Main tool : pangolin
Full documentation: https://cov-lineages.org/resources/pangolin.html
Phylogenetic Assignment of Named Global Outbreak LINeages
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda/envs/pangolin"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 20_gnu conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
argparse-dataclass 2.0.0 pyhd8ed1ab_1 conda-forge
attr 2.5.2 h39aace5_0 conda-forge
attrs 25.4.0 pyhcf101f3_1 conda-forge
biopython 1.86 py312h4c3975b_1 conda-forge
boost-cpp 1.78.0 h2c5509c_4 conda-forge
brotli-python 1.2.0 py312hdb49522_1 conda-forge
bzip2 1.0.8 hda65f42_9 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
certifi 2026.1.4 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py312h460c074_1 conda-forge
charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.12 h8b142ea_1 conda-forge
coin-or-cgl 0.60.7 h516709c_0 conda-forge
coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge
coin-or-osi 0.108.10 haf5fa05_0 conda-forge
coin-or-utils 2.11.11 hee58242_0 conda-forge
conda-inject 1.3.2 pyhd8ed1ab_0 conda-forge
configargparse 1.7.1 pyhe01879c_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
constellations 0.1.12 pypi_0 pypi
docutils 0.22.4 pyhd8ed1ab_0 conda-forge
dpath 2.2.0 pyha770c72_1 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
git-lfs 3.7.1 ha8f183a_1 conda-forge
gitdb 4.0.12 pyhd8ed1ab_0 conda-forge
gitpython 3.1.46 pyhd8ed1ab_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gofasta 1.2.3 h9ee0642_0 bioconda
h2 4.3.0 pyhcf101f3_0 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
humanfriendly 10.0 pyh707e725_8 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.11 pyhd8ed1ab_0 conda-forge
immutables 0.21 py312h4c3975b_2 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
jinja2 3.1.6 pyhcf101f3_1 conda-forge
joblib 1.5.3 pypi_0 pypi
jsonschema 4.26.0 pyhcf101f3_0 conda-forge
jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge
jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge
k8 1.2 h6618dc6_3 bioconda
kernel-headers_linux-64 6.12.0 he073ed8_5 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.45.1 bootstrap_ha15bf96_1 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcap 2.77 h3ff7636_0 conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcbor 0.10.2 hcb278e6_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libfido2 1.14.0 h4446dcb_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran-ng 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblapacke 3.11.0 5_h6ae95b6_openblas conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
liblzma-devel 5.8.2 hb03c661_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libopenssl-static 3.6.1 hb03c661_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libudev1 259.1 h6569c3e_0 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markupsafe 3.0.3 py312h8a5da7c_0 conda-forge
minimap2 2.28 he4a0461_3 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
mysql-connector-c 6.1.11 h659d440_1008 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.4.2 py312h33ff503_1 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssh 9.6p1 h2d3b35a_0 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.3 pypi_0 pypi
pangolin 4.4 pypi_0 pypi
pangolin_assignment 1.37.1 pypi_0 pypi
pangolin_data 1.37.1 pypi_0 pypi
pip 26.0.1 pyh8b19718_0 conda-forge
platformdirs 4.9.2 pyhcf101f3_0 conda-forge
psutil 7.2.2 py312h5253ce2_0 conda-forge
pulp 2.8.0 py312hd0750ca_3 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.3 hab00c5b_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-fastjsonschema 2.21.2 pyhe01879c_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pypi_0 pypi
pyyaml 6.0.3 py312h8a5da7c_1 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
requests 2.32.5 pyhcf101f3_1 conda-forge
reretry 0.11.8 pyhd8ed1ab_1 conda-forge
rpds-py 0.30.0 py312h868fb18_0 conda-forge
scikit-learn 1.7.1 pypi_0 pypi
scipy 1.17.0 pypi_0 pypi
scorpio 0.3.19 pypi_0 pypi
setuptools 81.0.0 pyh332efcf_0 conda-forge
six 1.17.0 pypi_0 pypi
smart_open 7.5.0 pyhcf101f3_0 conda-forge
smmap 5.0.2 pyhd8ed1ab_0 conda-forge
snakemake-interface-common 1.22.0 pyhd4c3c12_0 bioconda
snakemake-interface-executor-plugins 9.3.9 pyhdfd78af_0 bioconda
snakemake-interface-logger-plugins 2.0.0 pyhd4c3c12_0 bioconda
snakemake-interface-report-plugins 1.3.0 pyhd4c3c12_0 bioconda
snakemake-interface-scheduler-plugins 2.0.2 pyhd4c3c12_0 bioconda
snakemake-interface-storage-plugins 4.3.3 pyh84498cf_0 bioconda
snakemake-minimal 9.16.3 pyhdfd78af_0 bioconda
sysroot_linux-64 2.39 hc4b9eeb_5 conda-forge
tabulate 0.9.0 pyhcf101f3_3 conda-forge
threadpoolctl 3.6.0 pypi_0 pypi
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
ucsc-fatovcf 473 he8037a5_0 bioconda
ucsc-stringify 472 he8037a5_0 bioconda
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
usher 0.6.3 hb389108_1 bioconda
wheel 0.46.3 pyhd8ed1ab_0 conda-forge
wrapt 1.17.3 py312h4c3975b_1 conda-forge
xz 5.8.2 ha02ee65_0 conda-forge
xz-gpl-tools 5.8.2 ha02ee65_0 conda-forge
xz-tools 5.8.2 hb03c661_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yte 1.9.4 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py312h4c3975b_3 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
As of pangolin version 4.3, pangoLEARN mode has been deprecated. More info can be found here on the v4.3 release page.
If
--analysis-mode fastor--analysis-mode pangolearnis given, pangolin v4.3 will print out a warning and use UShER mode instead, unless--datadiris also given specifying a directory with pangoLEARN model files. The next release of pangolin-data (v1.20) will no longer include the model files which have not been updated since v1.18.
The pangoLEARN model has not been updated since pangolin-data version 1.18. Only the the underlying UShER tree/protobuf file will be maintained for the forseeable future.
Please use the UShER mode of pangolin if you want to stay up-to-date with the most recent lineages. See pangolin-data release notes here for more details
# run Pangolin in the default mode (usher). Can optionally supply --analysis-mode usher
$ pangolin /pangolin/pangolin/test/test_seqs.fasta -o /data/test_seqs-output-pusher
# view the output CSV
$ column -t -s, /data/test_seqs-output-pusher/lineage_report.csv
taxon lineage conflict ambiguity_score scorpio_call scorpio_support scorpio_conflict scorpio_notes version pangolin_version scorpio_version constellation_version is_designated qc_status qc_notes note
India seq B.1.617.1 0.0 B.1.617.1-like 1.0 0.0 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.617.1(1/1)
b117 B.1.1.7 0.0 Alpha (B.1.1.7-like) 0.91 0.04 scorpio call: Alt alleles 21; Ref alleles 1; Amb alleles 1; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.1.7(2/2)
outgroup_A A 0.0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: A(1/1)
issue_57_torsten_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_has_6000_Ns_in_18000_bases Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_has_no_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
This_seq_is_too_short Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.9
This_seq_has_lots_of_Ns Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.98
This_seq_is_literally_just_N Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map
Japan_seq B 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash.
USA_seq B.1.314 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash.
Unassigned_omicron_seq BA.1 0.0 Probable Omicron (BA.1-like) 0.71 0.08 scorpio call: Alt alleles 42; Ref alleles 5; Amb alleles 9; Oth alleles 3 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.03 Usher placements: BA.1(1/1)