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 hbc8128a_2 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
bokeh 3.7.3 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
c-blosc2 2.19.0 h3122c55_0 conda-forge
ca-certificates 2025.6.15 hbd8a1cb_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
contourpy 1.3.2 py312h68727a3_0 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 py312h7201bc8_0 conda-forge
hdf5 1.14.6 nompi_h2d575fe_101 conda-forge
icu 75.1 he02047a_0 conda-forge
infernal 1.1.5 pl5321h7b50bb2_4 bioconda
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.44 h1423503_0 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libblas 3.9.0 32_h59b9bed_openblas conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_0 conda-forge
libpng 1.6.50 h943b412_0 conda-forge
libsqlite 3.50.2 h6cd9bfd_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libtiff 4.7.0 hf01ce69_5 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h4bc477f_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 3.0.2 py312h178313f_1 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 1.45.0 pyhe01879c_0 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.5 pyhe01879c_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.10.2 py312h6a710ac_100 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.0 py312hf9745cd_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 11.3.0 py312h80c1187_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_1 conda-forge
ppanggolin 2.2.4 h0fa9677_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_0 bioconda
pytables 3.10.2 py312h09a4e84_6 conda-forge
python 3.12.11 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 7_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h178313f_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
scipy 1.16.0 py312hf734454_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
tenacity 9.1.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tornado 6.5.1 py312h66e93f0_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typing-extensions 4.14.1 h4440ef1_0 conda-forge
typing_extensions 4.14.1 pyhe01879c_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xyzservices 2025.4.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.4 h7955e40_0 conda-forge
zstd 1.5.7 hb8e6e7a_2 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