Main tool: MetaPhlAn
Code repository: https://github.com/biobakery/MetaPhlAn
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
_r-mutex 1.0.1 anacondar_1 conda-forge
anyio 4.9.0 pyh29332c3_0 conda-forge
argcomplete 3.6.2 pyhd8ed1ab_0 conda-forge
argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py312h66e93f0_5 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.5 pyh29332c3_0 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
bcbio-gff 0.7.1 pyh7e72e81_2 bioconda
beautifulsoup4 4.13.4 pyha770c72_0 conda-forge
binutils_impl_linux-64 2.44 h4bf12b8_1 conda-forge
bioconductor-biobase 2.66.0 r44h3df3fcb_0 bioconda
bioconductor-biocgenerics 0.52.0 r44hdfd78af_3 bioconda
bioconductor-biomformat 1.34.0 r44hdfd78af_0 bioconda
bioconductor-biostrings 2.74.0 r44h3df3fcb_1 bioconda
bioconductor-data-packages 20250625 hdfd78af_0 bioconda
bioconductor-genomeinfodb 1.42.0 r44hdfd78af_2 bioconda
bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0 bioconda
bioconductor-iranges 2.40.0 r44h3df3fcb_2 bioconda
bioconductor-microbiome 1.28.0 r44hdfd78af_0 bioconda
bioconductor-multtest 2.62.0 r44h3df3fcb_1 bioconda
bioconductor-phyloseq 1.50.0 r44hdfd78af_0 bioconda
bioconductor-rhdf5 2.50.0 r44h77050f0_1 bioconda
bioconductor-rhdf5filters 1.18.0 r44h77050f0_1 bioconda
bioconductor-rhdf5lib 1.28.0 r44h15a9599_0 bioconda
bioconductor-s4vectors 0.44.0 r44h3df3fcb_2 bioconda
bioconductor-ucsc.utils 1.2.0 r44h9ee0642_1 bioconda
bioconductor-xvector 0.46.0 r44h15a9599_2 bioconda
bioconductor-zlibbioc 1.52.0 r44h3df3fcb_2 bioconda
biom-format 2.1.16 py312h66e93f0_2 conda-forge
biopython 1.85 py312h66e93f0_1 conda-forge
blast 2.16.0 h66d330f_5 bioconda
bleach 6.2.0 pyh29332c3_4 conda-forge
bleach-with-css 6.2.0 h82add2a_4 conda-forge
bowtie2 2.5.4 he96a11b_6 bioconda
brotli 1.1.0 hb9d3cd8_3 conda-forge
brotli-bin 1.1.0 hb9d3cd8_3 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_3 conda-forge
bwidget 1.10.1 ha770c72_1 conda-forge
bx-python 0.13.0 py312h5e9d817_1 bioconda
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.7.14 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
capnproto 1.0.2 h766bdaa_3 conda-forge
certifi 2025.7.14 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge
click 8.2.1 pyh707e725_0 conda-forge
cmseq 1.0.4 pyhb7b1952_0 bioconda
comm 0.2.2 pyhd8ed1ab_1 conda-forge
contourpy 1.3.2 py312h68727a3_0 conda-forge
curl 8.14.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
debugpy 1.8.15 py312h8285ef7_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
diamond 2.1.12 h13889ed_3 bioconda
entrez-direct 22.4 he881be0_0 bioconda
exceptiongroup 1.3.0 pyhd8ed1ab_0 conda-forge
executing 2.2.0 pyhd8ed1ab_0 conda-forge
fasttree 2.1.11 h7b50bb2_5 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.59.0 py312h8a5da7c_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gcc_impl_linux-64 15.1.0 h4393ad2_3 conda-forge
gfortran_impl_linux-64 15.1.0 h3b9cdf2_3 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graphite2 1.3.14 h5888daf_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 15.1.0 h6a1bac1_3 conda-forge
h11 0.16.0 pyhd8ed1ab_0 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.14.0 nompi_py312h3faca00_100 conda-forge
harfbuzz 11.2.1 h3beb420_0 conda-forge
hclust2 1.0.0 pyh864c0ab_1 bioconda
hdf5 1.14.6 nompi_h6e4c0c1_102 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
htslib 1.22.1 h566b1c6_0 bioconda
httpcore 1.0.9 pyh29332c3_0 conda-forge
httpx 0.28.1 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.7.0 pyhe01879c_1 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 9.4.0 pyhfa0c392_0 conda-forge
ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge
iqtree 3.0.1 h503566f_0 bioconda
isoduration 20.11.0 pyhd8ed1ab_1 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jq 1.8.1 h73b1eb8_0 conda-forge
json5 0.12.0 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py312h7900ff3_1 conda-forge
jsonschema 4.25.0 pyhe01879c_0 conda-forge
jsonschema-specifications 2025.4.1 pyh29332c3_0 conda-forge
jsonschema-with-format-nongpl 4.25.0 he01879c_0 conda-forge
jupyter-lsp 2.2.6 pyhe01879c_0 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.8.1 pyh31011fe_0 conda-forge
jupyter_events 0.12.0 pyh29332c3_0 conda-forge
jupyter_server 2.16.0 pyhe01879c_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge
jupyterlab 4.4.5 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_1 conda-forge
k8 1.2 he8db53b_6 bioconda
kernel-headers_linux-64 5.14.0 he073ed8_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 py312h68727a3_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lark 1.2.2 pyhd8ed1ab_1 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 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
libbrotlicommon 1.1.0 hb9d3cd8_3 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_3 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_3 conda-forge
libcblas 3.9.0 32_he106b2a_openblas conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.22 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_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-devel_linux-64 15.1.0 h4c094af_103 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
libgfortran-ng 15.1.0 h69a702a_3 conda-forge
libgfortran5 15.1.0 hcea5267_3 conda-forge
libglib 2.84.1 h2ff4ddf_0 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
libsanitizer 15.1.0 h97b714f_3 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.50.3 hee844dc_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-devel_linux-64 15.1.0 h4c094af_103 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libtiff 4.7.0 hc4654cb_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.51.0 hb9d3cd8_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 2.13.8 h4bc477f_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
make 4.4.1 hb9d3cd8_2 conda-forge
markupsafe 3.0.2 py312h178313f_1 conda-forge
mash 2.3 hb105d93_9 bioconda
matplotlib-base 3.10.3 py312hd3ec401_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
metaphlan 4.2.2 pyhdfd78af_0 bioconda
minimap2 2.30 h577a1d6_0 bioconda
mistune 3.1.3 pyh29332c3_0 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
muscle 5.3 h9948957_2 bioconda
nbclient 0.10.2 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.6 pyh29332c3_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
notebook 7.4.4 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge
numpy 2.3.1 py312h33ff503_1 conda-forge
oniguruma 6.9.10 hb9d3cd8_0 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.1 py312hf79963d_0 conda-forge
pandoc 3.7.0.2 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.56.3 h9ac818e_1 conda-forge
parso 0.8.4 pyhd8ed1ab_1 conda-forge
patsy 1.0.1 pyhd8ed1ab_1 conda-forge
pcre2 10.44 hc749103_2 conda-forge
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_1 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
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
phylophlan 3.1.1 pyhdfd78af_0 bioconda
pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge
pillow 11.3.0 py312h80c1187_0 conda-forge
pip 25.1.1 pyh8b19718_0 conda-forge
pixman 0.46.4 h537e5f6_0 conda-forge
platformdirs 4.3.8 pyhe01879c_0 conda-forge
prometheus_client 0.22.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.51 pyha770c72_0 conda-forge
