Main tool :
Additional tools installed via micromamba:
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aria2 1.37.0 hbc8128a_2 conda-forge
blast 2.16.0 h66d330f_5 bioconda
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.6.15 hbd8a1cb_0 conda-forge
curl 8.14.1 h332b0f4_0 conda-forge
diamond 2.1.12 h13889ed_2 bioconda
entrez-direct 22.4 he881be0_0 bioconda
fastme 2.1.6.3 h7b50bb2_1 bioconda
fasttree 2.1.11 h7b50bb2_5 bioconda
gawk 5.3.1 hcd3d067_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
icu 75.1 he02047a_0 conda-forge
iqtree 2.4.0 h503566f_0 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.43 h1423503_5 conda-forge
libasprintf 0.24.1 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
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
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.24.1 h5888daf_0 conda-forge
libgfortran 15.1.0 h69a702a_3 conda-forge
libgfortran-ng 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
liblapack 3.9.0 32_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libmpdec 4.0.0 hb9d3cd8_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_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
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_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
mafft 7.526 h4bc722e_0 conda-forge
mcl 22.282 pl5321h7b50bb2_4 bioconda
mmseqs2 17.b804f hd6d6fdc_1 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
muscle 3.8.1551 h9948957_8 bioconda
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.3.1 py313h17eae1a_0 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.5.0 h7b32b05_1 conda-forge
orthofinder 2.5.5 hdfd78af_2 bioconda
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 3.04 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321hbf60520_1 conda-forge
perl-compress-raw-zlib 2.202 pl5321hadc24fc_0 conda-forge
perl-encode 3.21 pl5321hb9d3cd8_1 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.201 pl5321h503566f_5 bioconda
perl-io-zlib 1.15 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.03 pl5321h9948957_4 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge
perl-scalar-list-utils 1.69 pl5321hb9d3cd8_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pip 25.1.1 pyh145f28c_0 conda-forge
python 3.13.5 hec9711d_102_cp313 conda-forge
python_abi 3.13 7_cp313 conda-forge
raxml 8.2.13 h7b50bb2_3 bioconda
raxml-ng 1.2.2 h6747034_2 bioconda
readline 8.2 h8c095d6_2 conda-forge
rpsbproc 0.5.0 hd6d6fdc_3 bioconda
scipy 1.16.0 py313h86fcf2b_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tzdata 2025b h78e105d_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Basic information on how to use this tool:
- executable: orthofinder
- help: -h
- version: NA
- description: Phylogenetic orthology inference for comparative genomics
Full documentation: https://davidemms.github.io/
orthofinder -f directory_with_data/