTATATTTATGTAGAATAACCAATGCCATGTTGCAAATTCTAATATGCCACCACCTAGAAGTGG
+TCCAATGATACTCGAAATCCCCCAAACGCTACCAACGATACCCATAATTTTATAGCGTAATGGAATTTCAAACGCTAATT
+TAGGTACAATTTGTGACAAGGACATCATGACACCAGATCCAAACCCTTGAATTACACGTGATATAATCAACATACTAAAA
+TGTGTGCTTAAACCTGACATTAAACTACCAACCGTGAATAGTGTAAGACCTGCGATAGCAATATAAATAATTTTAAAACG
+AGTTAATAATTCACCTACTATTGGATTCGCAATCACTAATGCAATAAAGTAAGCCGTAAATATTAATGAAATTAAATTCC
+CTGCATTTAAATCTTGCTTAATTGTTGGTAACGCTAAAGAAATAATTGATGATTCGATTGCAGCCATAAACATGATTAGT
+ATTAAAGCTATTACAGTTACAATTGATTTTAAACGCATGCTATACCTCCTTTTATAATAATGATAGTGCTATGTAATTTC
+TAATTTTACTATTTCCTATCTTATCCTCTTTTAAATTCAAATTAGTTTTTTTAAAATCTATTTGTTACACCTACTAAAAA
+ATTCAAATAAACGTATCCATCAAATGTCTGATTAATACAAATTAAGTGCACTCCCAGCTTTAAAAATCATACCGATTTTA
+AAAAAGCAAAACAATCCTCTATTAGAATGAATTAAGTAATAAAAAAAGCGGAGTTTCCCCCACCTTCTGATAAACTATTA
+CATAAAATATAAAATAGCAATTAAATGCAATAATGATGCTATAACGATAAAAATATGCCATATCATATGAAAATATGGTC
+TGTTTTTTTGTGCATAAAACCAGGCACCAATTGTATATGACACACCACCTAAGAAAATGAATAATATGAATATCCATGAT
+GTGCGAATAAAAATAATTGGTAACAAGATAATACCTACCCAGCCCATCACTAAATAGACAATTAAACTTAACTTTTGATT
+AACTTTGACAGCTATGGATTTATATAAAATTCCCCAAAGAGTCGTTCCCCATAATAAAATAAATACTGTCCAACCTATCC
+AACCACCTACAATTGTTAACAAAATAGGAGTGTATGTACCTGAAATTGCTACGTAAATCATACTATGATCAATAATCCTT
+AAAATATATTTATGGGGTGTTTCATTTTGCATAGAGTGATAAATTGTTGATGAAATAAACATCATAAAGATAGAAATAAC
+ATAAATTGACATACTAACTGATGCAAGTGTGCCATTTGCAATATAACTATGTACAGCCGCATAAGGTAAGACTAATAGTG
+TTAACAGCGCTGCCAGACCATGAGATGCAGCATTGCCTATTTCTTCTCCAAATGACAATGGAATGATATCCTTAAATGTT
+TCTACAATTGTGTCATTACTTTTTTTACTTGATTTGGACATCATAGTCACCGCCTAACATTAAATTAAACCCATTCTACG
+TAAATCTTCAGTCGCTGTTGCAACACTATCTTTACCTTCTTTATTTTTTAGAGGTGAGAACTCTTCTTCTCTAGGAACTT
+GTAACGTGACAAAACTAGTTCCATAAGTAAATATGTCAAAATAGAACAATTCGAATTTTAAAGTTGGTTGTTCAATAACA
+CCAAAGTTCTCATCTAATTGCTTCAAATTCTTAATAGCTAAATGATAAGGTAATTCACGATTTACAGCATTTATAATAAA
+TCCAAGTTTAAATGCATGAATACCGATATTAGCATTGTTAAATTGATTTGCAACTTCTGGATCTAATTCTGAATACTCCA
+ATACTGTATCTTTACAATCGACATTAACTAATCGTCCAACACTTTCTCCTGGTTTTGGTTGAATCGTTTTAGAAGTAATA
+TCGTAATCATGTTCTACCGTAAATCCTGCAAATAGTGGATCCAACACTTTTACTAAAACATTGTCGATATTATTCAAGAA
+AATATACTTAACGCCATTATTAGACATTTCTTCTAAGTATCCTGACTTGTCTAAAGATTTAAACACGCCACCATTACCAT
+TTGGCGTTTCCATAATACGACCTTGTTGATTTAAAATTAACTTCCCTTCTTCACTAAGCGCCACAATATTATCTTGTTTA
+AAGAAATGTATTGCTTCTTGATCATAACCAAAGTAGTTATGCGATTCAAAATAAGCTAAAGTTTCTTCATGATTGATATC
+ACTTGTCATAATGTACCATTGAATTATATGACCAGTTTGTCGATGTAGTTCTTTTAATTGTTTTGCCTGAAGTTCAAATA
+AACTTACACCTTCAATTTCGAATGAACCTTTAGGTCCTTTATATCCAAGTCTTGTTCCTTGTCCACCTGCCATCAAAAGT
+ACTGCAAATTGTCCTTCTTTAATAGCTTGAAGTCCTTGTTCCTCTAAACGCTTAATCTCATCATCACTCATTTGTGATTT
+AATATCATATTTCACTTCAGAAACTGCAGATACATCATCTATTGTTTTCTTATTGATGTATAAATCGTTATATAATTTGG
+CAATAAAATCTAAATCTAATGACGCTACCTTCTCTTCAAGCGCTTCTTTTTCATTATTACTCATTATTTTTTCATATTCA
+CATAAATGATCTTGTTTATATTTAGCTAATTGATTTTTATCTAGCATTTTACGCCTCCTGCTGAGTTTGTAACCTTTAAT
+AATTTATTTTCTATAAAAACTTAGTATTCCAGTTGCTTATTATATCATTGATGAAAGGCTGAAATAAAACATAAACTGTT
+CCGACCATTAACGCAGTAGCTAAAGATAAGTCTACAAGTCCACCTGTTTTAAATTGAATCGGTGTCTTCACATTAAACGG
+TAACGGATAAAATAATTTCACGCCTTTTGGTGTTATCATATCTAGTATAACATGTGACACTAATCCAATTATAATTGCTG
+CCATATAATAATTAGGCGTCTGAATAATTTGCAATAAAAATGCTATGATTGCGATAAATAATATTGAATGCGTAAAGGTT
+>PZRR01000017.1 Staphylococcus aureus strain CM179 PROKKA_contig000017, whole genome shotgun sequence
+TGAATCGTCTACACTTAATTGGACAAATTCTATGAGAATAGATATTGTTAATTTAAGAAAGTAGGCGATTTTATTATGAC
+AAGAGAAAGAAGATCATTTAGTTCAGAGTTTAAGTTACAAATGGTTAGATTATATGAAAATGGTAAGCCTAGGAATGAAA
+TTATACGCGAGTATGATTTAACACCTTCGGCGTTAGGAAAATGGATAAAGCAACATCAAAACACGGGTACATTCAATCAC
+CAAGATAACTTATCAGATGAAGAAAAAGAGCTGATTAAATTACGTAAAGAAGTTCAACATTTAAAAATGGAGAACGATAT
+TTTAAAGCAAGCAGCGCTGATCATGGGACGAAAATAGAAGTCATTCAAAAGAATGCACATCAATATTCAGTATCAGCAAT
+GTGTAAAGTCCTAAAAATACCAAGAAGTACCTATTATGATTCTATAAAAAGAAAAGATAATAAAATCACTAAAGATGATT
+CAAACGTAGAACGTGCTGTCATAAATATTTTTAATTCTAATAGAAAAGTCTTTGGTACAAGACGAATTAAAAATAATTTA
+AATGATAAGGGTCTTACTGTATCAAGACGAAAGATAGGTCGTATCATGAAAAAACATAATCTAGTTTCTGTTTATACGAA
+AGCTAAATACAAAAATCATCCAAAAGAAACTAATAAAAAACGAATTAAAAATCATTTGAATCGCGCTTTTAATAGAGAAC
+AACCAATGGAGACATTAGTAAGTGATTTGACATATGTAAAAGTCGCAGGAACATGGCATTACATATGTTTATTTATAGAT
+CTATTTAATAGAGAAATTGTTGGTTACAGTGCAGGTAAAAATAAGGACGCAAATTTAGTATCAAAAGCAATCAGCAGAAT
+AAATCATAATCTTGAACAAATCAAACTATTCCACACTGATAGAGGCAAAGAATTTGATAATCATTTGATAGATGAAGTCC
+TAGAAACATTTAAAATCAAACGTTCATTAAGTACCAAAGGTTGTCCTTATGATAACGCAGTTGCGGAAGCAACGATGAAA
+GCAATGAAAACCGAATTTGTAAAACAAATGCAATTTGAAAACTTAGAACAGTTAGAAACAGAATTATTTGATTATGTAAA
+TTGGTACAACAATTTTAGACCACATTCTTCATTACAGTATTTGACGCCAGTGGCATTTAAAAATCTACACATGAAAACTG
+TCTAAAAAATTGTTGACATACCA
diff --git a/tools/phylophlan/test-data/GCA_003236765_trunc.fna b/tools/phylophlan/test-data/GCA_003236765_trunc.fna
new file mode 100644
index 0000000000..d9ea458369
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_003236765_trunc.fna
@@ -0,0 +1,114 @@
+>PZTC01000001.1 Staphylococcus aureus strain CM178 PROKKA_contig000001, whole genome shotgun sequence
+TAACAATACTAACAGCAATTATTATTATACTAGAGATTTTATTTAAAAATAATATATATTTACCTGTTCTATCTATAGAA
+CCTAAAACCTTACCTAATATTGCTAACAGAAAAAACCATAGCCAAGAAACCATAATTGTGGCAATACAAAAAAGTATCTT
+TTCTAAACCAGAATAGACAGATGCGCTTGATCCAATTACACCAACTGTATCCATAATTGCATGTGGATTTAACAACGAAA
+CAGATATAGCAAAACCTATTTGCTTTTTTGTACTCATCGGTTCATAGTTCTCTAGAGTGTTAGGCTTTTCTTTCCATAAA
+GACCAAGCCATGTACAATAGAAAAAACAAACCAACTATATAAATAAATAATTGTAGAACTGGTAATGACATTAATATTAG
+TGAAACACCCAGTACAGCAATTATTATTAAAAAAGTGTCACATAATCCAGCCGTTATAACAACCGGCAATGCGTTTATCA
+TTTTTTTTTGATTAGCACCTTGATTAAATACAAACACGTTTTGCGCTCCTAGGGGCAAAATAAGCCCCAATGCTAATAAA
+ATACCGTGTAAAACTGGTTGTATCAATTCGCATCCTCCCCCTTCCCAACAATGTTCGGTGTACAAATATCTTTTACTACA
+CTATAAAAACCCGGTAGTGTCGTCTTGAAGAACCCAGTACAATGGTGTGCTTCTCTATATTTTTGATCTTTCATTAATAT
+AATATGTGCTTTTTTCAAATTATAATGTGGAATTGCTGGGAATAAATGGTGAACTAAGTGAAAATTATCATGGTGAGGAT
+GAAATAAAAATATTGTCCAAGGCATACCAAAAGTATTCCGACTTGCTGTTAACTCACTATCATTATTCAATCCAGAGTGT
+TCAGCCATTTCTGCCCAATAACGAATAATCTGAAAAGTTGTTAAAAGTGGTATAAACCAATAAAGAATAACATATAACCA
+AAAATTAAACATAATTGATAACGTAATAATTGTTACCCAGAAAATATTTCTAGTCCATATTTCTGATTTAGGTGTATCCC
+TACTGTATAAGTTAGCTGAAACTGTACCTAAAACATATTTAGGCACATGGAATAAAAATAGTACCTTTACAATGTGATTA
+ATTATAAATTTTTTCACATCTTTTTGCGGCTTATCTAAACCTACAATGCGATATCGTTTAGTATCTGGGTCTTTTTCCTC
+ATCCCATAAATTTCTATGATGTTTAAAATGAGAATTACAATATGTAGTAAAGCTTGTAAATATAGGGAATGCTACTAAAA
+GACAAGCAATCCATTTATTATAAAACTTATTTGTAAATAATGAACGATGACATGCTTCGTGCATTAAGTTATCAAACGCC
+CTCATTCGACTTCCAATTAAAATAATACTTATAATATAAATAATGAGATTACTCATATAGATACTTATACATGCACTCCC
+GAGAATTACCAACCAGTCAAAAATCAAAGCGAAAATATTGTGGTAATTATCCTTTTTCATTAATAACTTCAAATCTTTTT
+TTATCTCCATTGAAAATACAGCTTTTTCTAATTTTAGTGTCAATTTAACCGCCTCCCTTATTTAATATGTTATAATAATC
+TGAAAATTAAAAAACCTACCAGATTCTAATAAAAATTCCAACCAGATTGAGGATGACATTTATGACTAAATTTCAATATA
+AAAAAATTATTGATGATATTATTAATAAAATTAACAACGGTATTTTATCTCCTGGAGATAAATTGTACTCGCAAAGAAAA
+TTAGCTAAGTACTATAATGTAAATAAATCCACAGTTATACAAGCTTTAGATATTCTAAAAAGCTATGGCATCTTAGATAC
+AATTGAAAAAAAAGGTATTTATGTATCCCAGTATAAATGGAATTCTTATATTACCAATAATATTCATTGGCAAGATTATA
+TAGGCAACAGCTTTTCTAAAAATAACCAGTATTATATTCAAAAAATTAATGAAATAGAATTTAATACTGATATCGTCCGA
+TTAGGTACTGGAGAACTATCACCAAAACTAATTCCAAACCATATATTTAAAAAAATATTAACTAATGATATTGAAGAATC
+TTTACAAACTAACTATGAAGAACCTAAAGGAAATCTAAAGTTAAGGATAGAAATAGTAAAGTATATGAAGCGAAGAGGAG
+TTGATTGTAATATCAATAATATATGTATTACATCCGGTGCTGTACAAGGTTTAAAACTAATTGCAGACGGACTGTTAATT
+CCACAATCTAAAATTATAATTGAAACACCATCATACATTAATTCCATACGTACTTGGCATAATATCAGAGCGAAAATTAT
+TCCTTTGTCCATCAATTACATCAAACAGAATATTAACAATATCTTTAAATTAAATAGTGATTATAGGCACAGTATTTTTT
+ACTGTATACCTACGCTGCATAACCCTACTCAAAATACTTATAGTAAAGAAGAGAAGCAAAAAATTATAGATCAATGTCAT
+AAAGAAGGTATTCCAATTGTGGAAGATAGTATATACTCTGATTTATGGTTCAGCCCTAACCAACAAATTTCTATGAAAGC
+TTTAAAAAATAGTGATAATGTTTTATATTTAGGTAGTTTATCTAAAACTGTAAGTCCCGGTTTACGTATTGGTTGGATTA
+TAGCAGATGAAAAAGTAATTCATCATTTAGCCGATTTAAAAATGCAAAATGATTATGGTGCAAGTTCTATATCACAGTAT
+ATTGCCACAACGTGGTTAAGTAATTATCATGAAGATCATTTATATAAATTAAAAATCGAACTAAAATTACGAAAATCTAT
+TTTTATAAAGTCATTAAAGAAACATCTATCTAAGTTTGGATATTGGAATGAACCCCAAGGCTCATTTTATATCTGGTTTA
+AGCTATCTGTTCCAGTAAATATAAAGCTCTTATTTAACGAAGCAATAAAAGAAAATATACTAATACACCCAGGAGAAATA
+TATGACATTAACTCTAAAAGCTATATCCGCTTTTCATACTCATATATCGACAAGGAAGAAATTGACCAAAGCTTAAAAAA
+ATTAAGTGAAATTATAAATAGAATACGAACTTAGTTAACATTTATCACCCTTTATATAATTCATTTTATACATGCGTGTT
+ATAATATTAAGCACAATACGCATTACATTTCATAAAAAACCTAAAATGCATTTTGTTATAAGATATTGGGATATTATACA
+CATTTACAAATATTGACAATATGATCTATATCATCAAATATTATTTCATTGTATGAATATAGAAGTTTTATTAAAAGATA
+ATAATGAGTACTATTAAAAAGGGAATTCCCCAAAAAATGTTTTGATTGGAAATTCCCTTTTTTAATTTTTATGTGGCGAA
+TTGTTGCACTTAATTTGACAACCTAAAACTTAAGAAAATATTCAGTCACACAACCTATCTTACTTATTACTTATTTAATT
+CCGTATACCCATCTCACAAATCCATCTATAATACAAACTATCATTTTATATAAGCAGAATTTACCCTGTCTTCCACACAA
+ACTGTTTTCGTCACTTTAATATGTCTTCTATTCAAAAAAGTCACTCATAACAAATTGCGCATTTTAATAAATTTAGCAAT
+GCCATTTGCATGCTGCAAAAATACTCATATTAATATTTATATTTTATATTATTTAAGTTTTTTAAATCCATATTTTTATA
+ACACTTGCTATGTGATAAAATTAATTTTATATATATAATCTTAAGATTCAGATTATTTAATAGCAAAGGAGATAGTGATA
+TGGATGTTTTAACAATAGAACATTTAACAAAGAAGATAGGTAATAAAACGATTCTCGACGATGTATCATTTAAGCTGAAA
+CGCGGACAAATAGTTGGTCTTGTTGGAGCGAATGGTGCAGGTAAAACAACTTTAATGAAAGTTATATTAGGTTACTCTAG
+TTTCCAAAGCGGGAATTTTAATGTTATTAACAGCAAGGATAGCAAAAGCAATATCGGTGCATTGATTGAAAATCCAGGAA
+TATATCCTTTTATGTCTGGATATGAAAACTTGAAGTTATTGAATGAATCAAAAAACACTCAAGATATCGATAAAATTGTC
+TCACAACTTCATATGGATGAATACATTCATAAAAAAGCTAAAACGTATTCTCTTGGTATGAAACAAAAATTAGGAATTGC
+TATAGCATTTTTAAATGAACCTCAATTTATTATCTTAGATGAACCAATGAATGGCTTAGATCCAAAAGCTGTGCGAGATG
+TACGTGAATTGATTGTCCAAAAAGCGCAAGAAGGTGTCACTTTCTTAATTTCGAGTCATATTTTAAGTGAATTAGTTAAA
+ATCACAAACTCTATCCTTATTATTAACAAAGGTAAAATTGTTACAGAAACATCGGAAGAAGAACTTAAACAATTTAAAGA
+TAATGATTTAGAAAATGTATTACTAGACATCATAGAAAGGGAGGATCAAGCATAAAATGGGAACTTTAATTAAACAAGAA
+TGTTTCAAATTATTTAAAAAGAAATCAACTTTTATCGCACCTATTGTCTTTATTCTACTAATGGTTGCTCAAGGTTATAT
+TGCTACAAAATACAATGAAATTTTTACACCACAGGAATCTTTTACATCTGCTTATAATGGTTTTTCATGGTTTGCATTTT
+TATTAATTATTCAAGCAAGTACAATCATTTCAATGGAATTTCATTACGGTACGATTAAAAATTTACTCTATCGTGAATAT
+TCAAGAACAACTATGATTGTTAGCAAAATCATCACATTATTTATTATTTCTTTAATTTATTTTGTTATTACAATTATTGC
+TTCAATTGTTATTGGGTCTTTATTCTTTAATGATTTAAATATATTTGAAAGTAGCGGTAATCAATTATCTTTATTGAATC
+AATTATTATTAGTTAGTTTAGGTACATTTGTTGGTGTTTGGTTAGTTTTAAGCTTAACGTTGCTATTATCATCTGCAACT
+AATTCAACGGGTGTAGCCATTGCTGTAGGTATTGTTTTTTATTTTGCAAGTTCTATTTTAGCAGTTATTCAAACGGCACT
+TTTAGAAAAAATAGACTGGCTAAAGTGGAATCCTATTAATATGATGAATATTATGCTTCAAACAGTTGAAAAAGGCTTTA
+GTAAGTCGACGAAATTAGAACTTCATGAATTGTTTATTGGTAATATTGCTTATATTTCTATTTTCTTAATACTTGTAGTA
+TTTATTTTCAAGAAGAAAAATATTTAGTAACTTAAAGTATTAGATGAATAAATACACACATATTTCATCGTAATTCAAAA
+TTATTTTCAAATCCCTTCACCCAAATAATGGTGCAGGGATTTTTGATATGTCAGCATGCCACTCATTCTATCTTTAATAT
+ATTTCAAAATCCCCCCACTTGTAATGTACAAAATATGCTCACTTAAACGATAATCGTATCTCTGCCAAGCTATTTCAACT
+CTGCTTTAATATAAAAATTATTCTCCCGGATGGGATGCTTATATCTCTATCATGATATTTCAACGCCGCTTCAACAACTT
+TATCACTTCATATTTATGCGGGTACACTTCAACGCTACTAATATGAATGATACAACCACAGATTCTCAACACTAAAATTC
+ACAATATGTTTACTCTATTTTTATCAATTCAAGCATACTTATTGAAAAATGTTAACGTTTTCTTGATAATCATTGTAAGC
+GTATTAATTTTACAAACCAATGATTGAAATATACTACAGGAGTGACACACAATGACTCAAATTACTGAAAGAGAATTAAA
+AAAGAAATATTTGGATTTATTATCTCAACATTTCGATACTCCAGAAAAGCTTGCGACTGAAATTATTAATTTAGAATCTA
+TTTTAGAATTGCCTAAAGGTACGGAGCATTTCGTCAGCGATTTACATGGTGAATATGAAGCTTTCCAACACGTATTACGC
+AACGGTTCTGGGAACGTGCGAGCGAAAATTAATGATATTTTCAAAGACAAGTTATCAACGAAAGAACTTAACGATTTGAC
+TGCCCTTGTTTACTATCCAGAAGACAAATTGCAACTTATTAAATGTGATTTTCAAAATTATGGACAATTAAATGTTTGGT
+ATATTACGACGATTGAACACCTCATTCAGCTAATTAAATATTGTTCTTCAAAATATACGCGTTCAAAACTTCGACGTGCC
+TTGCCGGAGCAATACGTTTTCATCGTAGAAGAGTTATTATATAAGAACAACGAATTTAAAAATAAAAAATCTTACTACGA
+AACACTTGTAAACCAAGTGATTGAGCTTAAGCAAGCGGATGATTTAATTATAGGGCTTGCGTATTCTGTACAACGCTTAG
+TCGTCGATCATTTACACGTTGTCGGCGATATTTATGATCGTGGCCCGCAACCAGATAAAATCATGGACACGCTGATTAAT
+TATCATTCTCTGGATATTCAATGGGGTAATCATGATGTGCTGTGGGTTGGTGCGTATGCAGGGTCTAAAGTATGTTTAGC
+TAATTTACTACGTATTTGTGCACGTTATGACAATCTAGATATCGTTGAAGATGCATACGGTATTAATTTAAGACCTTTGC
+TAACATTAGCCGAAAAATACTATGATGCAGATAATCCTGCTTTTAAACCTAAAAAAAGGCCTGACAAACATGAACGTTTA
+ACTCAACGCGAAGAAAGTCAGATTACTAAAATTCATCAAGCAATTGCGATGATTCAATTCAAACTGGAAATACCGGTTAT
+TAAGCGACGTCCAAACTTTGAAATGGACGAACGACTTGTACTTGAAAAAGTTAATTATGATACTAATGAAATAACAGTAT
+ACGGAAAAACATATCCATTAAAAGATACATGCTTCCAAACTGTTAACCGTGATAACCCAGCAAAGTTACTACCTGAAGAA
+GAAGAAGTCATGAACAAACTATTATTGTCATTCCAGCAATCTGAAAAATTACGTCGTCATATGTCTTTCTTGATGCGTAA
+AGGCTCACTTTACTTACCTTGTAATGGCAATTTACTCATTCATGGTTGTATTCCAGTTGATGAAAATGGTGAGATGGAAT
+CATTCGAAATTGATGGTCAGACATACAGTGGCCAAGAGTTATTAGATGTGTTTGAATATCATGTCCGTAAATCATTTGAT
+GAAAAAGAAAATACTGATGACTTATCCACTGATTTAGTTTGGTATTTATGGACTGGGAAATACTCTTCACTATTTGGTAA
+ACGTGCGATGACTACGTTTGAACGATACTTTATTGCAGATAAAGCTTCTCATAAAGAAGAAAAGAATCCGTACTATCATC
+TTCGTGAAGATGTGAATATGGTTCGTAAAATGCTCAGTGATTTCGGATTAAATCCAGATGAAGGACGCATTATTAATGGT
+CACACACCAGTGAAAGAAATTAATGGCGAAGATCCTATCAAAGCTGATGGAAAGATGCTTGTCATTGATGGCGGCTTTTC
+AAAAGCTTATCAGTCAACAACTGGCATTGCAGGCTATACATTGTTGTATAATTCATTCGGAATGCAACTCGTTGCACATC
+AACAATTTAACGCAAAAGAAAAAATTCTTTCCGAAGGTATCGACGAACTGTCAATTAAACGGATTGTTGATAAAGAATTA
+CAACGTAAAAAAATCCGCAATACAAATAAAGGTAAAGAGCTTCAGGCTCAAATAGATATTTTGAAAATGTTAATGCATGA
+TCGTTACTTAGACTAAAGACGACTTTTGATGCACGTGTCGTACACTTATTTAGAGGTGCTGTGTTTACGCATTGGCTACG
+CAAACGCGATGGTAAATAGGCGACCTAGCTACACCGAAAAAATCCCCTCACTATTACGAGTAGTGAGGGGATTGGTGTAT
+>PZTC01000055.1 Staphylococcus aureus strain CM178 PROKKA_contig000055, whole genome shotgun sequence
+ATTAAAACACTTCTTTCACAATCAATCTCTCATGCCATATCCACTCATTATGATTGTTCCAATAAATGCGACACCAACCA
+TCTATAATTTCAAACACATATATTAATGTTCCAGGCGCGTATACAGCCTGTCCAACATCGAATCTATAGTTAGTACGATT
+ATCACCGTATCTAGTGGCTGAAGTAGCACCTAAGCCGTCGATTTTCGCATTAAAATAAGCACCTTTTGACCATTTAAGGT
+TATAAGGCGCTTTACTTCCAACTGTTATTTTACTTGCAGATTTACCGACTGCTTTTTGAGCAGGTGGTTTAACTTTATTT
+GTGATCTTATTCATTAAGCCCTCACTTTTATACTTAGGTCTAATAAAGTGAGTACAGCCGTAATAATTATCCCAACGTAA
+CTTTGCAGGCGTATTTGCGTTACCGTCATAGTTCTGTTCCAAAATTAAAAATTGATTTGTATTACCACCATTAAACACTA
+AACCAATATGACCGTATTGTTTATATATTCCTTTGGTAAATACAGCCACATCACCTATTTGTGGAACAAACGATGGTGTG
+TTTTCATATACTGTTGCCATGTTTTTAAAATCGTTATTGATTGCATCTTTTGCATTTCCCCACATTCTAATTTCTAACAA
+CCAATAAATGTAATCAACTGCTAAATCTGCACATTGGTAACCATACCAACCGTCAAAATCAATATATCTACCTTGATACC
+AACGTAACCTTGCTCTTGCTTCACTGTATGTTTTCATTATTTTACCTCCTAGTATTTTCTTCTTGGTTCTTCATATTCTA
+AAGCTTGGTGGCTATCACCTATACCTTTAGTAGTCGGGTCTTGAATCACACCAGTTAATACTAAAAATCCTAATATAGCG
+TTTAAACCGTCTGTTAATTGCTCTGTATAAACTTGAATATCATACCCAATAGCTTTGGCGATGTTTTGAGCAAATAAAAA
+GATAGCTGACAATATCGCTACCCAAAATGATTTTTGTTTCATTCTAATTTTCCAATTAATCATATTCTTATCTCCTTTTA
+TCCAAAATAAAAAGACGACTAA
diff --git a/tools/phylophlan/test-data/GCA_003236795_trunc.fna b/tools/phylophlan/test-data/GCA_003236795_trunc.fna
new file mode 100644
index 0000000000..d5ab4745d9
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_003236795_trunc.fna
@@ -0,0 +1,119 @@
+>PZTE01000001.1 Staphylococcus aureus strain CM175 PROKKA_contig000001, whole genome shotgun sequence
+GTATTGACATTAATATCTAATTGTAATGTATCGATTAAGTATTGAAACGACACGCCTTTTTCATATTCTTGAAACATATA
+TAGCAGTACATCTATGTCTACTTTAGGTTTTATTGACATAAATAAAGGTCCCTTCAAAGTTTTCATTTTTTCAATGTCTA
+CTTTGAAGGGAGCATTTCAATATGCTTAAGTCCGAACTCATTGTTTATACTTATAAATTTTACGGGTTTAATATAATACT
+TATTTACCTGTAATATATGATAATTCTTCAGCGGCAGATGCGTTGATAGTTCTATGAGAAATGATACCTAATCCTTTAAC
+ATTGGATTCTGAAATAACGATAGAACCATCACTGTTAACTTTTTCAACAAATGCTACATGACCGTAATGTTGATCTGCAC
+CAAATTGTCCAGCCTCAAATACAACAGCAGCATGACGTTTTGGTGTATGACTTACTTGATAATCACGGTATTGAGCTCGA
+TTATTCCAATTATGTGCATCACCTAAATCACCTGAGATAGATGTACCAAATTGTTTCATACGGTTATATACGTACCAAGT
+ACATTGGCCATGTGGATATGGCATACTATCAGATACCTCGCGGAAAGGTTTGAATTCATCTGATGAATCATCATAATCCT
+TGATAGAACGTTCATATTTATCTAAATCTGGCATGCGTTCATCGTCAAACTGAGTTAATTGATAGTGTTTAATAATACTG
+TTTAATTTCTTAGCATAGTTTGGATCTGTAGCATATGTTTTAGATAAGTGTGATGTTGCATCTTTATAAGAATCGGCTTC
+CGATTTCCATGTTGGTTTATAAATTGTTCGATTGCCATCAATACCATTTTTAATAAGGTCAGAGTAATCTTTTAGTGATT
+CTTTCGTGCTTGGATATTTTCGGAATCCAGCATTAATACTATACAATTGATTACCATCAGCTTCTAATGTGTTAAAAGGA
+ACAGAATTCCCTTCAAAAGCACCTTTGATACCGAATAAATTATGGTTTGGTGACTTAGCTAAAGCACTACGACCTGAGTC
+AGATTCTAAGATTGCTTGGGCAATCATGACAGACGCATAAATATCGTTATCTTGACCAATGCGATGTGCATCTTTAGCAA
+TTGATTTTACAAATTGACGTGTATCTTTTGAGTCAACAACGTTAAATTGTCCACTATCATCATTGTTAGATATACTAGGA
+TCTGTTTCGAATAATGATGTTGCACGTGTATCCTTTTGATTAACATCGTTATTGAATGATTGAGCAGGTTTAGATTTATG
+TTTCAATTCATCTTGTGTTGGTAACTGTGGATTCTTTGTATTAGATTTTTCATTTTTGTCTTTTTTAGATTGAGATGCGT
+AATCTTTTTGTGTTTTCTTTGCATCTTCACTGTATTGATCCAAAATAGAGTCTAAAGCCGAATCTGACATTGATTGATTA
+CCTTTCGATGAAGATTTTTGATTTGCTTTATCGTCACTTGCTGGTTGACTATTTGATTGATTTGGTTGTGTTGGCTTTGG
+CGAATTTGGTTGCTTGTTAGATGTACTTGGTTTTGAATTGTTTGATTTAGGTGCTTTTTGATTGTCTGCTTTATCTTGTT
+TAGATGATTGCGTATCAGTGTCATTTTTGATGCTATTGTCACTGTTTTTATTCGAATCATTTGTTGACTTTTCACCATTA
+CGAGGTTGTTCGTAATCAGAAATATCCGAATTTAAATTGAATAAGTTTTGGATTAAAGTTGTTAATGAGTAATTATCATC
+GTATTTATTTTTGGTTAGCAATTGGTTTATATTGGTTTGTGGTAAATTCTTATAAATAAAATCAATGATATTGTTAGAGT
+CTGAAGTGCTGTCGTCTATAGTTTTAAATTTTTTGTCGTTATTGTCTTGGTTACTTGTATTATTGTTGTCTGCTTTATCA
+ATATCTTTACTTGTAGTATCCTTAGAAGTTTCATCGTCATTAGATTTTTTTGAATCATGAGATGTTGTCTTAGCTGTAGT
+ATCTTTTTGAGGTGTATCAGCATAAGCGGTAGGTGAAACTAAAGTAGGTAATACGAGCGTAGTTGATAGCAAATAAATTA
+AAATTTTATTTTTAGGCATATTTCGTATTCTCCCTTGAAAAATATAATAATTAAGTGTGATAATAAACTATGATTTGTTA
+TAATTTATCGTATGCTGAAAATAGTTGATAGGTATCAATCGACTAAATATCTTCCAGTAAATTGATTATACTAATTCACA
+ACGCAAAAATAAATTAATTTACAAAAAATATATAAAAAATATGAATAATTCCTACATAGGAGTGTGACAATGAAGAACGC
+ATTTAAATTATTTAAAATGGATCTGAAGAAAGTAGCTAAGACGCCAGCTGTGTGGATTATCTTAGCAGGCTTAGCTATTT
+TACCATCGTTCTACGCTTGGTTTAACTTATGGGCAATGTGGGATCCATATGGCAACACGGGACACATCAAGGTCGCAGTC
+GTTAATGAAGATAAAGGCGACACAATCAGAGGGAAAAAAGTTAATGTCGGTAATACGATGGTTAATACACTCAAGAAAAA
+TAAAAGCTTTGATTGGCAGTTTGTAAGTAGAGAGAAAGCTGATCATGAGATAAAAATGGGTAAATATTTTGCAGGTATTT
+ACATCCCATCTAAGTTTACACATGAAATTACTGGAACACTACGTAAGCAGCCTCAAAAAGCAGATGTAGAATTTAAGGTG
+AATCAGAAGATTAACGCTGTTGCGTCTAAGCTAACAGATACTGGTTCGTCAGTTGTCGTTGAAAAAGCGAATGAACAATT
+TAATAAAACAGTAACTCGAGCATTATTAGAAGAAGCTAACAAAGCAGGTTTAACTATTGAAGAAAATGTGCCGACAATTA
+ACAAGATAAAAAATGCGGTATATTCAGCAGATAAAGCTTTACCTAAGATTAATGACTTTGCGAATAAAATTGTATATTTG
+AATAACCACCAAGCGGATTTAGATAAATATGCGAATGATTTTAGAAAACTAGGAAATTATAAAGGTGATATTTTAGATGC
+TCAGAAAAAATTAAACGAAGTCAATGGTGCTATTCCGCAACTTAATGAAAAGGCTAAGTTGATATTAGCTTTAAATAATT
+ATATGCCGAAAATTGAAAAAGCGTTAAATTTTGCAGCTGATGACGTGCCAGCGCAGTTCCCTAAAATTAATCAAGGACTT
+AACATTGCGAGTCAAGGTATTGATCAAGCTAATGGACAGTTAAATGATGCCAAAGGCTTCGTCACACAAGTTAGAAGTAG
+AGTCGGTGATTATCAAGATGCAATTCGACGCGCGCAAGATTTAAATCGAAGAAATCAGCAACAGATTCCTCAAAATAGCG
+CGGCGAACAACGAAACATCAAATAGTGCACCTGCAGCTGGTAATGGTGTAGCACCAACGCCACCAAGTGCACCAAGTGGC
+GATACCGCACCAAATAATAATGTTACGCAAAATACCGCACCAAATAGTAATAATGCGCCTGTATCGACTACACCACAAAG
+TACAAGCGGGAAAAAAGATGGGCAAAGTTTTGCAGATATAACAACAACACAAGTCAGCACAGCTAACGAGAACACACAAA
+ACATTACAGATAAAGATGTTAAATCAATGGAAGCGGCATTAACGGGCTCTTTATTATCATTATCAAATAATTTAGATACC
+CAAGCGAAAGCCGCACAAAAAGATAGTCAGGCATTACGTAATATTTCGTATGGCATTTTAGCATCGGACAAGCCTTCTGA
+TTTTAGAGAGTCTTTAGATAATGTTAAGTCCGGTTTAGAATACACAACTCAATATAATCAACAATTTATCGATACATTAA
+AAGAGATTGAGAAGAATGAAAATGTTGATTTATCAAAAGAAATTGATAAGGTAAAGGCAGCTAATAATAGAATTAATGAA
+TCACTAAGGTTAGTTAATCAATTAAGCAATGCATTAAAGAATGGTAGTTCAGGAACTGCTGAAGCTACTAAATTACTAGA
+TCAACTGTCAAAACTAGATTCATCATTATCATCATTTAGAGATTATGTTAAAAAAGATATTAACAGCTCTTTAGTATCAA
+TATCACAACGTATTATGGATGAATTGAATAAAGGGCAAACGGCATTGTCTAATGTTCAGTCTAAGCTAAATACAATTGAT
+CAAGTCATTAACAGTGGACAAGCTATTTTAAAAAATGGTAAAACACGTATCGATCGTTTACAAACAGTATTACCAAGTAT
+TGAACAACAATACATTAGTGCTGTTAAAAATGCTCAAGCAAACTTCCCTAAAGTGAAAAGTGATGTAGCGAAAGCAGCTA
+ACTTTGTACGTAACGATTTACCACAGTTGGAGCAACGTTTAACCAATGCGACAGCAAGTGTGAATAAAAATTTACCAACG
+TTATTAAATGGTTATGATCAAGCGGTAGGATTACTAAATAAAAATCAGCCACAAGCGAAAAAGGCTTTATCAGATTTAGC
+TGATTTTTCTCAAAATAAATTGCCTGATGTTGAAAAAGATTTGAAAAAAGCGAATAAAATTTTCAAGAAATTAGACAAAG
+ATGATGCAGTCGATAAATTAATCGACACGCTTAAGAATGATTTGAAAAAGCAAGCGGGTATTATTGCAAATCCTATTAAT
+AAGAAGACTGTTGATGTTTTCCCAGTTAAGGATTATGGTTCAGGTATGACACCATTCTATACTGCACTGTCAGTATGGGT
+AGGTGCACTCTTGATGGTAAGTTTATTAACGGTTGATAATAAACATAAGAGTCTAGAGTCAGTGTTAACGACACGACAAG
+TGTTCTTAGGTAAGGCAGGATTCTTTATAATGCTTGGTATGTTGCAAGCACTCATTGTATCGGTTGGAGATTTGTTAATC
+CTAAAAGCAGGGGTTGAGTCACCTGTATTATTCGTACTTATAACGATTTTCTGTTCGATTATTTTCAACTCAATCGTATA
+CACGTGCGTTTCATTACTTGGTAACCCAGGTAAAGCCATTGCAATCGTATTGCTTGTATTACAAATTGCAGGTGGTGGAG
+GAACATTCCCAATTCAAACTACGCCACAATTTTTCCAAAACATTTCGCCATACTTACCATTTACGTATGCAATTGATTCA
+TTACGTGAAACAGTAGGCGGTATTGTTCCGGAAATCTTAATTACAAAATTAATTATATTAACGTTATTTGGCATAGGATT
+CTTCGTTGTAGGTTTAATTTTAAAACCTGTAACAGATCCATTGATGAAGCGCGTATCTGAAAAAGTTGACCAAAGTAACG
+TTACAGAATAAAAATTAAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGA
+TAGTAATTTCTGTCTTTTATGGGACGGGTGTTATCATTGCTATTATCCAGGATGACTTACTATAGCACTAATATTACCGA
+CAAAGTGAATATCCTCGTCTTCCGTAGTTAAAATAAAGCTAGAACCTTTTTGGATGTCATAGTGCTTATCGTTTACTGCT
+AAAGTGCCAGTACCATCGATAATTGTAACTAAGCAATAAGCATGTGGTTTATTGAATTTTAAATCTCCATGAATATCCCA
+TTTATATACTGCAAAATACTGATTATCTACAAATTGAGTTACAGTGTGTGTGTCGATGTGAGTTGTTATAGGAGTAGTAT
+TTGGTTCATGATTGCCTAATTCAATCACATCTTTACTTTGCTCTAAGTGCAAATCACGCAATTGACCATTTTGATCTCGT
+CTATCATAGTCATAAATACGGTATGTCGTATCGGATGATTGTTGTGTCTCTAAAATTAAAATACCCGAACCAATGGCATG
+GACAGTGCCAGCAGGAACATAATAAAAATCACCGGGCTTAACAGGTATACGTTTGAAAAGACTGTCAAATTCATGATTAT
+CAATCATGTCGATTAACGTCTGTTTATTATGTGCATGTACGCCATATATAATTTCAGCACCTGGGGCTGCATCTAAAATA
+TACCAACATTCTGTTTTACCTAGTTCGCCTTCGTGTTTTAAAGCGTAATCATCATCCGGATGAACTTGAACAGATAATTT
+ATCATTGGCATCTAATACTTTAGTTAGCAGAGGGAAACTATCTCGTGAATCATTATCGAATAATTCACGATGTTGTGACC
+AAAGTTGATCTAGGGTCATATCCTTGTATGGACCATTGATAATTGTATTAGGACCATTTGGATGTGCAGAAATTGCCCAG
+CATTCACCAGTTGTTTTATTAGGGATATCATAGTTAAATGCTTTTAATGCATGACCGCCCCAAATTCTGTCTTTAAAAAC
+GGGTTGTAAAAATAATGCCATAGTTAAAACTCCTCTATATTTTCATTAATAAGTTGTAAATTTCTGTAGTACTGTTTGCA
+TTAATTAGTGATTGGCGTGTCTCATCATTCATTAACGCTTTAGATAAGCGCTGAAGTATTTTTAAATGTGTATCCTGACT
+GTTGTTTGGTACGGCAATTAAGAATATCAATTGAGGTAGACTACCATCTAGGCTCTCCCATTTAACTCCATGATTATTTT
+TCATAACAGCTACAATCGGTTGTTTTACAACATCAGACTTTGCATGTGGAATGGCCACGTTCATGCCAATAGCCGTCGTA
+GACTCCATTTCACGTTCTAGGATTGCATTTTTTAAATGCGATGTGTGCTCAACATAACGGCAAATTTTAAGTTTATGAAT
+CAACATATCAATTGCTTCGTTTCGAGACATGTCGTGATCAGTAATTACCATAGTTTGTTGATCAAAAACATGAGAAGGTT
+TATTGAGATGTGAATGTTTCGCGGTGTTATCTACATTGTCAACCTCTGTATCATGTTGTGTTATATCTGTATCATGAAGT
+TGCGTGTGTTGCGCTGGTGCATCTACTGCTATAACTGGTGTATTGCGTTTTAATAATAGTACAGTAATCATTGTGACAAG
+ACTACCTACTATCACTGCAAAGGTAAACCATAATATATGATCAATACCACCTAATACAGCCACAATTGGACCTCCATGTG
+CGACTCTATCGCCGACACCACCAATGGCTGCAATGACTGATGCAATCATTGCACCAATGATGTTTGCAGGTATAATGCGC
+AATGGATCTTGCGCTGCGAAAGGAATAGCACCTTCAGTAATACCAAATAGTCCCATAGTGAAGGAAGCCTTACCCATTTC
+TCTTTCGGAATGATTGAATTTATACTTTTGAACAAACGTTGCTAAACCTAAACCGATTGGTGGTGTACATACAGCAACTG
+CGACCATACCCATAACGGCGTAATTACCTTCAGCAATAAGTGCTGAGCCAAATAAAAATGCTACTTTGTTTACTGGACCG
+CCCATATCGAAGGCGATCATCGCACCTATAATCATCGCAAGTATAATAATATTAGCACCTTGCATACTTTTTAACCAGGT
+TGTTAATGCCTCAAAAATATTAGAAATTGGTGCACCGATTAAAAATATAAATATCAATCCTACAACGACCGATGAAATAA
+TGGGAATAATAATGATAGGCATAATTGGTGCCATTGCTTTTGGAACTTTAATATCTTTAATCCACTTTGCGATATAACCT
+GCTAAGAAACCAGCAACAATACCACCTAAAAATCCTGCGCCTGCATCACTGCCATAAAAACTACCGTCAGCAGCGATAGC
+GCCGCCAATCATACCAGGAACGAGACCGGGCTTGTCAGCGATACTAACAGCGATATATCCAGCTAGTATTGGGACCATAA
+ATTTAAAGGCTAAACTACCAATGTTTTCAATGGATTTCCAAAATGAATCATCTGGGATGACTAATCCTTTTGATGTCGTT
+>PZTE01000044.1 Staphylococcus aureus strain CM175 PROKKA_contig000044, whole genome shotgun sequence
+GGTTCTCCACCAAATGTGGTGGGTATATAATTTAAAGAACTATTTTAAATTACAACTTTTAGAGTTTTTATTATTAGGCG
+GCCAGTCCATTATTGGGCTTGGTTGTCTTCTTTTTTTCTCCTTTGTACAAGCTGAAAATCATCATTATACGTGCTTTAAA
+GTTGTTGAAATTTCTGTAACCAAAAGAAATTCGCTTGATTAATTTTATCTTATTATTAATTCCTTCTATAGCACCATTAT
+TAAATGCTGGGTAATAAATTGTATTTCTTAACATCCTTTGATGTTTTCTATAATATTTAACCACTTTCCATACACCCTTA
+CTCACAGACTTTTTACTAACTGAATTTAAACGATTAATAAATTTAGGCCAATTACATAACCTTAGGTCTTTTCGTAATCC
+TTGGACAAGTTCGTAGGAGTGTCGTAGTATATCGTCTTTTGAAAGCATGAATTCTACAATGTCAGATGAGCGTTTATAAG
+CCTTAAAAGATTTATTCCATCTGTATTTACTAAATATGGTTTTACTAGTATCCATCAATAGAACTTTCCAGTTATTCTTA
+AAAATTGTATAATTAGGTCCTTTTTTATTACGGTATTCATTCATAACTTGTACACGATACTTATTAAGTTCTCTATTTAA
+ATGTTGAACGATATGGAATCTGTCAAAAATAATAGCCGCATTAGGAAATAGGTCGCGAAATAATCGGACATAGGGTTCAT
+ACATGTCAATAGTAACCGTCTTAACTTGTTGTCGATTTTTTAAATCGAATCGCTCGAAATAGGCACGCAAGAATCTTGTA
+GTTCTATTTTCTAAAATATCTATAACATCATGAGTATCATTATCTATAAAAATGAAACTCATTGACCCAGTTACATTTTT
+AACGCTTTTAAATTCATCCATAGCGATGTGTTCTGGCAAACAATTAAACGGTTTAATTCGCAATGAATTAGCCGCTTTAG
+TTCTAATACGACTTACAGTAGATGGAGAGATACAGTTGTCTTCTGCAGTATCAATCTCTGTTTTAACTTTAGTAGCTTCT
+TCTATAACTTTTTGAGTAACACATCTTGAGATAAAACACGACTCATCAACAATTGATGTTTTAGCAGTAAAAGTGCCATT
+GCATTCTAAGCATTTAAAACGTTGTTTAGCTAAGTTGAGGTATGTGTTATACCCTTGAGTTTTAAGTAAAGTAATACGAG
+AAACACGCTTACCATGTTTATGAATTTGTCCTTCATTTTTAACACCACAACAATAACAGGCCGAAGGCTTATACGTTAGT
+ACAGCATTAACCACTGTTGCTTTTTTTCCTTTGATAATGACGTCAATTTCTTGGTTTATATAATTTATATTTTCATCTTT
+TATTCTTAGTAATTCTAAGGTATCATTACACATAGGCGCACTTGTCTCCTTTAGTTTGGGTTTGGTCACTTTAAATTATA
+GAGGCAATTGCGCTTTTTGTGTATTAAAAAAAGCAGGAAGTTTTACCTTCCCACCATAAAAGATGAAGAACC
diff --git a/tools/phylophlan/test-data/GCA_003236805_trunc.fna b/tools/phylophlan/test-data/GCA_003236805_trunc.fna
new file mode 100644
index 0000000000..d827341e42
--- /dev/null
+++ b/tools/phylophlan/test-data/GCA_003236805_trunc.fna
@@ -0,0 +1,118 @@
+>PZRU01000001.1 Staphylococcus aureus strain CM173 PROKKA_contig000001, whole genome shotgun sequence
+TTTGTTTTCAAACCAATGTTATATTGGAATGGCCATCGCATAGCTTTAACATGATTAGTTTTTTTATAGTTGTAATATGT
+TGTTCTAGAGCTAATGAATCCTTGCATCTTTAATATCAAAGCATCTTTGTTATATTTTTTATCCTTCACAAAATCAAATT
+GAATATTTTGAGTCACGCCCCATTTATTACTAGTTTTATCTTCTGTCCTTTTGATAATTTCTATATCGCTTCCTTTACCG
+ATGTCTTCAGTATCGTTGGCAGCTTTAGCATTTTCTAATAACGGATTGGCAAGAGGGGCAAGTAAGCTCACAGATAAAGT
+TGTAGCTAATATTTTATTTCTAAGCATAAGTTTCACTTTCTTTCTATAATTTTATTTAACTTAATTAAATAATAATATAT
+TTTGAACGTTATTATAATTAACTGTTCATTAACAATTGACCATTATCAACTTTTTTTACAATTAAGTTAAAAATGCCATA
+ATTCCGTTCGATTTAACCTTTTTTGTTTGGAATGCTAAAATCTAATTTTGTGAGAAATATAGTTAATAAAACCTTGGTAT
+TGTTGACAGTTGTAAACAATTTAAGGTAACCGATTGCACGAATGTCTTGCTTTTATTTTTAATTAATGTTTGTAAAATAC
+AAATTGTTCTTTTTTAAGATTTTTGATGTATCCATCTAAAAGTTAATTATTTATTAACTTGAGAATATTTTATTTAAGCT
+TTCAAGTTAAATTGCTTCATTTGTATTATTTGTGTATCTACTATGGTGTGATATTTTGTTCTTATAAAAATCAGTTGTTA
+TTATTAAATTTAATGTACGATAAAATAATTTAATGTTATGAGACTGATTCAATATGTTAAAAAATCCTGAGACAAGTATG
+AAGTGTCCCAGGATTTTATAAAATGATTGAACTGTTTACTTAGGTGTGATGCTTTTAATTTTTACTTCATGTGTTTTCCA
+GTTCACTTCATATTTAACTGTAACGTTTCGGTTTTTAAAAGCATCATGTTTTCTATCAACGGCTAAACGATGTCTTGTCA
+CGTATGCATAAGTAGCATCCATGTTTCTGCCGTAAGTGATTTCAAACTCGCTTTTATCACCTTTACCTCTTTCGTGTGAC
+AATGTTGTAATAAATGATGGATTAAAGCCACTTTGAATTAAAGGAGGTAGTTGATTATCTGGGACGAAATAGTCTCTTGC
+TGCTGGACCAGTTGGGTCTTGTGCAAATAAGTATTGATCATATGCAGATACTTGACCATTCGGTGTAACGAATGAATTTG
