Main tool: PPanGGOLiN
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aragorn 1.2.41 h7b50bb2_5 bioconda
archspec 0.2.5 pyhd8ed1ab_0 conda-forge
aria2 1.37.0 h4e1c2bf_3 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
bokeh 3.8.1 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
c-blosc2 2.22.0 hc31b594_1 conda-forge
ca-certificates 2025.11.12 hbd8a1cb_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.3 py312hd9148b4_3 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.2.1 py312hcaba1f9_2 conda-forge
hdf5 1.14.6 nompi_h1b119a7_104 conda-forge
icu 75.1 he02047a_0 conda-forge
infernal 1.1.5 pl5321h7b50bb2_4 bioconda
jinja2 3.1.6 pyhcf101f3_1 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.45 default_hbd61a6d_105 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcurl 8.17.0 h4e3cde8_1 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libfreetype 2.14.1 ha770c72_0 conda-forge
libfreetype6 2.14.1 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgcc-ng 15.2.0 h69a702a_16 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libpng 1.6.53 h421ea60_0 conda-forge
libsqlite 3.51.1 h0c1763c_1 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.9 h04c0eec_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
markupsafe 3.0.3 py312h8a5da7c_0 conda-forge
mmseqs2 15.6f452 pl5321h6a68c12_3 bioconda
mpc 1.3.1 h24ddda3_1 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
narwhals 2.14.0 pyhcf101f3_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.14.1 py312h88efc94_101 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.3 py312hf79963d_1 conda-forge
pcre2 10.45 hc749103_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 12.0.0 py312h50c33e8_2 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_1 conda-forge
ppanggolin 2.2.6 py312h0fa9677_0 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
pyrodigal 3.6.3.post1 py312h0fa9677_1 bioconda
pytables 3.10.2 py312hefc0c3f_10 conda-forge
python 3.12.12 hd63d673_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.3 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.3 py312h8a5da7c_0 conda-forge
readline 8.3 h853b02a_0 conda-forge
scipy 1.16.3 py312h54fa4ab_2 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
tenacity 9.1.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tornado 6.5.4 py312h961da02_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c h8577fbf_0 conda-forge
wget 1.25.0 hc2d8bac_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xyzservices 2025.11.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.2 hceb46e0_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Code repository: https://github.com/labgem/PPanGGOLiN
Basic information on how to use this tool:
- executable: ppanggolin
- help: --help
- version: --version
- description: |
PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes.
Additional information:
PPanGGOLiN only creates the pangenome graphs. It is recommended to use another tool to visualize them. Please read https://github.com/labgem/PPanGGOLiN/wiki for more information.
Full documentation: https://github.com/labgem/PPanGGOLiN/wiki
ppanggolin annotate --fasta organisms.fasta.list --output output
# many of the commands manipulate the 'pangenome.h5' file in place
ppanggolin cluster -p pangenome.h5
ppanggolin graph -p pangenome.h5
ppanggolin partition -p pangenome.h5
ppanggolin draw -p pangenome.h5 --ucurve
# there are some human-readable files that can be generated as well
ppanggolin write -p pangenome.h5 --stats --output stats