genotree

Pipeline for making phylogenetic trees out of a dataset of genomes and exons. The scripts are written to run on a high performance cluster using SLURM. The pipeline consists of multiple scripts working together. Input files and folders are set inside the scripts.

Main Pipeline:

1_make_alignments.sh

• calls 1-1_process_genomes.sh, 1-3_align_loci.sh and utilities/speciesinfo.py
• Creates working directory and required subfolders while running.

1-1_process_genomes.sh

• calls 1-2_find_hits.py
• finds hits for each locus in specified genome file.

1-2_find_hits.py

• uses nhmmer-tables to create fasta files that contain hits for each locus

1-3_align_loci.sh

• aligns hits for specified locus.

2_process_alignments.sh

• calls 2-1_rate_alignments.sh, 2-2_filter_alignments.py and utilities/total_score.py
• generates AliGROOVE-Scores for all alignments and returns .fasta-files that are filtered to not contain any sequences with a score below the supplied threshold (0.35)

2-1_rate_alignments.sh

• generates AliGROOVE matrices with similarity scores for all sequence alignments.

2-2_filter_alignments.py

• filters the supplied sequence alignments for the score threshold

3_make_trees.sh

• calls 3-1_rename_trees.py
• creates individual phylogenetic trees from the supplied alignments and combines them into a supertree

3-1_rename_trees.py

• renames tree tips to make postprocessing easier

4_color_trees.R

• calls 4-3_functions.R and 4-1_load_trees.R
• gets a phylogenetic tree and makes several differently annotated versions of it that get saved as pdfs or jpegs.

4-1_compare_trees.R

• calls 4-3_functions.R and 4-1_load_trees.R
• gets multiple phylogenetic trees and makes tanglegrams out of them

4-2_load_trees.R

• contains the preamble for 4_color_trees.R to load phylo and plot trees into the workspace

4-3_functions.R

• provides a multitude of custom functions for tree annotation

Utilities:

speciesinfo.py - gets general information for specified taxon

total_score.py - calculates total mean and median scores for supplied AliGROOVE matrices

align_cry.sh - align the gene files for cryptochrome 4 and 5

filter_alignments.sh - runs 2-2_filter_alignments.py for all given alignment files and re-aligns them with mafft afterwards

rename_taxa.sh - calls rename_script.sh for all supplied .fasta-files

rename_script.py - renames genes in supplied .fasta file for processing with AliGROOVE

count_sequences.sh - counts all sequences within a folder of multiple sequence alignment files

calculate_pairwise_time.sh - calculates the time it takes to perform pairwise comparisons on sequences in provided files

rename_trees.sh - calls 3_2_rename_trees.py to rename tips in generated gene trees to the corresponding IDX

combine_trees.sh - uses ASTER to combine all given gene trees into consensus trees