+CTTTCACTCCCCATTTAACACCTTTAGAGTTCTGACTTTCTACTTCAGTAACATAGTTTTTTTGATTATAACTAATTGTT
+TTAGAGTAGTTGAATGAGCCACTGCCTCCGATTGATGGCGCTGATTGGAAGTTTCCGCCGATATTATAGCCTAATTTCTG
+ACTAACATCTGCTGAATCAATTTTATTTTTAGGAAGATAATTGATTAAATCAACATTAGAGTCTTTCGTTTTCAAACTGA
+TATTATATTGAAATGGCCATATCATTCTTTTAATATATGGATATTTTTTTAAGTCTGAATATGTTGTTCTAGAGCTGATG
+AAGCCTTGCATCTTAACAACTAGAGCATCTTTGTTATATTTTTTATCTTTTACAAAATCAAATTGAATGTTTTGAGTTAT
+AGCTAATCGTTTGCTAGTAATGTCTTGAGTTCTTTTGATGATTTCTGCACCTTGGCCGATATCTTCTATCTTATTTTCTG
+CTTTAGAAATTTCTATAAATGGATTGGCTAAAGGGGCTATTAAACCAACTGCTAAAGTTGCTGTTAATATTTTATTTTTA
+ATCATAGAAATCACTTTCTTTCTATTTAATTTTAAGTTCATATATATAATAATCTATTTGTAAGCGTTTTCGAATTAACT
+GTTCGTTAAAAGTTAATTACTATCAACATGTATTGAAGAGACATTTTAGCATTGTTAAATGATGTTTTTGCATTATGTTA
+TGTTTAAAAGATTTATTGGTCGTAGGCGTTTATATAGCTACATAACTATGTTTTGCAAGTCTTATTCTATTGAATTGTTG
+TTTAATTATGGTGCTTGTAGTGGAAGAGGAATGGATTGCGCAATAGTTTGTGAAAATTTGAAGTTAATAAAGTTGTGCTG
+ATTCAACTAAATGATGAACTATTCGTTAACGATGTAAGGATTATTTAACAAGTTGCAGGTAAAAAAGTAGGCTGACAAAT
+AGCGAAGAAACATTTAATTGATGGAAAATAAAAAAAGAACCGCAGATTCGATTGAGAATCAACGGTTCTTTTTAATCACG
+GTTTATTACGAAAATTATTTAAAAAATGATGTAAAACTAGAGAAGATATTTTTGATTGATGATGCTGTTTCAGCTGTAGT
+TATAGCAGCTTTAACTACTTTTGGATTTTGATAAAATGCATATAATACTTTACCTGTGTTTAAAGTTTCAGTTACATAGT
+TTCTTACTTGTGCATATGATTTAGATACATAATTTTTTTGATCTTCAACTTTTAATGGTTGGATGTATGATTTGTATCCA
+TTACCAAAAACTGATAGTACAGTTTTATCTATTGTACCTTTATATTTAAAATATTTATCAGTGTAGTACTTTGCTGTATC
+ATATTTTTCTTTATAGCTTTTATAAGTATCTGTTAAATATTTGTAACCATAGTTAAATGAATCTTTTAATGATTGGTAGT
+AACCTAATAATTTAGATTGAGGAACCTCAACTTTTGGTGATTGAATTTGAGGGACTTCAACTTTTGGTGATTCTGCTTTA
+GGTTTTTCAATTTGTGGTGATTGAATTTGAGGAGCCTCAACTTTTGGCGCCACTTTCTTTTCAGCATCTTTTTGAGCTAC
+TAATGCGTCTAATTGTTTCTGTAAATGCTTTTGTACATCCATAGGTGCTTTATTAACTTCACGTTGTGCTAAACGTCTGT
+TTTCAATTGAATCTTTTTCATTTAATTTTGAGATTGCATCATTTGCTGATTTCACACGCTCATCATGACGAACGATTGCT
+TTTTCAATTGAAACTTTTTCTACAAAGCGGTTATTTTTATCGCGTAAATCTTTAGGTAATTTTGAGTTAGCTTCATATGC
+TGCTGATTTATCGTGTGGTGCTTTGTTATCTTGGAAATCTTTAATTGCTTTATCCGCATTTTCAATATTTTGACGTTCTT
+TAGCTTTAGAAGATTGTACTGATTCTACCCAAACTTGTTGGCTTCTATCAGGGTTTTCTTTAATTTGTGCAATGTAATTA
+TTTTTTTCTTGTTCAGTTAAGTTATCATTTTTAAGAACATTGTAAAAAGCGTTTTGTTGTGCAACACGTCGGTCTGGGTT
+CTTGCTGTCTTTAAGTGATTCAGAGAATACTTCTTGTGCACGTTCTGGGTGTTCGCGTAATGTTTTGATGTATTGGTTAC
+GTTGTTCTTCTGTGATACCTTTTAGATGCAATACTTGATAAAAAGCTTTTTGTTGATCTGTTACGTAGTTGTTTTGAGTT
+GTTTGGTGCTTAGTTGAAGTTTGTTGCGTGTTTTCACTCGCTTTTGCTTCCCCATTTGAAATCATTGTAGCTAAAGTAAT
+TGTTGCTGCCCCAACTAGCAACTTCGAGATATATTTATTTTTCATGTGTATTCCCTTTCTTTTTACATATTAAATTTATT
+GTATGCTTTTAGAATTTATCACATGAGAATACAAATGGAAATTAACTAATTATTAACTAATGTTAACTAATAGATTAACT
+AGTGTTAACTATGTAAAAAAGCGTTTAATTCAGAACATTCAGCGTATTTTAAGTAAGGAAGTACTATATGGAGAAATGCA
+ATGGTTTGCTAATAAATAGAGGAGAAAATTGTCTTTCGAAGAGAGTTTGGTAGAGTAGAAATCACATTTGATTTGTCACT
+GATGCACTTTTTCTTCTATATAATTAGGTCACGACATTAGATAGCTTCGCAACTCATGCATAGGGTCCCAACATAGAAAC
+TTTCGAGGCGAAAGTTAACAAGTAGGAAGAGTTGGGCGCCTTTCTAACAAATAATTTCGCAGAAAATAAAGGAACGCAGT
+TGGACGTAAAACGTCAACTGCATAAGCCTTTCTAGCTCATAAAATTCGCAGAAAATAAAGGAACGCATTAGATAGCTTCG
+CTACTAATGCATAAGCCTTTCTAACAAATAAATTTGAAGAAAGGCTAAAAAATATTTTTAGGGGTTGCGAATGAATAAAT
+TAGTTTAATTTTATAAAAATTTATAAAAATTAAAAACGTTGTAAATTTAAAATAAATCATTCATAATATTGTTACTATAC
+TAATTCAAGGTGGTTCAACGCATGTCTCATAATGAAAATCTTAAATTGGCGCAACGCGGTGCTTATTTGAGTTTAATTGT
+ATATATAATCTTATCTATTGTTAAGTATGTCACGGGTTTTGTCTTTAACTCTGCAGCTGTAAGAGCCGACGCATTAAACA
+ATATGACAGATATTATCGTTTCTTTAGCTGTTATTATTGGATTGAAAATTTCAATTAAACCTGCCGATCGAAATCATCCT
+TATGGCCATTTGAAGTCTGAAAATATTTCTTCATTATTGGTGTCATTTGTCATTATGTTTGTAGGTATCCAAGTAGTTAT
+TCAAAATGCACTTCGTTTGTTCAAAGAAGATGACGTTGTACCTAACGCAATAACAATTATCGTCAGCTTAATCAGTGGTC
+TTGTAATGTTGATTGTATTTGCAGTCAATCAAAGACTAGCGAAAAGAACGAAAAGTAGTTCTTTAAATTCTGCTGCCAAA
+GATAATTTATCAGATAGTTTAGTCAGCATTGGAACGGCGATAGGATTAATTTTTACGCAAATCGGTTTCCCAATTGTCGA
+TATTATTTTAGCAACATTGCTAGGCTTACTAATCGTTTATACTGGTTTTGGTATTTTTAAAGAAGCAATTTTTATGTTGA
+GTGATGGTTTCAATGAAACTGAATTAGAAGCGTATCGCAATGATATTTTAGAAGTTGATGAAGTACAAGAAGTTAAAAGT
+ATTAAAGGGCGTTACCATGGAAGTAGTGTGTTTATTGATGTCACAATTGTTGTAGATGCTAACCTTTCCTTAGTAGAAGC
+CCATCAAATTTGTGACAATGTCGAACATCATTTGCACAAAAAAGGTATTTCCTCAGTATACGTTCACCCAGAACCAGACC
+ATCTATAATGTATTTAAACGTCTTCATAGATATATAAATATCTGAGGAGGCGTTTTTATTACATTTATTTTTAGGCGCGC
+CTAAAAATATTTTTTAAACCTTAGAAAAATAGCGGACAAAGGTGTATAATATGATTTATTATTAGGTGGTTATTGATTCA
+TTTATGAATTAAAAAATGAAAATGGGGAATAGGATTTATGTATTTAATGTCTAGTGATAATTGATTTAATCATTGAATTT
+TAAAACATATTGAAAAGAAAATTACTAAGATTAAATCATCTTAAAATATCCCTGAAATAACGTCCTAAAGATTAAAGGAA
+AGAGGTTATAAGTTATGCCAAAATTAATTTTATGTCGTCATGGACAAAGCGAGTGGAATGCTAAAAACTTATTTACTGGA
+TGGGAAGATGTTAATTTATCTGAACAAGGTATTAATGAAGCGACTAGAGCAGGTGAAAAAGTAAGAGAAAATAACATTGC
+CATCGATGTAGCTTTTACATCGTTATTAACACGTGCTTTAGATACAACGCATTATATTTTAACTGAATCTAAACAACAAT
+GGATTCCTGTATATAAAAGCTGGCGTTTAAATGAACGCCACTATGGTGGATTGCAAGGCTTAAATAAAGATGATGCTAGA
+AAAGAATTTGGAGAAGAACAAGTACATATTTGGCGTCGTTCTTATGATGTGAAACCACCTGCTGAAACTGAAGAACAACG
+TGAAGCTTACTTAGCTGATCGTCGATATAATCATTTAGATAAACGTATGATGCCTTATTCTGAAAGTCTGAAAGATACTT
+TAGTTCGAGTGATACCATTTTGGACAGATCATATTTCACAATATTTGCTAGATGGTCAAACGGTATTAGTTTCTGCACAC
+GGAAATTCAATTCGCGCATTGATTAAATATCTTGAAGATGTGTCAGATGAAGATATCATTAATTATGAAATTAAAACAGG
+TGCACCGCTTGTTTATGAATTAACGGATGATTTAGAAGTTATAGATAAATACTACTTATAAAAAAAGAGCTGAATGTACA
+CAAGGAGTGAGTGTATATGCAGCTCTTAAATATGTGAAGTAATGTAAGGAAATAGTTAAGTATAGAGTTTATATTAACGA
+GCTAGGGATACTCGAAAATATAGTTAGACATACAATATAGTCAAATTAAAACAATTATTTCGCTCTTTTATGTTGTTTAA
+TAATCTTTAAAGCACGCTTTCTTGTTTTAATGTTAGGGCTATTTAAATTACGACGAGCAGTCTGTAAATCTAATTTCATC
+TCTATCCCTCCTTGTAAATATATTATGACCGATAACTACTCATATGTAAATAGTAATGATTACGTTTTAAAGAAATTGTA
+ATAAAGTCGTGATAATTTTTTTGAAAATGGGTATAATTACCGGATATCTAAAAATGAGTGTCGTTTTTTAGATGATGAGG
+GGGAAGCTTTAAATGTCGAAGAAACAAAAATTAACGAGGATTATTACTATGCTGATGGGTGGATTTTTTGGATTATTAAA
+TGAAACACTATTAGTGACGGCTTTACCAAGTATTATGAAAGATTTTGAAATTTCATATACACAAGTTCAATGGCTGACAA
+CAGCTTTTTTATTGACTAATGGGATTGTTATTCCTTTGTCCGCGCTTGTTATACAACGTTATACAACAAGACAAGTGTTT
+TTAGTGGGTATTACTATCTTTTTCTTAGGTACATTACTCGGCGGTTTGAGTCCGCACTTTGCAACATTATTAGTTGCTAG
+AATTATTCAGGCGTTAGGTGTAGGTATTATGATGCCATTGATGATGACAACGATTTTGGATGTGTTCCAACCGCACGAAC
+GCGGTAAATATATGGGGATATTTGGTTTGGTAATTGGTTTAGCACCAGCTATTGGACCTACTCTTTCAGGTTACCTTGTT
+GAATATTTTAACTGGAGATCGCTTTTCCATGTTGTCGCTCCAATTGCAGCTGTAACATTTTTAATTGGATTTAAAACGAT
+AAAAAATGTTGGAACTACAATTAAAGTACCTATTGATTTTATTTCTGTCATTTTTTCTGTACTAGGTTTCGGTGGGTTAT
+TGTATGGAACGAGTTCAATTTCAGAAAAAGGTTTTGATAATCCTATCGTATTGGTATCTATGATTGGTGGTATTGCTTTA
+GTCGCATTATTTGTATTACGTCAATATCGACTATCAACACCATTATTAAATTTTGCTGTATTTAAAAATAAACAATTTAC
+AGTTGGTATCATTATTATGGGTGTCACAATGGTATCGATGATTGGTTCGGAAACGATTTTACCTATCTTTGTGCAAAATT
+TATTGCATCGTTCAGCTTTAGATTCTGGGTTAACTTTATTACCAGGAGCAATTGTTATGGCATTTATGTCGATGACTTCG
+GGTGCTTTATATGAAAAGTTTGGTCCTAGAAAGCTTGCTTTAGTAGGTATGGCGATTGTTGTTATTACTACGGCTTATTT
+TGTTGTAATGGATGAACAAACATCAACAATCATGTTGGCAACAGTTTATGCGATTCGAATGGTTGGTATCGCGTTAGGAT
+TAATTCCAGTAATGACCCATACGATGAATCAATTAAAGCCAGAAATGAATGCACACGGTTCATCTATGACAAACACAGTA
+>PZRU01000091.1 Staphylococcus aureus strain CM173 PROKKA_contig000091, whole genome shotgun sequence
+CAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCTTAGAATT
+ACTAAGAATAAAAGATGAAAATATAAATTATATAAACCAAGAAATTGACGTCATTATCAAAGGAAAAAAAGCAACAGTGG
+TTAATGCTGTACTAACGTATAAGCCTTCGGCCTGTTATTGTTGTGGTGTTAAAAATGAAGGACAAATTCATAAACATGGT
+AAGCGTGTTTCTCGTATTACTTTACTTAAAACTCAAGGGTATAACACATACCTCAACTTAGCTAAACAACGTTTTAAATG
+CTTAGAATGCAATGGCACTTTTACTGCTAAAACATCAATTGTTGATGAGTCGTGTTTTATCTCAAGATGTGTTACTCAAA
+AAGTTATAGAAGAAGCTACTAAAGTTAAAACAGAGATTGATACTGCAGAAGACAACTGTATCTCTCCATCTACTGTAAGT
+CGTATTAGAACTAAAGCGGCTAATTCATTGCGAATTAAACCGTTTAATTGTTTGCCAGAACACATCGCTATGGATGAATT
+TAAAAGCGTTAAAAATGTAACTGGGTCAATGAGTTTCATTTTTATAGATAATGATACTCATGATGTTATAGATATTTTAG
+AAAATAGAACTACAAGATTCTTGCGTGCCTATTTCGAGCGATTCGATTTAAAAAATCGACAACAAGTTAAGACGGTTACT
+ATTGACATGTATGAACCCTATGTCCGATTATTTCGCGACCTATTTCCTAATGCGGCTATTATTTTTGACAGATTCCATAT
+CGTTCAACATTTAAATAGAGAACTTAATAAGTATCGTGTACAAGTTATGAATGAATACCGTAATAAAAAAGGACCTAATT
+ATACAATTTTTAAGAATAACTGGAAAGTTCTATTGATGGATACTAGTAAAACCATATTTAGTAAATACAGATGGAATAAA
+TCTTTTAAGGCTTATAAACGCTCATCTGACATTGTAGAATTCATGCTTTCAAAAGACGATATACTACGACACTCCTACGA
+ACTTGTCCAAGGATTACGAAAAGACCTAAGGTTATGTAATTGGCCTAAATTTATTAATCGTTTAAATTCAGTTAGTAAAA
+AGTCTGTGAGTAAGGGTGTATGGAAAGTGGTTAAATATTATAGAAAACATCAAAGGATGTTAAGAAATACAATTTATTAC
+CCAGCATTTAATAATGGTGCTATAGAAGGAATTAATAATAAGATAAAATTAATCAAGCGAATTTCTTTTGGTTACAGAAA
+TTTCAACAACTTTAAAGCACGTATAATGATGATTTTCAGCTTGTACAAAGGAGAAAAAAAGAAGACAACCAAGCCCAATA
+ATGGACTGGCCGCCTAATAATAAAAACTCTAAAAGTTGTAATTTAAAATAGTTCTTTAA
diff --git a/tools/phylophlan/test-data/bin2meta.tsv b/tools/phylophlan/test-data/bin2meta.tsv
new file mode 100644
index 0000000000..8a4b82c1da
--- /dev/null
+++ b/tools/phylophlan/test-data/bin2meta.tsv
@@ -0,0 +1,369 @@
+CM_ethiopia__CM_A01_I1_18__bin.19	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.31	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.42	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.51	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.52	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.5	A01_I1
+CM_ethiopia__CM_A01_I1_18__bin.73	A01_I1
+CM_ethiopia__CM_A01_M0_18__bin.21	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.30	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.31	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.43	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.56	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.59	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.60	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.62	A01_M0
+CM_ethiopia__CM_A01_M0_18__bin.63	A01_M0
+CM_ethiopia__CM_A04_I1_18__bin.1	A04_I1
+CM_ethiopia__CM_A04_I1_18__bin.2	A04_I1
+CM_ethiopia__CM_A04_I1_18__bin.42	A04_I1
+CM_ethiopia__CM_A04_M0_18__bin.15	A04_M0
+CM_ethiopia__CM_A04_M0_18__bin.16	A04_M0
+CM_ethiopia__CM_A04_M0_18__bin.8	A04_M0
+CM_ethiopia__CM_A06_I1_18__bin.31	A06_I1
+CM_ethiopia__CM_A06_I1_18__bin.32	A06_I1
+CM_ethiopia__CM_A06_I1_18__bin.34	A06_I1
+CM_ethiopia__CM_A06_I1_18__bin.37	A06_I1
+CM_ethiopia__CM_A06_I1_18__bin.46	A06_I1
+CM_ethiopia__CM_A06_I1_18__bin.54	A06_I1
+CM_ethiopia__CM_A06_M0_18__bin.19	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.24	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.2	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.31	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.34	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.36	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.39	A06_M0
+CM_ethiopia__CM_A06_M0_18__bin.9	A06_M0
+CM_ethiopia__CM_D02_I1_18__bin.21	D02_I1
+CM_ethiopia__CM_D02_I1_18__bin.24	D02_I1
+CM_ethiopia__CM_D02_I1_18__bin.2	D02_I1
+CM_ethiopia__CM_D02_I1_18__bin.31	D02_I1
+CM_ethiopia__CM_D02_I1_18__bin.46	D02_I1
+CM_ethiopia__CM_D02_I1_18__bin.49	D02_I1
+CM_ethiopia__CM_D02_M0_18__bin.17	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.21	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.23	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.25	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.3	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.49	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.4	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.61	D02_M0
+CM_ethiopia__CM_D02_M0_18__bin.62	D02_M0
+CM_ethiopia__CM_D03_I12_18__bin.27	D03_I12
+CM_ethiopia__CM_D03_I12_18__bin.33	D03_I12
+CM_ethiopia__CM_D03_I12_18__bin.34	D03_I12
+CM_ethiopia__CM_D03_I12_18__bin.5	D03_I12
+CM_ethiopia__CM_D03_M0_18__bin.30	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.44	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.45	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.62	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.63	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.64	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.65	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.67	D03_M0
+CM_ethiopia__CM_D03_M0_18__bin.69	D03_M0
+CM_ethiopia__CM_D04_I1_18__bin.12	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.1	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.26	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.33	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.35	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.36	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.39	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.44	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.47	D04_I1
+CM_ethiopia__CM_D04_I1_18__bin.8	D04_I1
+CM_ethiopia__CM_D04_M0_18__bin.42	D04_M0
+CM_ethiopia__CM_D04_M0_18__bin.47	D04_M0
+CM_ethiopia__CM_D04_M0_18__bin.76	D04_M0
+CM_ethiopia__CM_D05_I1_18__bin.27	D05_I1
+CM_ethiopia__CM_D05_I1_18__bin.37	D05_I1
+CM_ethiopia__CM_D05_I1_18__bin.7	D05_I1
+CM_ethiopia__CM_D05_M0_18__bin.24	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.27	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.42	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.4	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.50	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.52	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.54	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.57	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.59	D05_M0
+CM_ethiopia__CM_D05_M0_18__bin.93	D05_M0
+CM_ethiopia__CM_D06_I1_18__bin.21	D06_I1
+CM_ethiopia__CM_D06_I1_18__bin.42	D06_I1
+CM_ethiopia__CM_D06_I1_18__bin.43	D06_I1
+CM_ethiopia__CM_D06_M0_18__bin.10	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.22	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.39	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.40	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.41	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.42	D06_M0
+CM_ethiopia__CM_D06_M0_18__bin.7	D06_M0
+CM_ethiopia__CM_D07_I1_18__bin.13	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.1	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.23	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.30	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.32	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.38	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.44	D07_I1
+CM_ethiopia__CM_D07_I1_18__bin.48	D07_I1
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diff --git a/tools/phylophlan/test-data/database_trunc.faa b/tools/phylophlan/test-data/database_trunc.faa
new file mode 100644
index 0000000000..9e9dce750e
--- /dev/null
+++ b/tools/phylophlan/test-data/database_trunc.faa
@@ -0,0 +1,78 @@
+>s--Staphylococcus-aureus_UniRef90-A0A2X2MCQ2_0
+MINWKIRMKQKSFWVAILSAIFLFAQNIAKAIGYDIQVYTEQLTDGLNAILGFLVLTGVI
+QDPTTKGIGDSHQALEYEEPRRNTRR
+>s--Staphylococcus-aureus_UniRef90-A0A380E267_0
+MKTYSEARARLRWYQGRYIDFDGWYGYQCADLAVDYIYWLLEIRMWGNAKDAINNDFKNM
+ATVYENTPSFVPQIGDVAVFTKGIYKQYGHIGLVFNGGNTNQFLILEQNYDGNANTPAKL
+RWDNYYGCTHFIRPKYKSEGLVNKITNKINPPVQKVVGKSASKITVGSKAPYNLKWSKGA
+YFNAKIDGLGATSATRYGDNRTNYRFDVGQAVYAPGTLIYVFEIIDGWCRIYWNNHNEWI
+WHERLIVKEVY
+>s--Staphylococcus-aureus_UniRef90-A0A7U7JQN2_0
+MLTVDQVKELVGEIKDPIIDVPLKETEGIVEVSIKEEKEHVSVKLAMAQLGGAPQLDLQM
+AVVNVLKENGAKTVGIRFETLPEDKVNQFKPKEENKPKTIEGLLSQNNPVEFIAIASGKG
+GVGKSTVAVNLAVALAREGKKVGLVDADIYGFSVPDMMGIDEKPGIKGKEVIPVERHGVK
+VISMAFFVEENAPVIWRGPMLGKMLTNFFTEVKWGDIEYLILDLPPGTGDVALDVHTMLP
+SSKEIIVTTPHPTAAFVAARAGAMAKHTEHSILGVIENMSYFESKETGNKEYVFGKGGGT
+KLADELNTQLLGELPLEQPSWNPKDFSPSIYQPDDRLGKIYSSIAQKVIASTNK
+>s--Staphylococcus-aureus_UniRef90-P31716_0
+MLKNKILATTLSVSLLAPLANPLLENAKAANDTEDIGKGSDIEIIKRTEDKTSNKWGVTQ
+NIQFDFVKDTKYNKDALILKMQGFISSRTTYYNYKKTNHVKAMRWPFQYNIGLKTNDKYV
+SLINYLPKNKIESTNVSQTLGYNIGGNFQSAPSLGGNGSFNYSKSISYTQQNYVSEVEQQ
+NSKSVLWGVKANSFATESGQKSAFDSDLFVGYKPHSKDPRDYFVPDSELPPLVQSGFNPS
+FIATVSHEKGSSDTSEFEITYGRNMDVTHAIKRSTHYGNSYLDGHRVHNAFVNRNYTVKY
+EVNWKTHEIKVKGQN
+>s--Staphylococcus-aureus_UniRef90-Q2FVK8_0
+MPKLILCRHGQSEWNAKNLFTGWEDVNLSEQGINEATRAGEKVRENNIAIDVAFTSLLTR
+ALDTTHYILTESKQQWIPVYKSWRLNERHYGGLQGLNKDDARKEFGEEQVHIWRRSYDVK
+PPAETEEQREAYLADRRYNHLDKRMMPYSESLKDTLVRVIPFWTDHISQYLLDGQTVLVS
+AHGNSIRALIKYLEDVSDEDIINYEIKTGAPLVYELTDDLEVIDKYYL
+>s--Staphylococcus-aureus_UniRef90-Q2FW81_0
+MLDKNQLAKYKQDHLCEYEKIMSNNEKEALEEKVASLDLDFIAKLYNDLYINKKTIDDVS
+AVSEVKYDIKSQMSDDEIKRLEEQGLQAIKEGQFAVLLMAGGQGTRLGYKGPKGSFEIEG
+VSLFELQANQLKTLNHQSGHTIQWYIMTSDINHEETLAYFEAHSYFGYDQEAIHFFKQDN
+IVALSEEGKLILNQQGRIMETPNGNGGVFKSLDKAGYLEEMSNNGVKYIFLNNIDNVLVR
+VLDPLFAGFTVEHDYDITSKTIQPKPGESVGRLVNVDCKDTVLEYSELDPEVANQFNNAN
+IGIHAFKLGFILNAVNRELPYHLAIKNLKQLDENFGVIEQPTLKFELFYFDIFTYGTSFV
+TLQVPREEEFSPLKNKEGKDSVATATEDLRRMGLI
+>s--Staphylococcus-aureus_UniRef90-Q2FW85_0
+MAKVELTTRRRNFIVAVMLISAFVAILNQTLLNTALPSIMRELNINESTSQWLVTGFMLV
+NGVMIPLTAYLMDRIKTRPLYLAAMGTFLLGSIVAALAPNFGVLMLARVIQAMGAGVLMP
+LMQFTLFTLFSKEHRGFAMGLAGLVIQFAPAIGPTVTGLIIDQASWRVPFIIIVGIAILA
+FVFGLVSISSYNEVKYTKLDKRSVMYSTIGFGLMLYAFSSAGDLGFTSPIVIGALILSMV
+IIYLFIRRQFNITNALLNLRVFKNRTFALCTISSMIIMMSMVGPALLIPLYVQNSLSLSA
+LLSGLVIMPGAIINGIMSVFTGKFYDKYGPRPLIYTGFTILTITTIMLCFLHTDTSYTYL
+IVVYAIRMFSVSLLMMPINTTGINSLRNEEISHGTAIMNFGRVMAGSLGTALMVTLMSFG
+AKIFLSTSPSHLTATEIKQQSIAIGVDISFAFVAVLVMAAYVIALFIREPKEIESNRRKF
+>s--Staphylococcus-aureus_UniRef90-Q2G1T0_0
+MVTAIIHGFILAIGLILPLGAQNVFIFNQGANQPKYRYVLPAIITAGLSDSLLIIIAVVG
+VSIIIMSLPVLQAIIYIVGLIFLMYMAWTIWHDKPSTDGETQIMSPMKQVSFALSVSLLN
+PHAILDTIGVIGSSAALYSGSNKIAFTIACISVSWLWFFLLAILGKMVGSIDKTGKLLTI
+INKISSIIIIIVALMILQKLIQLLF
+>s--Staphylococcus-aureus_UniRef90-Q2G222_0
+MPKNKILIYLLSTTLVLPTLVSPTAYADTPQKDTTAKTTSHDSKKSNDDETSKDTTSKDI
+DKADKNNTSNQDNNDKKFKTIDDSTSDSNNIIDFIYKNLPQTNINQLLTKNKYDDNYSLT
+TLIQNLFNLNSDISDYEQPRNGEKSTNDSNKNSDNSIKNDTDTQSSKQDKADNQKAPKSN
+NTKPSTSNKQPNSPKPTQPNQSNSQPASDDKANQKSSSKDNQSMSDSALDSILDQYSEDA
+KKTQKDYASQSKKDKNEKSNTKNPQLPTQDELKHKSKPAQSFNNDVNQKDTRATSLFETD
+PSISNNDDSGQFNVVDSKDTRQFVKSIAKDAHRIGQDNDIYASVMIAQAILESDSGRSAL
+AKSPNHNLFGIKGAFEGNSVPFNTLEADGNQLYSINAGFRKYPSTKESLKDYSDLIKNGI
+DGNRTIYKPTWKSEADSYKDATSHLSKTYATDPNYAKKLNSIIKHYQLTQFDDERMPDLD
+KYERSIKDYDDSSDEFKPFREVSDSMPYPHGQCTWYVYNRMKQFGTSISGDLGDAHNWNN
+RAQYRDYQVSHTPKRHAAVVFEAGQFGADQHYGHVAFVEKVNSDGSIVISESNVKGLGII
+SHRTINAAAAEELSYITGK
+>s--Staphylococcus-aureus_UniRef90-Q5HDD6_0
+MIKNKILTATLAVGLIAPLANPFIEISKAENKIEDIGQGAEIIKRTQDITSKRLAITQNI
+QFDFVKDKKYNKDALVVKMQGFISSRTTYSDLKKYPYIKRMIWPFQYNISLKTKDSNVDL
+INYLPKNKIDSADVSQKLGYNIGGNFQSAPSIGGSGSFNYSKTISYNQKNYVTEVESQNS
+KGVKWGVKANSFVTPNGQVSAYDQYLFAQDPTGPAARDYFVPDNQLPPLIQSGFNPSFIT
+TLSHERGKGDKSEFEITYGRNMDATYAYVTRHRLAVDRKHDAFKNRNVTVKYEVNWKTHE
+VKIKSITPK
+>s--Staphylococcus-aureus_UniRef90-Q931F4_0
+MKNKYISKLLVGAATITLATMISNGEAKASENTQQTSTKHQTTQNNYVTDQQKAFYQVLH
+LKGITEEQRNQYIKTLREHPERAQEVFSESLKDSKNPDRRVAQQNAFYNVLKNDNLTEQE
+KNNYIAQIKENPDRSQQVWVESVQSSKAKERQNIENADKAIKDFQDNKAPHDKSAAYEAN
+SKLPKDLRDKNNRFVEKVSIEKAIVRHDERVKSANDAISKLNEKDSIENRRLAQREVNKA
+PMDVKEHLQKQLDALVAQKDAEKKVAPKVEAPQIQSPQIEKPKAESPKVEVPQSKLLGYY
+QSLKDSFNYGYKYLTDTYKSYKEKYDTAKYYYNTYYKYKGAIDQTVLTVLGSGSKSYIQP
+LKVDDKNGYLAKSYAQVRNYVTESINTGKVLYTFYQNPTLVKTAIKAQETASSIKNTLSN
+LLSFWK
diff --git a/tools/phylophlan/test-data/output.tsv b/tools/phylophlan/test-data/output.tsv
new file mode 100644
index 0000000000..bfd7c8fa28
--- /dev/null
+++ b/tools/phylophlan/test-data/output.tsv
@@ -0,0 +1,2 @@
+#input_bin	[u|k]_[S|G|F]GBid:taxa_level:taxonomy:avg_dist
+CM_ethiopia__CM_A06_M0_18__bin.34 is not close to any SGB present in the ethiopia_tutorial database
diff --git a/tools/phylophlan/test-data/output_heatmap_counts.png b/tools/phylophlan/test-data/output_heatmap_counts.png
new file mode 100644
index 0000000000..5320c97d7c
Binary files /dev/null and b/tools/phylophlan/test-data/output_heatmap_counts.png differ
diff --git a/tools/phylophlan/test-data/output_heatmap_pres_abs.png b/tools/phylophlan/test-data/output_heatmap_pres_abs.png
new file mode 100644
index 0000000000..2bb08926ff
Binary files /dev/null and b/tools/phylophlan/test-data/output_heatmap_pres_abs.png differ
diff --git a/tools/phylophlan/test-data/output_metagenomic.tsv b/tools/phylophlan/test-data/output_metagenomic.tsv
new file mode 100644
index 0000000000..cab88ef52b
--- /dev/null
+++ b/tools/phylophlan/test-data/output_metagenomic.tsv
@@ -0,0 +1,365 @@
+#input_bin	[u|k]_[S|G|F]GBid:taxa_level:taxonomy:avg_dist
+CM_ethiopia__CM_A01_I1_18__bin.19	uSGB_4894:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_unclassified_SGB4894|t__SGB4894:0.0321575902631579
+CM_ethiopia__CM_A01_I1_18__bin.31	kSGB_4350:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_bacterium|t__SGB4350:0.035591812592592594
+CM_ethiopia__CM_A01_I1_18__bin.42	kSGB_4563:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter|s__Ruminococcus_torques|t__SGB4563:0.037374750437317784
+CM_ethiopia__CM_A01_I1_18__bin.5	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.04053020105263159
+CM_ethiopia__CM_A01_I1_18__bin.51	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03559054139475368
+CM_ethiopia__CM_A01_I1_18__bin.52	kSGB_4940:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_inulinivorans|t__SGB4940:0.04562117861072903
+CM_ethiopia__CM_A01_I1_18__bin.73	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.032458176190476196
+CM_ethiopia__CM_A01_M0_18__bin.21	kSGB_1333:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB1333:0.024229557692307693
+CM_ethiopia__CM_A01_M0_18__bin.30	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.022375910814094777
+CM_ethiopia__CM_A01_M0_18__bin.31	kSGB_9209:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9209:0.015718422018348624
+CM_ethiopia__CM_A01_M0_18__bin.43	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04064938601986249
+CM_ethiopia__CM_A01_M0_18__bin.56	kSGB_9203:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9203:0.01644279676470588
+CM_ethiopia__CM_A01_M0_18__bin.59	uSGB_19976:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__GGB12851|s__GGB12851_SGB19976|t__SGB19976:0.030983433333333334
+CM_ethiopia__CM_A01_M0_18__bin.60	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.024005437423312886
+CM_ethiopia__CM_A01_M0_18__bin.62	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.021870221544715445
+CM_ethiopia__CM_A01_M0_18__bin.63	kSGB_15467:Species:k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio_piger|t__SGB15467:0.023819577638888895
+CM_ethiopia__CM_A04_I1_18__bin.1	kSGB_4716:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora_amygdalina|t__SGB4716:0.037654118810679614
+CM_ethiopia__CM_A04_I1_18__bin.2	uSGB_14439:Genus:k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_SGB14439|t__SGB14439:0.06418826730769231
+CM_ethiopia__CM_A04_I1_18__bin.42	kSGB_19444:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter_jejuni|t__SGB19444:0.01665842264392324
+CM_ethiopia__CM_A04_M0_18__bin.15	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.022711207845528457
+CM_ethiopia__CM_A04_M0_18__bin.16	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.022738580923450786
+CM_ethiopia__CM_A04_M0_18__bin.8	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.030365172766048203
+CM_ethiopia__CM_A06_I1_18__bin.31	uSGB_1437:Other:k__Bacteria|p__Bacteroidetes|c__CFGB544|o__OFGB544|f__FGB544|g__GGB1123|s__GGB1123_SGB1437|t__SGB1437:0.02269366791262136
+CM_ethiopia__CM_A06_I1_18__bin.32	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.0218392411299435
+CM_ethiopia__CM_A06_I1_18__bin.34	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.024418974191980556
+CM_ethiopia__CM_A06_I1_18__bin.37	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.021414286354166662
+CM_ethiopia__CM_A06_I1_18__bin.46	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.033303842259543616
+CM_ethiopia__CM_A06_I1_18__bin.54	kSGB_2075:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2075:0.019615276206896553
+CM_ethiopia__CM_A06_M0_18__bin.19	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.021415001979166667
+CM_ethiopia__CM_A06_M0_18__bin.2	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.02487240189550425
+CM_ethiopia__CM_A06_M0_18__bin.24	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02168037502824859
+CM_ethiopia__CM_A06_M0_18__bin.31	kSGB_4285:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii|t__SGB4285:0.04570293804561542
+CM_ethiopia__CM_A06_M0_18__bin.34	kSGB_66053:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_sp_MUC_MUC_530_WT_4D|t__SGB66053:0.059212150000000005
+CM_ethiopia__CM_A06_M0_18__bin.36	kSGB_2075:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2075:0.0198921175862069
+CM_ethiopia__CM_A06_M0_18__bin.39	kSGB_7061:Species:k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus_ruminis|t__SGB7061:0.02888113339517625
+CM_ethiopia__CM_A06_M0_18__bin.9	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.034505634763275755
+CM_ethiopia__CM_D02_I1_18__bin.2	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.037184771315789476
+CM_ethiopia__CM_D02_I1_18__bin.21	kSGB_4940:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_inulinivorans|t__SGB4940:0.040451880055020636
+CM_ethiopia__CM_D02_I1_18__bin.24	kSGB_1475:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1475:0.024409391818181816
+CM_ethiopia__CM_D02_I1_18__bin.31	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03249809963744935
+CM_ethiopia__CM_D02_I1_18__bin.46	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.03509609662447257
+CM_ethiopia__CM_D02_I1_18__bin.49	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.042205436287242167
+CM_ethiopia__CM_D02_M0_18__bin.17	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.02257218024390244
+CM_ethiopia__CM_D02_M0_18__bin.21	kSGB_8595:Species:k__Bacteria|p__Candidatus_Melainabacteria|c__Candidatus_Melainabacteria_unclassified|o__Candidatus_Gastranaerophilales|f__Candidatus_Gastranaerophilales_unclassified|g__Candidatus_Gastranaerophilales_unclassified|s__Candidatus_Gastranaerophilales_bacterium|t__SGB8595:0.01280233394736842
+CM_ethiopia__CM_D02_M0_18__bin.23	uSGB_4890:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_unclassified_SGB4890|t__SGB4890:0.02620155625
+CM_ethiopia__CM_D02_M0_18__bin.25	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.0300982457880145
+CM_ethiopia__CM_D02_M0_18__bin.3	kSGB_1853:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_fragilis|t__SGB1853:0.021933116666666665
+CM_ethiopia__CM_D02_M0_18__bin.4	kSGB_714:Species:k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714:0.022009852936910802
+CM_ethiopia__CM_D02_M0_18__bin.49	uSGB_1437:Other:k__Bacteria|p__Bacteroidetes|c__CFGB544|o__OFGB544|f__FGB544|g__GGB1123|s__GGB1123_SGB1437|t__SGB1437:0.0230746927184466
+CM_ethiopia__CM_D02_M0_18__bin.61	kSGB_9202:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis|s__Victivallis_vadensis|t__SGB9202:0.018689171962616824
+CM_ethiopia__CM_D02_M0_18__bin.62	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.02604421055900621
+CM_ethiopia__CM_D03_I12_18__bin.27	uSGB_14980:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__GGB9568|s__GGB9568_SGB14980|t__SGB14980:0.024585907200000003
+CM_ethiopia__CM_D03_I12_18__bin.33	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02024565118644068
+CM_ethiopia__CM_D03_I12_18__bin.34	kSGB_3548:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3548:0.02412463823529412
+CM_ethiopia__CM_D03_I12_18__bin.5	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.021216877375000002
+CM_ethiopia__CM_D03_M0_18__bin.30	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.02347683251533742
+CM_ethiopia__CM_D03_M0_18__bin.44	kSGB_2021:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2021:0.03222965960264901
+CM_ethiopia__CM_D03_M0_18__bin.45	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.032545289285714284
+CM_ethiopia__CM_D03_M0_18__bin.62	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.021596757853107343
+CM_ethiopia__CM_D03_M0_18__bin.63	uSGB_1024:Other:k__Archaea|p__Euryarchaeota|c__CFGB343|o__OFGB343|f__FGB343|g__GGB781|s__GGB781_SGB1024|t__SGB1024:0.027763024661246614
+CM_ethiopia__CM_D03_M0_18__bin.64	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.028853236459627327
+CM_ethiopia__CM_D03_M0_18__bin.65	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.025928870909090913
+CM_ethiopia__CM_D03_M0_18__bin.67	kSGB_1404:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1404:0.016574511313131316
+CM_ethiopia__CM_D03_M0_18__bin.69	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.037718670263157894
+CM_ethiopia__CM_D04_I1_18__bin.1	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04149574178762414
+CM_ethiopia__CM_D04_I1_18__bin.12	kSGB_4335:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_bacterium|t__SGB4335:0.022550591692307692
+CM_ethiopia__CM_D04_I1_18__bin.26	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03944625904243975
+CM_ethiopia__CM_D04_I1_18__bin.33	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.032972708333333337
+CM_ethiopia__CM_D04_I1_18__bin.35	kSGB_4540:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Anaerostipes|s__Anaerostipes_hadrus|t__SGB4540:0.03343807104123946
+CM_ethiopia__CM_D04_I1_18__bin.36	uSGB_2240:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1632|s__GGB1632_SGB2240|t__SGB2240:0.03582656050955414
+CM_ethiopia__CM_D04_I1_18__bin.39	kSGB_1475:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1475:0.02569116299465241
+CM_ethiopia__CM_D04_I1_18__bin.44	kSGB_14993:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Agathobaculum|s__Agathobaculum_butyriciproducens|t__SGB14993:0.035852457205623904
+CM_ethiopia__CM_D04_I1_18__bin.47	kSGB_6754:Species:k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Faecalibacillus|s__Faecalibacillus_intestinalis|t__SGB6754:0.031273649734395746
+CM_ethiopia__CM_D04_I1_18__bin.8	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.021270506700564976
+CM_ethiopia__CM_D04_M0_18__bin.42	kSGB_2075:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2075:0.02010362379310345
+CM_ethiopia__CM_D04_M0_18__bin.47	kSGB_15447:Species:k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrionaceae_unclassified|s__Desulfovibrionaceae_bacterium|t__SGB15447:0.022900349822064056
+CM_ethiopia__CM_D04_M0_18__bin.76	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02028208033898305
+CM_ethiopia__CM_D05_I1_18__bin.27	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.021683595806451614
+CM_ethiopia__CM_D05_I1_18__bin.37	uSGB_4664:Other:k__Bacteria|p__Firmicutes|c__CFGB1424|o__OFGB1424|f__FGB1424|g__GGB3490|s__GGB3490_SGB4664|t__SGB4664:0.026189018749999998
+CM_ethiopia__CM_D05_I1_18__bin.7	uSGB_4890:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_unclassified_SGB4890|t__SGB4890:0.02281281875
+CM_ethiopia__CM_D05_M0_18__bin.24	uSGB_4372:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4372|t__SGB4372:0.020020442857142856
+CM_ethiopia__CM_D05_M0_18__bin.27	uSGB_2237:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1629|s__GGB1629_SGB2237|t__SGB2237:0.03719957027027026
+CM_ethiopia__CM_D05_M0_18__bin.4	uSGB_13976:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9059|s__GGB9059_SGB13976|t__SGB13976:0.02635656379781421
+CM_ethiopia__CM_D05_M0_18__bin.42	kSGB_4262:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bicirculans|t__SGB4262:0.03198925178845171
+CM_ethiopia__CM_D05_M0_18__bin.50	kSGB_1855:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_fragilis|t__SGB1855:0.017717912779661015
+CM_ethiopia__CM_D05_M0_18__bin.52	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.020903162500000003
+CM_ethiopia__CM_D05_M0_18__bin.54	kSGB_4285:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii|t__SGB4285:0.03201108596146284
+CM_ethiopia__CM_D05_M0_18__bin.57	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.02145104725806451
+CM_ethiopia__CM_D05_M0_18__bin.59	kSGB_4938:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_sp_AF02_12|t__SGB4938:0.02524454456780333
+CM_ethiopia__CM_D05_M0_18__bin.93	kSGB_9210:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9210:0.019514726373626372
+CM_ethiopia__CM_D06_I1_18__bin.21	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03673517719298246
+CM_ethiopia__CM_D06_I1_18__bin.42	uSGB_4327:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB3277|s__GGB3277_SGB4327|t__SGB4327:0.027861904666234606
+CM_ethiopia__CM_D06_I1_18__bin.43	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.03363195357142858
+CM_ethiopia__CM_D06_M0_18__bin.10	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.03613631054852321
+CM_ethiopia__CM_D06_M0_18__bin.22	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.02828699814459373
+CM_ethiopia__CM_D06_M0_18__bin.39	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.021422726011299433
+CM_ethiopia__CM_D06_M0_18__bin.40	kSGB_3539:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3539:0.015086198863636362
+CM_ethiopia__CM_D06_M0_18__bin.41	kSGB_714:Species:k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714:0.017517191007976798
+CM_ethiopia__CM_D06_M0_18__bin.42	uSGB_26990:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB18271|s__GGB18271_SGB26990|t__SGB26990:0.01416074142857143
+CM_ethiopia__CM_D06_M0_18__bin.7	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.02138389541666667
+CM_ethiopia__CM_D07_I1_18__bin.1	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.021332762789101605
+CM_ethiopia__CM_D07_I1_18__bin.13	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.02847675687530803
+CM_ethiopia__CM_D07_I1_18__bin.23	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.02353445337423313
+CM_ethiopia__CM_D07_I1_18__bin.30	kSGB_1408:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1408:0.025046275641025642
+CM_ethiopia__CM_D07_I1_18__bin.32	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.021253345423728812
+CM_ethiopia__CM_D07_I1_18__bin.38	kSGB_2295:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_shahii|t__SGB2295:0.017644593427970555
+CM_ethiopia__CM_D07_I1_18__bin.4	kSGB_9226:Species:k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia_muciniphila|t__SGB9226:0.022643940591467356
+CM_ethiopia__CM_D07_I1_18__bin.44	kSGB_1949:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_merdae|t__SGB1949:0.01594793287222809
+CM_ethiopia__CM_D07_I1_18__bin.48	kSGB_4285:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii|t__SGB4285:0.029072833326779395
+CM_ethiopia__CM_D07_I1_18__bin.49	uSGB_13976:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9059|s__GGB9059_SGB13976|t__SGB13976:0.02688394453551913
+CM_ethiopia__CM_D07_I1_18__bin.53	kSGB_1965:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella|s__Barnesiella_intestinihominis|t__SGB1965:0.01897670766252955
+CM_ethiopia__CM_D07_I1_18__bin.9	kSGB_1836:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_uniformis|t__SGB1836:0.023904933409807132
+CM_ethiopia__CM_D07_M0_18__bin.18	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.028727236024844716
+CM_ethiopia__CM_D07_M0_18__bin.19	uSGB_26990:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB18271|s__GGB18271_SGB26990|t__SGB26990:0.015226757142857145
+CM_ethiopia__CM_D07_M0_18__bin.23	kSGB_4272:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_sp_JE7A12|t__SGB4272:0.027610883665338645
+CM_ethiopia__CM_D07_M0_18__bin.40	kSGB_3546:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Treponema|s__Treponema_succinifaciens|t__SGB3546:0.02012432380952381
+CM_ethiopia__CM_D07_M0_18__bin.44	kSGB_2229:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_bacterium|t__SGB2229:0.024130417094017094
+CM_ethiopia__CM_D07_M0_18__bin.73	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02030263152542373
+CM_ethiopia__CM_D07_M0_18__bin.78	kSGB_3548:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3548:0.022464210294117645
+CM_ethiopia__CM_D07_M0_18__bin.80	uSGB_4328:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB3278|s__GGB3278_SGB4328|t__SGB4328:0.021747616975308644
+CM_ethiopia__CM_D07_M0_18__bin.81	kSGB_4262:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bicirculans|t__SGB4262:0.03087436561062851
+CM_ethiopia__CM_D08_I1_18__bin.1	kSGB_5115:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_sp_OM04_5BH|t__SGB5115:0.017265259798994976
+CM_ethiopia__CM_D08_I1_18__bin.21	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.020066164745762713
+CM_ethiopia__CM_D08_I1_18__bin.22	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03401490985284709
+CM_ethiopia__CM_D08_I1_18__bin.24	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.024617650813008127
+CM_ethiopia__CM_D08_I1_18__bin.5	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03866051754385965
+CM_ethiopia__CM_D08_M0_18__bin.1	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.0199903340625
+CM_ethiopia__CM_D08_M0_18__bin.14	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.02349544459295261
+CM_ethiopia__CM_D08_M0_18__bin.17	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.023360407419354835
+CM_ethiopia__CM_D08_M0_18__bin.18	kSGB_714:Species:k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714:0.016190648498912257
+CM_ethiopia__CM_D08_M0_18__bin.21	kSGB_3546:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Treponema|s__Treponema_succinifaciens|t__SGB3546:0.01888655894179894
+CM_ethiopia__CM_D08_M0_18__bin.24	kSGB_5065:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio_crossotus|t__SGB5065:0.028811107293666028
+CM_ethiopia__CM_D08_M0_18__bin.29	kSGB_1475:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1475:0.024320632192513368
+CM_ethiopia__CM_D08_M0_18__bin.3	kSGB_4285:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii|t__SGB4285:0.04425564889893826
+CM_ethiopia__CM_D08_M0_18__bin.31	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03719356475438597
+CM_ethiopia__CM_D08_M0_18__bin.34	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.0356452894514768
+CM_ethiopia__CM_D08_M0_18__bin.41	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.026033423512476006
+CM_ethiopia__CM_D08_M0_18__bin.43	kSGB_2075:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2075:0.018980628620689655
+CM_ethiopia__CM_D09_I1_18__bin.17	kSGB_1473:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1473:0.023315838333333335
+CM_ethiopia__CM_D09_I1_18__bin.19	kSGB_6783:Species:k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenibacterium|s__Catenibacterium_sp_AM22_15|t__SGB6783:0.0383189283295711
+CM_ethiopia__CM_D09_I1_18__bin.39	uSGB_4886:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3614|s__GGB3614_SGB4886|t__SGB4886:0.022254304488778055
+CM_ethiopia__CM_D09_I1_18__bin.50	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03665488789473684
+CM_ethiopia__CM_D09_M0_18__bin.11	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03707280315789473
+CM_ethiopia__CM_D09_M0_18__bin.22	uSGB_1024:Other:k__Archaea|p__Euryarchaeota|c__CFGB343|o__OFGB343|f__FGB343|g__GGB781|s__GGB781_SGB1024|t__SGB1024:0.02888795149051491
+CM_ethiopia__CM_D09_M0_18__bin.25	kSGB_8021:Species:k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_lutetiensis|t__SGB8021:0.01528407674033149
+CM_ethiopia__CM_D09_M0_18__bin.28	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03013315607805502
+CM_ethiopia__CM_D09_M0_18__bin.37	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.021090136451313277
+CM_ethiopia__CM_D09_M0_18__bin.39	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.028159944603252836
+CM_ethiopia__CM_D09_M0_18__bin.40	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.019142116249999997
+CM_ethiopia__CM_D09_M0_18__bin.9	kSGB_3546:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Treponema|s__Treponema_succinifaciens|t__SGB3546:0.020248204444444445
+CM_ethiopia__CM_D10_I1_18__bin.1	kSGB_2301:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_finegoldii|t__SGB2301:0.02510436442105263
+CM_ethiopia__CM_D10_I1_18__bin.10	kSGB_1613:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri|t__SGB1613:0.02915100620689655
+CM_ethiopia__CM_D10_I1_18__bin.13	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.0385965949456174
+CM_ethiopia__CM_D10_I1_18__bin.2	kSGB_4837:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Blautia|s__Blautia_wexlerae|t__SGB4837:0.05107277361154691
+CM_ethiopia__CM_D10_I1_18__bin.26	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.020753195833333335
+CM_ethiopia__CM_D10_I1_18__bin.29	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.03003536934450468
+CM_ethiopia__CM_D10_I1_18__bin.31	kSGB_5190:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Anaerotignum|s__Anaerotignum_faecicola|t__SGB5190:0.0310274795256917
+CM_ethiopia__CM_D10_I1_18__bin.32	kSGB_15316:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium_prausnitzii|t__SGB15316:0.032510090447598256
+CM_ethiopia__CM_D10_I1_18__bin.4	uSGB_4939:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_SGB4939|t__SGB4939:0.05174999090909091
+CM_ethiopia__CM_D10_I1_18__bin.41	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.036088981403508774
+CM_ethiopia__CM_D10_I1_18__bin.43	kSGB_4871:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Faecalicatena|s__Faecalicatena_fissicatena|t__SGB4871:0.025038668704663213
+CM_ethiopia__CM_D10_I1_18__bin.50	kSGB_6783:Species:k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenibacterium|s__Catenibacterium_sp_AM22_15|t__SGB6783:0.03784759616252822
+CM_ethiopia__CM_D10_I1_18__bin.55	kSGB_9273:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus_massiliensis|t__SGB9273:0.017259645991091314
+CM_ethiopia__CM_D10_I1_18__bin.9	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.03400034404761905
+CM_ethiopia__CM_D10_M0_18__bin.109	kSGB_4368:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_bacterium|t__SGB4368:0.018531030952380952
+CM_ethiopia__CM_D10_M0_18__bin.120	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.03478694345991561
+CM_ethiopia__CM_D10_M0_18__bin.129	kSGB_4883:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_bacterium|t__SGB4883:0.026223828205128204
+CM_ethiopia__CM_D10_M0_18__bin.140	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.032568390773809526
+CM_ethiopia__CM_D10_M0_18__bin.141	kSGB_6970:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadales_unclassified|g__Selenomonadales_unclassified|s__Selenomonadales_bacterium|t__SGB6970:0.019997668421052633
+CM_ethiopia__CM_D10_M0_18__bin.145	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03629123457894737
+CM_ethiopia__CM_D10_M0_18__bin.20	kSGB_19694:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19694:0.024437433962264152
+CM_ethiopia__CM_D10_M0_18__bin.26	uSGB_5099:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3751|s__GGB3751_SGB5099|t__SGB5099:0.01863289090909091
+CM_ethiopia__CM_D10_M0_18__bin.31	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.025934238181818177
+CM_ethiopia__CM_D10_M0_18__bin.50	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02179893775141243
+CM_ethiopia__CM_D10_M0_18__bin.53	kSGB_9203:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9203:0.016550575686274507
+CM_ethiopia__CM_D10_M0_18__bin.57	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.027513782608695653
+CM_ethiopia__CM_D10_M0_18__bin.59	kSGB_3548:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3548:0.02181751029411764
+CM_ethiopia__CM_D10_M0_18__bin.6	uSGB_4373:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4373|t__SGB4373:0.11444471913580247
+CM_ethiopia__CM_D10_M0_18__bin.60	kSGB_9210:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9210:0.019368654505494506
+CM_ethiopia__CM_D10_M0_18__bin.62	uSGB_4383:Other:k__Bacteria|p__Firmicutes|c__CFGB1358|o__OFGB1358|f__FGB1358|g__GGB3314|s__GGB3314_SGB4383|t__SGB4383:0.023548200000000002
+CM_ethiopia__CM_D10_M0_18__bin.67	kSGB_4200:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcaceae_unclassified|s__Ruminococcaceae_bacterium|t__SGB4200:0.019383474285714287
+CM_ethiopia__CM_D10_M0_18__bin.73	kSGB_2229:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_bacterium|t__SGB2229:0.024503928205128204
+CM_ethiopia__CM_D10_M0_18__bin.74	uSGB_1024:Other:k__Archaea|p__Euryarchaeota|c__CFGB343|o__OFGB343|f__FGB343|g__GGB781|s__GGB781_SGB1024|t__SGB1024:0.027872528997289973
+CM_ethiopia__CM_D10_M0_18__bin.76	kSGB_14205:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_bacterium|t__SGB14205:0.11534651428571428
+CM_ethiopia__CM_D10_M0_18__bin.77	kSGB_17244:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_adolescentis|t__SGB17244:0.02472740579310345
+CM_ethiopia__CM_D10_M0_18__bin.8	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.023576634024390246
+CM_ethiopia__CM_D10_M0_18__bin.82	uSGB_9243:Other:k__Bacteria|p__Proteobacteria|c__CFGB2394|o__OFGB2394|f__FGB2394|g__GGB6544|s__GGB6544_SGB9243|t__SGB9243:0.01981209159663866
+CM_ethiopia__CM_D10_M0_18__bin.97	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.021690822916666668
+CM_ethiopia__CM_D11_I1_18__bin.16	kSGB_6817:Species:k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified|o__Firmicutes_unclassified|f__Firmicutes_unclassified|g__Firmicutes_unclassified|s__Firmicutes_bacterium_AM41_11|t__SGB6817:0.013849751061946905
+CM_ethiopia__CM_D11_I1_18__bin.19	kSGB_9273:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus_massiliensis|t__SGB9273:0.016540447906458797
+CM_ethiopia__CM_D11_I1_18__bin.23	kSGB_4936:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_hominis|t__SGB4936:0.024950490716180374
+CM_ethiopia__CM_D11_I1_18__bin.32	kSGB_1934:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_distasonis|t__SGB1934:0.022831115687096212
+CM_ethiopia__CM_D11_I1_18__bin.38	kSGB_1790:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Odoribacter|s__Odoribacter_splanchnicus|t__SGB1790:0.016398938586678055
+CM_ethiopia__CM_D11_I1_18__bin.41	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03819003903508771
+CM_ethiopia__CM_D11_I1_18__bin.43	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02119712497175141
+CM_ethiopia__CM_D11_I1_18__bin.47	kSGB_7061:Species:k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Ligilactobacillus|s__Ligilactobacillus_ruminis|t__SGB7061:0.028093501298701296
+CM_ethiopia__CM_D11_I1_18__bin.57	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.020593590340574848
+CM_ethiopia__CM_D11_I1_18__bin.58	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.034769342278481004
+CM_ethiopia__CM_D11_I1_18__bin.67	kSGB_9283:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_wadsworthensis|t__SGB9283:0.0233507723542989
+CM_ethiopia__CM_D11_I1_18__bin.69	kSGB_15452:Species:k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Bilophila|s__Bilophila_wadsworthia|t__SGB15452:0.023001601151761517
+CM_ethiopia__CM_D11_I1_18__bin.71	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.042388908174178765
+CM_ethiopia__CM_D11_I1_18__bin.73	kSGB_5190:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Anaerotignum|s__Anaerotignum_faecicola|t__SGB5190:0.03145028529644269
+CM_ethiopia__CM_D11_M0_18__bin.11	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03706913798245614
+CM_ethiopia__CM_D11_M0_18__bin.14	uSGB_2240:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1632|s__GGB1632_SGB2240|t__SGB2240:0.033622282802547775
+CM_ethiopia__CM_D11_M0_18__bin.29	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02071046485875706
+CM_ethiopia__CM_D11_M0_18__bin.39	uSGB_4372:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4372|t__SGB4372:0.02026614761904762
+CM_ethiopia__CM_D11_M0_18__bin.52	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.022798438821385176
+CM_ethiopia__CM_D11_M0_18__bin.55	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.030572115248453827
+CM_ethiopia__CM_D11_M0_18__bin.61	uSGB_1024:Other:k__Archaea|p__Euryarchaeota|c__CFGB343|o__OFGB343|f__FGB343|g__GGB781|s__GGB781_SGB1024|t__SGB1024:0.02766992466124661
+CM_ethiopia__CM_D11_M0_18__bin.64	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.02182924643558282
+CM_ethiopia__CM_D11_M0_18__bin.67	uSGB_4348:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB3293|s__GGB3293_SGB4348|t__SGB4348:0.023505065566391595
+CM_ethiopia__CM_D11_M0_18__bin.68	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.033016548809523816
+CM_ethiopia__CM_D11_M0_18__bin.70	kSGB_17244:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_adolescentis|t__SGB17244:0.023832747298850574
+CM_ethiopia__CM_D11_M0_18__bin.8	uSGB_4920:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3632|s__GGB3632_SGB4920|t__SGB4920:0.015620066666666666
+CM_ethiopia__CM_D11_M0_18__bin.9	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.030145264596273296
+CM_ethiopia__CM_D13_I1_18__bin.17	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.02767735608871828
+CM_ethiopia__CM_D13_I1_18__bin.25	kSGB_16955:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__SGB16955:0.01086989962264151
+CM_ethiopia__CM_D13_I1_18__bin.36	kSGB_12308:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_oryzihabitans|t__SGB12308:0.0245435984375
+CM_ethiopia__CM_D13_I1_18__bin.6	uSGB_6927:Other:k__Bacteria|p__Firmicutes|c__CFGB1872|o__OFGB1872|f__FGB1872|g__GGB4964|s__GGB4964_SGB6927|t__SGB6927:0.03409726279069768
+CM_ethiopia__CM_D13_M0_18__bin.11	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.021231454838709682
+CM_ethiopia__CM_D13_M0_18__bin.18	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.019654927932203387
+CM_ethiopia__CM_D13_M0_18__bin.19	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03655025675438596
+CM_ethiopia__CM_D13_M0_18__bin.2	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03231342654084026
+CM_ethiopia__CM_D13_M0_18__bin.22	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.02959525115820601
+CM_ethiopia__CM_D13_M0_18__bin.23	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04187566042780749
+CM_ethiopia__CM_D13_M0_18__bin.4	uSGB_4890:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_unclassified_SGB4890|t__SGB4890:0.0210063125
+CM_ethiopia__CM_D15_I1_18__bin.32	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.0292009301863354
+CM_ethiopia__CM_D15_M0_18__bin.5	kSGB_17244:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_adolescentis|t__SGB17244:0.02568076935057471
+CM_ethiopia__CM_D15_M0_18__bin.54	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.027952527777777778
+CM_ethiopia__CM_D15_M0_18__bin.6	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.032447703154761906
+CM_ethiopia__CM_D15_M0_18__bin.65	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.020352729583333333
+CM_ethiopia__CM_D21B_I12_18__bin.4	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.027357181168790958
+CM_ethiopia__CM_D21_I1_18__bin.10	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.027743261442582552
+CM_ethiopia__CM_D21_I1_18__bin.2	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.031152088774792065
+CM_ethiopia__CM_D21_I1_18__bin.21	kSGB_8768:Species:k__Bacteria|p__Verrucomicrobia|c__Opitutae|o__Opitutales|f__Opitutales_unclassified|g__Opitutales_unclassified|s__Opitutales_bacterium|t__SGB8768:0.020660228988764042
+CM_ethiopia__CM_D21_I1_18__bin.26	uSGB_2126:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__GGB1543|s__GGB1543_SGB2126|t__SGB2126:0.029611555686274507
+CM_ethiopia__CM_D21_I1_18__bin.31	kSGB_2318:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_putredinis|t__SGB2318:0.016858436284490963
+CM_ethiopia__CM_D21_I1_18__bin.32	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.036264767517543865
+CM_ethiopia__CM_D21_I1_18__bin.39	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.026600874363636368
+CM_ethiopia__CM_D21_I1_18__bin.44	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.020716957916666667
+CM_ethiopia__CM_D21_M0_18__bin.14	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.02671283618181818
+CM_ethiopia__CM_D21_M0_18__bin.30	kSGB_4910:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_bacterium_WCA3_601_WT_6H|t__SGB4910:0.028309220983015956
+CM_ethiopia__CM_D21_M0_18__bin.36	kSGB_8768:Species:k__Bacteria|p__Verrucomicrobia|c__Opitutae|o__Opitutales|f__Opitutales_unclassified|g__Opitutales_unclassified|s__Opitutales_bacterium|t__SGB8768:0.019424386292134832
+CM_ethiopia__CM_D21_M0_18__bin.42	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03175504916080187
+CM_ethiopia__CM_D21_M0_18__bin.48	kSGB_2318:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_putredinis|t__SGB2318:0.01525946214240406
+CM_ethiopia__CM_D21_M0_18__bin.58	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.027847230688516512
+CM_ethiopia__CM_D21_M0_18__bin.59	uSGB_20192:Other:k__Bacteria|p__Bacteroidetes|c__CFGB4422|o__OFGB4422|f__FGB4422|g__GGB13020|s__GGB13020_SGB20192|t__SGB20192:0.026230874761904766
+CM_ethiopia__CM_D21_M0_18__bin.7	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.02066290020833333
+CM_ethiopia__CM_D24_I1_18__bin.16	kSGB_3548:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3548:0.022377923529411762
+CM_ethiopia__CM_D24_I1_18__bin.21	uSGB_1701:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1267|s__GGB1267_SGB1701|t__SGB1701:0.021716905416666665
+CM_ethiopia__CM_D24_I1_18__bin.33	uSGB_26990:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB18271|s__GGB18271_SGB26990|t__SGB26990:0.014240885714285712
+CM_ethiopia__CM_D24_I1_18__bin.52	kSGB_4368:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_bacterium|t__SGB4368:0.018302542857142858
+CM_ethiopia__CM_D24_I1_18__bin.57	kSGB_15084:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcaceae_unclassified|s__Ruminococcaceae_bacterium|t__SGB15084:0.035313026250000004
+CM_ethiopia__CM_D24_I1_18__bin.59	kSGB_9210:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9210:0.019280890989010983
+CM_ethiopia__CM_D24_I1_18__bin.71	kSGB_1333:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB1333:0.02428298269230769
+CM_ethiopia__CM_D24_I1_18__bin.77	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.024894785093167702
+CM_ethiopia__CM_D24_I1_18__bin.82	kSGB_6970:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadales_unclassified|g__Selenomonadales_unclassified|s__Selenomonadales_bacterium|t__SGB6970:0.01973624035087719
+CM_ethiopia__CM_D24_M0_18__bin.18	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.021611797916666665
+CM_ethiopia__CM_D24_M0_18__bin.26	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04213284117647059
+CM_ethiopia__CM_D24_M0_18__bin.36	kSGB_3546:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Spirochaetaceae|g__Treponema|s__Treponema_succinifaciens|t__SGB3546:0.018794813227513227
+CM_ethiopia__CM_D24_M0_18__bin.58	kSGB_9210:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9210:0.020020817582417583
+CM_ethiopia__CM_D24_M0_18__bin.72	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.037580156118143464
+CM_ethiopia__CM_D24_M0_18__bin.9	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.03191376547619048
+CM_ethiopia__CM_D26AB_I1_18__bin.20	uSGB_4920:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3632|s__GGB3632_SGB4920|t__SGB4920:0.06605975
+CM_ethiopia__CM_D26AB_I1_18__bin.22	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.03655784101265823
+CM_ethiopia__CM_D26AB_I1_18__bin.25	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04199274713521772
+CM_ethiopia__CM_D26AB_I1_18__bin.38	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.021307665186440682
+CM_ethiopia__CM_D26AB_I1_18__bin.44	kSGB_5100:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_bacterium|t__SGB5100:0.017473495
+CM_ethiopia__CM_D26AB_I1_18__bin.8	kSGB_19692:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19692:0.021568808020833333
+CM_ethiopia__CM_D26AB_I1_18__bin.9	uSGB_4930:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3637|s__GGB3637_SGB4930|t__SGB4930:0.03330005789473684
+CM_ethiopia__CM_D26A_I13_18__bin.11	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03706791665789474
+CM_ethiopia__CM_D26A_I13_18__bin.13	uSGB_1680:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_SGB1680|t__SGB1680:0.032731439077155824
+CM_ethiopia__CM_D26A_I13_18__bin.25	kSGB_4910:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_bacterium_WCA3_601_WT_6H|t__SGB4910:0.02695052974781266
+CM_ethiopia__CM_D26A_I13_18__bin.31	kSGB_5904:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella_jalaludinii|t__SGB5904:0.023625802845528458
+CM_ethiopia__CM_D26A_I13_18__bin.33	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02041316615819209
+CM_ethiopia__CM_D26K_I12_18__bin.8	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.02512904894886217
+CM_ethiopia__CM_D26_M0_18__bin.18	uSGB_4373:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4373|t__SGB4373:0.024968250925925924
+CM_ethiopia__CM_D26_M0_18__bin.25	uSGB_1680:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_SGB1680|t__SGB1680:0.0326514602118003
+CM_ethiopia__CM_D26_M0_18__bin.26	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.026412663818181817
+CM_ethiopia__CM_D26_M0_18__bin.38	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.030845753081680527
+CM_ethiopia__CM_D26_M0_18__bin.57	kSGB_4910:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_bacterium_WCA3_601_WT_6H|t__SGB4910:0.024341045548121464
+CM_ethiopia__CM_D26_M0_18__bin.64	kSGB_5117:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__SGB5117:0.02213430023277467
+CM_ethiopia__CM_D33_I1_18__bin.10	kSGB_7967:Species:k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus_faecium|t__SGB7967:0.013812849596293844
+CM_ethiopia__CM_D33_I1_18__bin.13	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.020821249463852626
+CM_ethiopia__CM_D33_M0_18__bin.11	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03597226614035088
+CM_ethiopia__CM_D33_M0_18__bin.12	uSGB_4894:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Lachnospiraceae_unclassified_SGB4894|t__SGB4894:0.02622717157894737
+CM_ethiopia__CM_D33_M0_18__bin.19	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.029589739751552793
+CM_ethiopia__CM_D33_M0_18__bin.20	kSGB_714:Species:k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714:0.018459912472806383
+CM_ethiopia__CM_D33_M0_18__bin.3	kSGB_4546:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacteriaceae_unclassified|s__Eubacteriaceae_bacterium|t__SGB4546:0.08417412999999999
+CM_ethiopia__CM_D33_M0_18__bin.31	kSGB_1636:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri|t__SGB1636:0.0394016177631579
+CM_ethiopia__CM_D33_M0_18__bin.34	uSGB_2321:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1689|s__GGB1689_SGB2321|t__SGB2321:0.023868098969072167
+CM_ethiopia__CM_D39_I1_18__bin.13	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.04053677043859649
+CM_ethiopia__CM_D39_I1_18__bin.15	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.02083194812890242
+CM_ethiopia__CM_D39_I1_18__bin.22	kSGB_14762:Species:k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_sp_AK_207A|t__SGB14762:0.019462590000000002
+CM_ethiopia__CM_D39_I1_18__bin.29	kSGB_5862:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera_elsdenii|t__SGB5862:0.025090881273408243
+CM_ethiopia__CM_D39_I1_18__bin.9	kSGB_9273:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Duodenibacillus|s__Duodenibacillus_massiliensis|t__SGB9273:0.015058685679287306
+CM_ethiopia__CM_D39_M0_18__bin.15	kSGB_3548:Species:k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetia_unclassified|f__Spirochaetia_unclassified|g__Spirochaetia_unclassified|s__Spirochaetia_bacterium|t__SGB3548:0.0224373
+CM_ethiopia__CM_D39_M0_18__bin.23	uSGB_19976:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__GGB12851|s__GGB12851_SGB19976|t__SGB19976:0.08399291666666665
+CM_ethiopia__CM_D39_M0_18__bin.32	uSGB_14238:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9285|s__GGB9285_SGB14238|t__SGB14238:0.01312110188888889
+CM_ethiopia__CM_D39_M0_18__bin.35	uSGB_14980:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__GGB9568|s__GGB9568_SGB14980|t__SGB14980:0.027242376
+CM_ethiopia__CM_D39_M0_18__bin.36	uSGB_17345:Other:k__Bacteria|p__Firmicutes|c__CFGB3170|o__OFGB3170|f__FGB3170|g__GGB10690|s__GGB10690_SGB17345|t__SGB17345:0.024214035555555548
+CM_ethiopia__CM_D39_M0_18__bin.40	kSGB_4188:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcaceae_unclassified|s__Ruminococcaceae_bacterium|t__SGB4188:0.021926175000000003
+CM_ethiopia__CM_D39_M0_18__bin.44	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.023842498159509205
+CM_ethiopia__CM_D39_M0_18__bin.45	uSGB_1437:Other:k__Bacteria|p__Bacteroidetes|c__CFGB544|o__OFGB544|f__FGB544|g__GGB1123|s__GGB1123_SGB1437|t__SGB1437:0.02291870339805825
+CM_ethiopia__CM_D39_M0_18__bin.46	kSGB_2215:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_bacterium|t__SGB2215:0.02294027358490566
+CM_ethiopia__CM_D39_M0_18__bin.52	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.026268718712029158
+CM_ethiopia__CM_D39_M0_18__bin.64	uSGB_4373:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4373|t__SGB4373:0.021488724074074074
+CM_ethiopia__CM_D39_M0_18__bin.65	uSGB_13976:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9059|s__GGB9059_SGB13976|t__SGB13976:0.02665185232240437
+CM_ethiopia__CM_D39_M0_18__bin.66	kSGB_1333:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB1333:0.024211184615384615
+CM_ethiopia__CM_D40_I1_18__bin.11	kSGB_1814:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_vulgatus|t__SGB1814:0.020266540251533745
+CM_ethiopia__CM_D40_I1_18__bin.16	kSGB_4584:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter|s__Ruminococcus_gnavus|t__SGB4584:0.027413949829816202
+CM_ethiopia__CM_D40_I1_18__bin.19	kSGB_5862:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera|s__Megasphaera_elsdenii|t__SGB5862:0.023824916666666668
+CM_ethiopia__CM_D40_I1_18__bin.23	kSGB_17248:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_longum|t__SGB17248:0.0501009919504644
+CM_ethiopia__CM_D40_I1_18__bin.27	kSGB_15316:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium_prausnitzii|t__SGB15316:0.03170473258733624
+CM_ethiopia__CM_D40_M0_18__bin.10	kSGB_2021:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2021:0.03208925540838852
+CM_ethiopia__CM_D40_M0_18__bin.20	kSGB_5065:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Butyrivibrio|s__Butyrivibrio_crossotus|t__SGB5065:0.022000097792706334
+CM_ethiopia__CM_D40_M0_18__bin.21	kSGB_19694:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19694:0.02432507358490566
+CM_ethiopia__CM_D40_M0_18__bin.28	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.024695422360248447
+CM_ethiopia__CM_D40_M0_18__bin.34	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.026474718181818183
+CM_ethiopia__CM_D40_M0_18__bin.35	uSGB_19436:Family:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__GGB12503|s__GGB12503_SGB19436|t__SGB19436:0.03357034285714285
+CM_ethiopia__CM_D40_M0_18__bin.36	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.02195771367231639
+CM_ethiopia__CM_D40_M0_18__bin.62	uSGB_4372:Genus:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__Clostridia_unclassified|s__Clostridia_unclassified_SGB4372|t__SGB4372:0.02067538571428571
+CM_ethiopia__CM_D40_M0_18__bin.63	kSGB_2075:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_bacterium|t__SGB2075:0.019396263448275865
+CM_ethiopia__CM_D40_M0_18__bin.66	uSGB_1024:Other:k__Archaea|p__Euryarchaeota|c__CFGB343|o__OFGB343|f__FGB343|g__GGB781|s__GGB781_SGB1024|t__SGB1024:0.028231784281842812
+CM_ethiopia__CM_D40_M0_18__bin.71	uSGB_14238:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9285|s__GGB9285_SGB14238|t__SGB14238:0.013153862222222222
+CM_ethiopia__CM_D40_M0_18__bin.76	kSGB_9209:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9209:0.015802699082568806
+CM_ethiopia__CM_D43_I1_18__bin.13	uSGB_3677:Other:k__Bacteria|p__Proteobacteria|c__CFGB1062|o__OFGB1062|f__FGB1062|g__GGB2734|s__GGB2734_SGB3677|t__SGB3677:0.020400869468926556
+CM_ethiopia__CM_D43_I1_18__bin.18	kSGB_4925:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_faecis|t__SGB4925:0.026292968977243
+CM_ethiopia__CM_D43_I1_18__bin.20	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.02689805155279503
+CM_ethiopia__CM_D43_I1_18__bin.30	uSGB_4900:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3623|s__GGB3623_SGB4900|t__SGB4900:0.024630386046511632
+CM_ethiopia__CM_D43_I1_18__bin.36	uSGB_4920:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3632|s__GGB3632_SGB4920|t__SGB4920:0.020173433333333334
+CM_ethiopia__CM_D43_I1_18__bin.37	uSGB_2230:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_unclassified_SGB2230|t__SGB2230:0.02237896609963548
+CM_ethiopia__CM_D43_I1_18__bin.42	kSGB_10043:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shimwellia|s__Shimwellia_blattae|t__SGB10043:0.146706
+CM_ethiopia__CM_D43_I1_18__bin.49	uSGB_14238:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridia_unclassified|f__Clostridia_unclassified|g__GGB9285|s__GGB9285_SGB14238|t__SGB14238:0.014570531777777774
+CM_ethiopia__CM_D43_I1_18__bin.8	kSGB_9209:Species:k__Bacteria|p__Lentisphaerae|c__Lentisphaeria|o__Lentisphaeria_unclassified|f__Lentisphaeria_unclassified|g__Lentisphaeria_unclassified|s__Lentisphaeria_bacterium|t__SGB9209:0.01510988899082569
+CM_ethiopia__CM_D43_M0_18__bin.12	uSGB_5809:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__GGB4266|s__GGB4266_SGB5809|t__SGB5809:0.03525266333333333
+CM_ethiopia__CM_D43_M0_18__bin.16	kSGB_17256:Species:k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_bifidum|t__SGB17256:0.020424639705882354
+CM_ethiopia__CM_D43_M0_18__bin.28	uSGB_2238:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1630|s__GGB1630_SGB2238|t__SGB2238:0.034011544444444444
+CM_ethiopia__CM_D48_M0_18__bin.11	kSGB_4285:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii|t__SGB4285:0.029795503912701533
+CM_ethiopia__CM_D48_M0_18__bin.19	kSGB_4938:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_sp_AF02_12|t__SGB4938:0.028649695479777953
+CM_ethiopia__CM_D48_M0_18__bin.23	uSGB_4930:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3637|s__GGB3637_SGB4930|t__SGB4930:0.027672151754385962
+CM_ethiopia__CM_D48_M0_18__bin.24	uSGB_4303:Other:k__Bacteria|p__Firmicutes|c__CFGB1340|o__OFGB1340|f__FGB1340|g__GGB3256|s__GGB3256_SGB4303|t__SGB4303:0.028321308674223757
+CM_ethiopia__CM_D48_M0_18__bin.46	kSGB_1475:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1475:0.026731281550802143
+CM_ethiopia__CM_D50_I1_18__bin.10	kSGB_1644:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri|t__SGB1644:0.046138954773869346
+CM_ethiopia__CM_D50_I1_18__bin.2	kSGB_6922:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella_ratti|t__SGB6922:0.008928070652173914
+CM_ethiopia__CM_D50_I1_18__bin.23	kSGB_1949:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_merdae|t__SGB1949:0.022577076673706443
+CM_ethiopia__CM_D50_I1_18__bin.27	kSGB_10068:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068:0.028076913590484545
+CM_ethiopia__CM_D50_I1_18__bin.3	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.02186850806451613
+CM_ethiopia__CM_D50_I1_18__bin.4	kSGB_5765:Species:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium|s__Phascolarctobacterium_succinatutens|t__SGB5765:0.04288258372803667
+CM_ethiopia__CM_D50_I1_18__bin.8	uSGB_14439:Genus:k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_SGB14439|t__SGB14439:0.064952925
+CM_ethiopia__CM_D50_M0_18__bin.12	kSGB_4938:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_sp_AF02_12|t__SGB4938:0.027289032910388582
+CM_ethiopia__CM_D50_M0_18__bin.36	uSGB_1699:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__GGB1266|s__GGB1266_SGB1699|t__SGB1699:0.024195238077969174
+CM_ethiopia__CM_D50_M0_18__bin.39	kSGB_19688:Species:k__Bacteria|p__Elusimicrobia|c__Elusimicrobia|o__Elusimicrobiales|f__Elusimicrobiales_unclassified|g__Elusimicrobiales_unclassified|s__Elusimicrobiales_bacterium|t__SGB19688:0.01242276923076923
+CM_ethiopia__CM_D50_M0_18__bin.42	kSGB_714:Species:k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714:0.01796047839013778
+CM_ethiopia__CM_D50_M0_18__bin.43	kSGB_1855:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_fragilis|t__SGB1855:0.017164711101694916
+CM_ethiopia__CM_D50_M0_18__bin.46	kSGB_1404:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroidaceae_unclassified|s__Bacteroidaceae_bacterium|t__SGB1404:0.015718816464646464
+CM_ethiopia__CM_D50_M0_18__bin.49	uSGB_6973:Family:k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__GGB4979|s__GGB4979_SGB6973|t__SGB6973:0.03582619113924051
+CM_ethiopia__CM_D50_M0_18__bin.58	uSGB_2214:Family:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__GGB1617|s__GGB1617_SGB2214|t__SGB2214:0.027074628181818182
+CM_ethiopia__CM_D50_M0_18__bin.59	kSGB_19434:Species:k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacteraceae_unclassified|s__Campylobacteraceae_bacterium|t__SGB19434:0.022509777580645162
+CM_ethiopia__CM_D50_M0_18__bin.60	kSGB_4933:Species:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_unclassified|s__Eubacterium_rectale|t__SGB4933:0.03287236667732992
+CM_ethiopia__CM_D50_M0_18__bin.63	uSGB_5239:Family:k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__GGB3862|s__GGB3862_SGB5239|t__SGB5239:0.02704829732919254
+CM_ethiopia__CM_D50_M0_18__bin.64	kSGB_2229:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_bacterium|t__SGB2229:0.023970951282051286
+CM_ethiopia__CM_D50_M0_18__bin.67	uSGB_2076:Genus:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Bacteroidales_unclassified|s__Bacteroidales_unclassified_SGB2076|t__SGB2076:0.021426739687116562
+CM_ethiopia__CM_D50_M0_18__bin.72	kSGB_1676:Species:k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_sp_Marseille_P4119|t__SGB1676:0.024065360540540537
\ No newline at end of file
diff --git a/tools/phylophlan/test-data/phylophlan.tsv b/tools/phylophlan/test-data/phylophlan.tsv
new file mode 100644
index 0000000000..622f9a69ad
--- /dev/null
+++ b/tools/phylophlan/test-data/phylophlan.tsv
@@ -0,0 +1,400 @@
+p0000	PROTCATLG
+p0001	PROTCATLG
+p0002	PROTCATLG
+p0003	PROTCATLG
+p0004	PROTCATLG
+p0005	PROTCATCPREVF
+p0006	PROTCATLG
+p0007	PROTCATLG
+p0008	PROTCATLG
+p0009	PROTCATLG
+p0010	PROTCATLG
+p0011	PROTCATRTREV
+p0012	PROTCATLG
+p0013	PROTCATLG
+p0014	PROTCATLG
+p0015	PROTCATLG
+p0016	PROTCATLG
+p0017	PROTCATLG
+p0018	PROTCATLG
+p0019	PROTCATLG
+p0020	PROTCATLG
+p0021	PROTCATLG
+p0022	PROTCATLG
+p0023	PROTCATLG
+p0024	PROTCATLG
+p0025	PROTCATLG
+p0026	PROTCATLG
+p0027	PROTCATLG
+p0028	PROTCATLG
+p0029	PROTCATLG
+p0030	PROTCATLG
+p0031	PROTCATLG
+p0032	PROTCATRTREV
+p0033	PROTCATLG
+p0034	PROTCATRTREV
+p0035	PROTCATLG
+p0036	PROTCATLG
+p0037	PROTCATLG
+p0038	PROTCATLG
+p0039	PROTCATLG
+p0040	PROTCATLG
+p0041	PROTCATLG
+p0042	PROTCATLG
+p0043	PROTCATRTREV
+p0044	PROTCATLG
+p0045	PROTCATLG
+p0046	PROTCATLG
+p0047	PROTCATLG
+p0048	PROTCATRTREV
+p0049	PROTCATLG
+p0050	PROTCATLG
+p0051	PROTCATLG
+p0052	PROTCATLG
+p0053	PROTCATCPREVF
+p0054	PROTCATLG
+p0055	PROTCATLG
+p0056	PROTCATLG
+p0057	PROTCATLG
+p0058	PROTCATLG
+p0059	PROTCATLG
+p0060	PROTCATLG
+p0061	PROTCATLG
+p0062	PROTCATLG
+p0063	PROTCATLG
+p0064	PROTCATLG
+p0065	PROTCATRTREV
+p0066	PROTCATLG
+p0067	PROTCATLG
+p0068	PROTCATLG
+p0069	PROTCATLG
+p0070	PROTCATLG
+p0071	PROTCATLG
+p0072	PROTCATLG
+p0073	PROTCATLG
+p0074	PROTCATLG
+p0075	PROTCATRTREV
+p0076	PROTCATLG
+p0077	PROTCATLG
+p0078	PROTCATLG
+p0079	PROTCATLG
+p0080	PROTCATLG
+p0081	PROTCATLG
+p0082	PROTCATLG
+p0083	PROTCATLG
+p0084	PROTCATLG
+p0085	PROTCATLG
+p0086	PROTCATLG
+p0087	PROTCATLG
+p0088	PROTCATLG
+p0089	PROTCATLG
+p0090	PROTCATRTREV
+p0091	PROTCATLG
+p0092	PROTCATLG
+p0093	PROTCATLG
+p0094	PROTCATRTREV
+p0095	PROTCATLG
+p0096	PROTCATLG
+p0097	PROTCATLG
+p0098	PROTCATLG
+p0099	PROTCATLG
+p0100	PROTCATRTREV
+p0101	PROTCATLG
+p0102	PROTCATLG
+p0103	PROTCATLG
+p0104	PROTCATRTREV
+p0105	PROTCATLG
+p0106	PROTCATLG
+p0107	PROTCATLG
+p0108	PROTCATLG
+p0109	PROTCATRTREV
+p0110	PROTCATLG
+p0111	PROTCATRTREV
+p0112	PROTCATLG
+p0113	PROTCATLG
+p0114	PROTCATLG
+p0115	PROTCATLG
+p0116	PROTCATLG
+p0117	PROTCATLG
+p0118	PROTCATRTREV
+p0119	PROTCATLG
+p0120	PROTCATLG
+p0121	PROTCATLG
+p0122	PROTCATLG
+p0123	PROTCATLG
+p0124	PROTCATLG
+p0125	PROTCATLG
+p0126	PROTCATLG
+p0127	PROTCATLG
+p0128	PROTCATLG
+p0129	PROTCATVT
+p0130	PROTCATLG
+p0131	PROTCATLG
+p0132	PROTCATLG
+p0133	PROTCATLG
+p0134	PROTCATLG
+p0135	PROTCATLG
+p0136	PROTCATRTREV
+p0137	PROTCATLG
+p0138	PROTCATLG
+p0139	PROTCATVT
+p0140	PROTCATLG
+p0141	PROTCATLG
+p0142	PROTCATLG
+p0143	PROTCATLG
+p0144	PROTCATVT
+p0145	PROTCATLG
+p0146	PROTCATLG
+p0147	PROTCATLG
+p0148	PROTCATLG
+p0149	PROTCATCPREVF
+p0150	PROTCATLG
+p0151	PROTCATCPREVF
+p0152	PROTCATLG
+p0153	PROTCATLG
+p0154	PROTCATLG
+p0155	PROTCATLG
+p0156	PROTCATLG
+p0157	PROTCATLG
+p0158	PROTCATLG
+p0159	PROTCATRTREV
+p0160	PROTCATVT
+p0161	PROTCATRTREV
+p0162	PROTCATLG
+p0163	PROTCATLG
+p0164	PROTCATLG
+p0165	PROTCATLG
+p0166	PROTCATLG
+p0167	PROTCATRTREV
+p0168	PROTCATLG
+p0169	PROTCATRTREV
+p0170	PROTCATLG
+p0171	PROTCATLG
+p0172	PROTCATLG
+p0173	PROTCATLG
+p0174	PROTCATLG
+p0175	PROTCATLG
+p0176	PROTCATLG
+p0177	PROTCATLG
+p0178	PROTCATLG
+p0179	PROTCATRTREV
+p0180	PROTCATLG
+p0181	PROTCATLG
+p0182	PROTCATLG
+p0183	PROTCATLG
+p0184	PROTCATLG
+p0185	PROTCATBLOSUM62
+p0186	PROTCATLG
+p0187	PROTCATLG
+p0188	PROTCATLG
+p0189	PROTCATLG
+p0190	PROTCATLG
+p0191	PROTCATLG
+p0192	PROTCATLG
+p0193	PROTCATLG
+p0194	PROTCATRTREV
+p0195	PROTCATLG
+p0196	PROTCATPMB
+p0197	PROTCATLG
+p0198	PROTCATLG
+p0199	PROTCATLG
+p0200	PROTCATLG
+p0201	PROTCATLG
+p0202	PROTCATLG
+p0203	PROTCATLG
+p0204	PROTCATRTREV
+p0205	PROTCATRTREV
+p0206	PROTCATLG
+p0207	PROTCATLG
+p0208	PROTCATLG
+p0209	PROTCATLG
+p0210	PROTCATLG
+p0211	PROTCATRTREV
+p0212	PROTCATRTREV
+p0213	PROTCATLG
+p0214	PROTCATLG
+p0215	PROTCATLG
+p0216	PROTCATCPREVF
+p0217	PROTCATLG
+p0218	PROTCATLG
+p0219	PROTCATCPREVF
+p0220	PROTCATCPREVF
+p0221	PROTCATLG
+p0222	PROTCATRTREV
+p0223	PROTCATLG
+p0224	PROTCATLG
+p0225	PROTCATCPREV
+p0226	PROTCATLG
+p0227	PROTCATLG
+p0228	PROTCATRTREV
+p0229	PROTCATLG
+p0230	PROTCATRTREV
+p0231	PROTCATLG
+p0232	PROTCATLG
+p0233	PROTCATCPREV
+p0234	PROTCATRTREV
+p0235	PROTCATLG
+p0236	PROTCATRTREV
+p0237	PROTCATLG
+p0238	PROTCATLG
+p0239	PROTCATLG
+p0240	PROTCATCPREV
+p0241	PROTCATLG
+p0242	PROTCATLG
+p0243	PROTCATVT
+p0244	PROTCATLG
+p0245	PROTCATRTREV
+p0246	PROTCATRTREV
+p0247	PROTCATLG
+p0248	PROTCATLG
+p0249	PROTCATRTREV
+p0250	PROTCATLG
+p0251	PROTCATVT
+p0252	PROTCATLG
+p0253	PROTCATLG
+p0254	PROTCATLG
+p0255	PROTCATVT
+p0256	PROTCATRTREV
+p0257	PROTCATLG
+p0258	PROTCATVT
+p0259	PROTCATLG
+p0260	PROTCATLG
+p0261	PROTCATLG
+p0262	PROTCATCPREVF
+p0263	PROTCATLG
+p0264	PROTCATRTREV
+p0265	PROTCATLG
+p0266	PROTCATLG
+p0267	PROTCATLG
+p0268	PROTCATCPREVF
+p0269	PROTCATLG
+p0270	PROTCATLG
+p0271	PROTCATLG
+p0272	PROTCATLG
+p0273	PROTCATCPREVF
+p0274	PROTCATLG
+p0275	PROTCATRTREV
+p0276	PROTCATRTREV
+p0277	PROTCATLG
+p0278	PROTCATLG
+p0279	PROTCATLG
+p0280	PROTCATLG
+p0281	PROTCATRTREV
+p0282	PROTCATLG
+p0283	PROTCATVT
+p0284	PROTCATLG
+p0285	PROTCATLG
+p0286	PROTCATBLOSUM62
+p0287	PROTCATLG
+p0288	PROTCATLG
+p0289	PROTCATLG
+p0290	PROTCATLG
+p0291	PROTCATCPREVF
+p0292	PROTCATLG
+p0293	PROTCATLG
+p0294	PROTCATLG
+p0295	PROTCATLG
+p0296	PROTCATRTREV
+p0297	PROTCATLG
+p0298	PROTCATLG
+p0299	PROTCATLG
+p0300	PROTCATLG
+p0301	PROTCATLG
+p0302	PROTCATLG
+p0303	PROTCATLG
+p0304	PROTCATLG
+p0305	PROTCATLG
+p0306	PROTCATLG
+p0307	PROTCATLG
+p0308	PROTCATRTREV
+p0309	PROTCATLG
+p0310	PROTCATLG
+p0311	PROTCATLG
+p0312	PROTCATLG
+p0313	PROTCATLG
+p0314	PROTCATLG
+p0315	PROTCATBLOSUM62
+p0316	PROTCATLG
+p0317	PROTCATLG
+p0318	PROTCATRTREV
+p0319	PROTCATLG
+p0320	PROTCATRTREV
+p0321	PROTCATLG
+p0322	PROTCATLG
+p0323	PROTCATLG
+p0324	PROTCATLG
+p0325	PROTCATLG
+p0326	PROTCATLG
+p0327	PROTCATLG
+p0328	PROTCATCPREVF
+p0329	PROTCATRTREV
+p0330	PROTCATLG
+p0331	PROTCATLG
+p0332	PROTCATLG
+p0333	PROTCATLG
+p0334	PROTCATLG
+p0335	PROTCATRTREV
+p0336	PROTCATRTREV
+p0337	PROTCATLG
+p0338	PROTCATLG
+p0339	PROTCATLG
+p0340	PROTCATLG
+p0341	PROTCATRTREV
+p0342	PROTCATLG
+p0343	PROTCATCPREVF
+p0344	PROTCATCPREVF
+p0345	PROTCATLG
+p0346	PROTCATPMB
+p0347	PROTCATLG
+p0348	PROTCATLG
+p0349	PROTCATRTREV
+p0350	PROTCATLG
+p0351	PROTCATLG
+p0352	PROTCATLG
+p0353	PROTCATRTREV
+p0354	PROTCATLG
+p0355	PROTCATLG
+p0356	PROTCATLG
+p0357	PROTCATCPREVF
+p0358	PROTCATVT
+p0359	PROTCATRTREV
+p0360	PROTCATBLOSUM62
+p0361	PROTCATRTREV
+p0362	PROTCATLG
+p0363	PROTCATLG
+p0364	PROTCATLG
+p0365	PROTCATLG
+p0366	PROTCATRTREV
+p0367	PROTCATLG
+p0368	PROTCATCPREV
+p0369	PROTCATLG
+p0370	PROTCATRTREV
+p0371	PROTCATLG
+p0372	PROTCATLG
+p0373	PROTCATLG
+p0374	PROTCATVT
+p0375	PROTCATLG
+p0376	PROTCATLG
+p0377	PROTCATLG
+p0378	PROTCATLG
+p0379	PROTCATLG
+p0380	PROTCATLG
+p0381	PROTCATLG
+p0382	PROTCATLG
+p0383	PROTCATLG
+p0384	PROTCATVT
+p0385	PROTCATLG
+p0386	PROTCATLG
+p0387	PROTCATCPREVF
+p0388	PROTCATLG
+p0389	PROTCATLG
+p0390	PROTCATRTREV
+p0391	PROTCATLG
+p0392	PROTCATLG
+p0393	PROTCATLG
+p0394	PROTCATLG
+p0395	PROTCATLG
+p0396	PROTCATVT
+p0397	PROTCATLG
+p0398	PROTCATLG
+p0399	PROTCATLG
diff --git a/tools/phylophlan/test-data/phylophlan_markers_filtered.faa.gz b/tools/phylophlan/test-data/phylophlan_markers_filtered.faa.gz
new file mode 100644
index 0000000000..6afb4e910b
Binary files /dev/null and b/tools/phylophlan/test-data/phylophlan_markers_filtered.faa.gz differ
diff --git a/tools/phylophlan/validate_mapping_file.py b/tools/phylophlan/validate_mapping_file.py
new file mode 100644
index 0000000000..496679d122
--- /dev/null
+++ b/tools/phylophlan/validate_mapping_file.py
@@ -0,0 +1,12 @@
+import string
+import sys
+
+print("Validating --maas mapping file ...")
+allowed = set(string.ascii_letters + string.digits + '._-')
+for line in open(sys.argv[1], 'r'):
+    if line.startswith('#'):
+        continue
+    for s in line.strip().split('\t'):
+        if not set(s).issubset(allowed):
+            print(f"Invalid line in mapping file: {line}")
+            sys.exit(1)