psutil 7.0.0 py312h66e93f0_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pysam 0.23.3 py312h47d5410_0 bioconda
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.12.11 h9e4cc4f_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h178313f_2 conda-forge
pyzmq 27.0.0 py312hbf22597_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
r-ade4 1.7_23 r44hc2d650c_1 conda-forge
r-ape 5.8_1 r44hb79369c_0 conda-forge
r-askpass 1.2.1 r44h2b5f3a1_0 conda-forge
r-assertthat 0.2.1 r44hc72bb7e_5 conda-forge
r-backports 1.5.0 r44hb1dbf0f_1 conda-forge
r-base 4.4.2 hbab086e_1 conda-forge
r-base64enc 0.1_3 r44hb1dbf0f_1007 conda-forge
r-bayesm 3.1_6 r44hb424bfc_1 conda-forge
r-beeswarm 0.4.0 r44h2b5f3a1_4 conda-forge
r-biocmanager 1.30.26 r44hc72bb7e_0 conda-forge
r-bit 4.6.0 r44h2b5f3a1_0 conda-forge
r-bit64 4.6.0_1 r44h2b5f3a1_0 conda-forge
r-blob 1.2.4 r44hc72bb7e_2 conda-forge
r-boot 1.3_31 r44hc72bb7e_0 conda-forge
r-broom 1.0.8 r44hc72bb7e_0 conda-forge
r-bslib 0.9.0 r44hc72bb7e_0 conda-forge
r-cachem 1.1.0 r44hb1dbf0f_1 conda-forge
r-callr 3.7.6 r44hc72bb7e_1 conda-forge
r-caret 6.0_94 r44hdb488b9_2 conda-forge
r-cellranger 1.1.0 r44hc72bb7e_1007 conda-forge
r-class 7.3_23 r44h2b5f3a1_0 conda-forge
r-cli 3.6.5 r44h93ab643_0 conda-forge
r-clipr 0.8.0 r44hc72bb7e_3 conda-forge
r-clock 0.7.3 r44h93ab643_0 conda-forge
r-cluster 2.1.8.1 r44hb67ce94_0 conda-forge
r-codetools 0.2_20 r44hc72bb7e_1 conda-forge
r-colorspace 2.1_1 r44hdb488b9_0 conda-forge
r-commonmark 2.0.0 r44h2b5f3a1_0 conda-forge
r-compositions 2.0_8 r44h02ebe12_1 conda-forge
r-conflicted 1.2.0 r44h785f33e_2 conda-forge
r-cpp11 0.5.2 r44h785f33e_1 conda-forge
r-crayon 1.5.3 r44hc72bb7e_1 conda-forge
r-crul 1.5.0 r44h785f33e_0 conda-forge
r-curl 6.2.2 r44h2700575_0 conda-forge
r-data.table 1.17.6 r44he23165d_0 conda-forge
r-dbi 1.2.3 r44hc72bb7e_1 conda-forge
r-dbplyr 2.5.0 r44hc72bb7e_1 conda-forge
r-deoptimr 1.1_3_1 r44hc72bb7e_0 conda-forge
r-diagram 1.6.5 r44ha770c72_3 conda-forge
r-digest 0.6.37 r44h0d4f4ea_0 conda-forge
r-dplyr 1.1.4 r44h0d4f4ea_1 conda-forge
r-dtplyr 1.3.1 r44hc72bb7e_2 conda-forge
r-e1071 1.7_16 r44h93ab643_0 conda-forge
r-ellipsis 0.3.2 r44hb1dbf0f_3 conda-forge
r-emmeans 1.11.2 r44hc72bb7e_0 conda-forge
r-essentials 4.4 r44hd8ed1ab_2005 conda-forge
r-estimability 1.5.1 r44hc72bb7e_0 conda-forge
r-evaluate 1.0.4 r44hc72bb7e_0 conda-forge
r-fansi 1.0.6 r44hb1dbf0f_1 conda-forge
r-farver 2.1.2 r44ha18555a_1 conda-forge
r-fastmap 1.2.0 r44ha18555a_1 conda-forge
r-fillpattern 1.0.2 r44hc72bb7e_1 conda-forge
r-fontawesome 0.5.3 r44hc72bb7e_0 conda-forge
r-forcats 1.0.0 r44hc72bb7e_2 conda-forge
r-foreach 1.5.2 r44hc72bb7e_3 conda-forge
r-foreign 0.8_90 r44h2b5f3a1_0 conda-forge
r-formatr 1.14 r44hc72bb7e_2 conda-forge
r-fs 1.6.6 r44h93ab643_0 conda-forge
r-future 1.58.0 r44h785f33e_0 conda-forge
r-future.apply 1.20.0 r44hc72bb7e_0 conda-forge
r-gargle 1.5.2 r44h785f33e_1 conda-forge
r-generics 0.1.4 r44hc72bb7e_0 conda-forge
r-getopt 1.20.4 r44ha770c72_1 conda-forge
r-ggbeeswarm 0.7.2 r44hc72bb7e_2 conda-forge
r-ggnewscale 0.5.2 r44hc72bb7e_0 conda-forge
r-ggplot2 3.5.2 r44hc72bb7e_0 conda-forge
r-ggrepel 0.9.6 r44h93ab643_0 conda-forge
r-ggtext 0.1.2 r44hc72bb7e_3 conda-forge
r-gistr 0.9.0 r44hc72bb7e_3 conda-forge
r-glmnet 4.1_10 r44ha36cffa_0 conda-forge
r-globals 0.18.0 r44hc72bb7e_0 conda-forge
r-glue 1.8.0 r44h2b5f3a1_0 conda-forge
r-googledrive 2.1.1 r44hc72bb7e_2 conda-forge
r-googlesheets4 1.1.1 r44h785f33e_2 conda-forge
r-gower 1.0.1 r44hb1dbf0f_2 conda-forge
r-gridtext 0.1.5 r44h0d4f4ea_3 conda-forge
r-gtable 0.3.6 r44hc72bb7e_0 conda-forge
r-hardhat 1.4.1 r44hc72bb7e_0 conda-forge
r-haven 2.5.4 r44h0d4f4ea_1 conda-forge
r-hexbin 1.28.5 r44hb67ce94_0 conda-forge
r-highr 0.11 r44hc72bb7e_1 conda-forge
r-hms 1.1.3 r44hc72bb7e_2 conda-forge
r-htmltools 0.5.8.1 r44ha18555a_1 conda-forge
r-htmlwidgets 1.6.4 r44h785f33e_3 conda-forge
r-httpcode 0.3.0 r44ha770c72_4 conda-forge
r-httpuv 1.6.15 r44ha18555a_1 conda-forge
r-httr 1.4.7 r44hc72bb7e_1 conda-forge
r-ids 1.0.1 r44hc72bb7e_4 conda-forge
r-igraph 2.0.3 r44h510f1ce_1 conda-forge
r-ipred 0.9_15 r44hdb488b9_1 conda-forge
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r-sys 3.4.3 r44h2b5f3a1_0 conda-forge
r-systemfonts 1.2.3 r44h5c043a3_0 conda-forge
r-tensora 0.36.2.1 r44hb1dbf0f_1 conda-forge
r-textshaping 1.0.1 r44h16f7c1a_0 conda-forge
r-tibble 3.3.0 r44h2b5f3a1_0 conda-forge
r-tidyr 1.3.1 r44h0d4f4ea_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge
r-tidyverse 2.0.0 r44h785f33e_2 conda-forge
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r-timedate 4041.110 r44hc72bb7e_0 conda-forge
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r-triebeard 0.4.1 r44ha18555a_2 conda-forge
r-ttr 0.24.4 r44hdb488b9_1 conda-forge
r-tzdb 0.5.0 r44h93ab643_0 conda-forge
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r-utf8 1.2.6 r44h2b5f3a1_0 conda-forge
r-uuid 1.2_1 r44hdb488b9_0 conda-forge
r-vctrs 0.6.5 r44h0d4f4ea_1 conda-forge
r-vegan 2.7_1 r44h012206f_0 conda-forge
r-vipor 0.4.7 r44hc72bb7e_1 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge
r-vroom 1.6.5 r44h0d4f4ea_1 conda-forge
r-withr 3.0.2 r44hc72bb7e_0 conda-forge
r-xfun 0.52 r44h93ab643_0 conda-forge
r-xml2 1.3.8 r44h1bb2df6_0 conda-forge
r-xtable 1.8_4 r44hc72bb7e_6 conda-forge
r-xts 0.14.1 r44h2b5f3a1_0 conda-forge
r-yaml 2.3.10 r44hdb488b9_0 conda-forge
r-zip 2.3.3 r44h2b5f3a1_0 conda-forge
r-zoo 1.8_14 r44h2b5f3a1_0 conda-forge
raxml 8.2.13 h7b50bb2_3 bioconda
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.4 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rfc3987-syntax 1.1.0 pyhe01879c_1 conda-forge
rpds-py 0.26.0 py312h680f630_0 conda-forge
rpsbproc 0.5.0 hd6d6fdc_3 bioconda
samtools 1.22.1 h96c455f_0 bioconda
scipy 1.16.0 py312hf734454_0 conda-forge
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sed 4.9 h6688a6e_0 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
soupsieve 2.7 pyhd8ed1ab_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.5 py312h8b63200_0 conda-forge
sysroot_linux-64 2.34 h087de78_2 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tomlkit 0.13.3 pyha770c72_0 conda-forge
tornado 6.5.1 py312h66e93f0_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
trimal 1.5.0 h9948957_2 bioconda
types-python-dateutil 2.9.0.20250708 pyhd8ed1ab_0 conda-forge
typing-extensions 4.14.1 h4440ef1_0 conda-forge
typing_extensions 4.14.1 pyhe01879c_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
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wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xmltodict 0.14.2 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yq 3.4.3 pyhe01879c_2 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py312h66e93f0_2 conda-forge
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Basic information on how to use this tool:
- executable: metaphlan
- help: -h
- version: -v
- description: MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics.
Additional information:
Warning: running MetaPhlAn 4 requires a minimum of 25GB of memory or more.
The database can be downloaded from Segatalab FTP or via metaphlan with the following command:
metaphlan --install
Full documentation: https://github.com/biobakery/biobakery/wiki/metaphlan4
metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt