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environment.yml
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environment.yml
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name: phylo
channels:
- pytorch
- etetoolkit
- anaconda
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- aioeasywebdav=2.4.0=py39hf3d152e_1001
- aiohttp=3.7.4.post0=py39h3811e60_0
- alsa-lib=1.2.3.2=h166bdaf_0
- amply=0.1.5=pyhd8ed1ab_0
- appdirs=1.4.4=pyh9f0ad1d_0
- argon2-cffi=21.3.0=pyhd3eb1b0_0
- argon2-cffi-bindings=21.2.0=py39h7f8727e_0
- argtable2=2.13=0
- asttokens=2.0.5=pyhd3eb1b0_0
- async-timeout=3.0.1=py_1000
- attmap=0.13.2=pyhd8ed1ab_0
- attrs=20.2.0=py_0
- augur=18.1.2=pyhdfd78af_0
- backcall=0.2.0=py_0
- backports=1.1=pyhd3eb1b0_0
- backports.functools_lru_cache=1.6.4=pyhd3eb1b0_0
- backports.tempfile=1.0=pyhd3eb1b0_1
- backports.weakref=1.0.post1=py_1
- bcbio-gff=0.6.9=pyh5e36f6f_0
- bcrypt=3.2.0=py39h3811e60_1
- binutils_impl_linux-64=2.35.1=h27ae35d_9
- binutils_linux-64=2.35=h67ddf6f_30
- biopython=1.79=py39h3811e60_0
- blas=1.0=mkl
- bleach=4.1.0=pyhd3eb1b0_0
- boto3=1.26.1=pyhd8ed1ab_0
- botocore=1.29.1=pyhd8ed1ab_0
- bottleneck=1.3.4=py39hce1f21e_0
- brotli=1.0.9=he6710b0_2
- brotlipy=0.7.0=py39h27cfd23_1003
- bwidget=1.9.14=ha770c72_1
- bx-python=0.8.11=py39h5d76eff_1
- bzip2=1.0.8=h7b6447c_0
- c-ares=1.17.1=h7f98852_1
- ca-certificates=2022.9.24=ha878542_0
- cachecontrol=0.12.6=py_0
- cachetools=5.2.0=pyhd8ed1ab_0
- cairo=1.16.0=h488836b_1006
- certifi=2022.9.24=pyhd8ed1ab_0
- cffi=1.15.0=py39hd667e15_1
- chardet=4.0.0=py39hf3d152e_3
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.4=py39h06a4308_0
- clustalo=1.2.4=h4346872_0
- coincbc=2.10.5=hab63836_1
- commonmark=0.9.1=py_0
- conda=4.12.0=py39hf3d152e_0
- conda-package-handling=1.8.1=py39h7f8727e_0
- conda-verify=3.4.2=py_1
- configargparse=1.5.3=pyhd8ed1ab_0
- connection_pool=0.0.3=pyhd3deb0d_0
- cryptography=36.0.0=py39h9ce1e76_0
- curl=7.76.1=h979ede3_1
- cvxopt=1.2.6=py39heb1511d_0
- cycler=0.11.0=pyhd3eb1b0_0
- cython=0.29.28=py39h295c915_0
- dataclasses=0.8=pyhc8e2a94_3
- datrie=0.8.2=py39h3811e60_2
- dbus=1.13.18=hb2f20db_0
- debugpy=1.5.1=py39h295c915_0
- decorator=4.4.2=py_0
- defusedxml=0.7.1=pyhd3eb1b0_0
- dialigntx=1.0.2=hdce4c0c_0
- docutils=0.19=py39hf3d152e_1
- dpath=2.0.6=py39hf3d152e_2
- dropbox=11.35.0=pyhd8ed1ab_0
- dsdp=5.8=hd9d9efa_1203
- entrypoints=0.3=py39h06a4308_0
- ete3=3.1.2=pyh39e3cac_0
- executing=0.8.3=pyhd3eb1b0_0
- expat=2.4.4=h295c915_0
- fasttree=2.1=hdfd2403_0
- ffmpeg=4.3=hf484d3e_0
- fftw=3.3.9=h27cfd23_1
- filechunkio=1.8=py_2
- filelock=3.8.0=pyhd8ed1ab_0
- fontconfig=2.13.1=hba837de_1005
- fonttools=4.25.0=pyhd3eb1b0_0
- freetype=2.11.0=h70c0345_0
- fribidi=1.0.10=h36c2ea0_0
- ftputil=5.0.4=pyhd8ed1ab_0
- future=0.18.2=py39h06a4308_1
- gcc_impl_linux-64=7.5.0=hda68d29_13
- gcc_linux-64=7.5.0=h47867f9_30
- gettext=0.21.1=h27087fc_0
- gfortran_linux-64=7.2.0=24
- giflib=5.2.1=h7b6447c_0
- gitdb=4.0.9=pyhd8ed1ab_0
- gitpython=3.1.29=pyhd8ed1ab_0
- glib=2.68.4=h9c3ff4c_0
- glib-tools=2.68.4=h9c3ff4c_0
- glpk=4.65=h9202a9a_1004
- gmp=6.2.1=h2531618_2
- gnutls=3.6.15=he1e5248_0
- google-api-core=2.10.0=pyhd8ed1ab_0
- google-api-python-client=2.65.0=pyhd8ed1ab_0
- google-auth=2.14.0=pyh1a96a4e_0
- google-auth-httplib2=0.1.0=pyhd8ed1ab_1
- google-cloud-core=2.3.2=pyhd8ed1ab_0
- google-cloud-storage=2.5.0=pyh6c4a22f_0
- google-crc32c=1.1.2=py39hb81f231_0
- google-resumable-media=2.4.0=pyhd8ed1ab_0
- googleapis-common-protos=1.56.4=py39hf3d152e_1
- graphite2=1.3.13=h58526e2_1001
- grpcio=1.38.1=py39hff7568b_0
- gsl=2.6=he838d99_2
- gst-plugins-base=1.14.5=h0935bb2_2
- gstreamer=1.18.5=h76c114f_0
- gxx_impl_linux-64=7.5.0=h64c220c_13
- gxx_linux-64=7.5.0=h555fc39_30
- harfbuzz=2.7.2=ha5b49bf_1
- hdmedians=0.14.2=py39h6323ea4_1
- httplib2=0.21.0=pyhd8ed1ab_0
- icu=67.1=he1b5a44_0
- idna=3.3=pyhd3eb1b0_0
- importlib-metadata=2.0.0=py_1
- importlib_metadata=2.0.0=1
- iniconfig=1.1.1=py_0
- intel-openmp=2021.4.0=h06a4308_3561
- ipykernel=6.9.1=py39h06a4308_0
- ipython=8.1.1=py39h06a4308_0
- ipython_genutils=0.2.0=pyhd3eb1b0_1
- ipywidgets=7.6.5=pyhd3eb1b0_1
- iqtree=2.0.3=h176a8bc_1
- isa-l=2.30.0=ha770c72_4
- isodate=0.6.1=pyhd8ed1ab_0
- jedi=0.18.1=py39h06a4308_1
- jinja2=3.0.3=pyhd3eb1b0_0
- jmespath=1.0.1=pyhd8ed1ab_0
- joblib=0.17.0=py_0
- jpeg=9d=h7f8727e_0
- jsonschema=3.2.0=pyhd3eb1b0_2
- jupyter=1.0.0=py39h06a4308_7
- jupyter_client=7.1.2=pyhd3eb1b0_0
- jupyter_console=6.4.3=pyhd3eb1b0_0
- jupyter_core=4.9.2=py39h06a4308_0
- jupyterlab_pygments=0.1.2=py_0
- jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
- kalign=2.03=h29c49b8_0
- kernel-headers_linux-64=2.6.32=he073ed8_15
- kiwisolver=1.3.2=py39h295c915_0
- krb5=1.17.2=h926e7f8_0
- lame=3.100=h7b6447c_0
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.35.1=h7274673_9
- libarchive=3.5.1=h3f442fb_1
- libblas=3.9.0=12_linux64_mkl
- libcblas=3.9.0=12_linux64_mkl
- libclang=11.1.0=default_ha53f305_1
- libcrc32c=1.1.1=h9c3ff4c_2
- libcurl=7.76.1=hc4aaa36_1
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.10=h9b69904_4
- libffi=3.3=he6710b0_2
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=9.3.0=h7864c58_19
- libgcc-ng=12.2.0=h65d4601_19
- libgfortran-ng=7.5.0=ha8ba4b0_17
- libgfortran4=7.5.0=ha8ba4b0_17
- libglib=2.68.4=h3e27bee_0
- libgomp=12.2.0=h65d4601_19
- libiconv=1.17=h166bdaf_0
- libidn2=2.3.2=h7f8727e_0
- liblapack=3.9.0=12_linux64_mkl
- libllvm11=11.1.0=hf817b99_2
- libnghttp2=1.43.0=h812cca2_0
- libopenblas=0.3.17=hf726d26_1
- libpng=1.6.37=hbc83047_0
- libpq=12.3=h255efa7_3
- libprotobuf=3.17.2=h780b84a_1
- libsodium=1.0.18=h7b6447c_0
- libsolv=0.7.19=h780b84a_5
- libssh2=1.9.0=ha56f1ee_6
- libstdcxx-devel_linux-64=9.3.0=hb016644_19
- libstdcxx-ng=12.2.0=h46fd767_19
- libtasn1=4.16.0=h27cfd23_0
- libtiff=4.2.0=h85742a9_0
- libunistring=0.9.10=h27cfd23_0
- libuuid=2.32.1=h7f98852_1000
- libuv=1.40.0=h7b6447c_0
- libwebp=1.2.2=h55f646e_0
- libwebp-base=1.2.2=h7f8727e_0
- libxcb=1.14=h7b6447c_0
- libxkbcommon=1.0.3=he3ba5ed_0
- libxml2=2.9.10=h68273f3_2
- libxslt=1.1.33=hf705e74_1
- lockfile=0.12.2=py39h06a4308_0
- logmuse=0.2.6=pyh8c360ce_0
- lxml=4.8.0=py39hb9d737c_3
- lz4-c=1.9.3=h295c915_1
- lzo=2.10=h516909a_1000
- mafft=6.861=h7f9ae3c_0
- make=4.3=hd18ef5c_1
- mamba=0.7.8=py39hda673b1_0
- markupsafe=2.0.1=py39h27cfd23_0
- matplotlib=3.5.1=py39h06a4308_1
- matplotlib-base=3.5.1=py39ha18d171_1
- matplotlib-inline=0.1.2=pyhd3eb1b0_2
- metis=5.1.0=h58526e2_1006
- mistune=0.8.4=py39h27cfd23_1000
- mkl=2021.4.0=h06a4308_640
- mkl-service=2.4.0=py39h7f8727e_0
- mkl_fft=1.3.1=py39hd3c417c_0
- mkl_random=1.2.2=py39h51133e4_0
- mpfr=4.1.0=h9202a9a_1
- msgpack-python=1.0.2=py39hff7bd54_1
- multidict=5.1.0=py39h3811e60_1
- munkres=1.1.4=py_0
- muscle=3.8.31=he5e28f3_0
- mysql-common=8.0.25=ha770c72_0
- mysql-libs=8.0.25=h935591d_0
- natsort=7.0.1=py_0
- nbclient=0.5.11=pyhd3eb1b0_0
- nbconvert=6.3.0=py39h06a4308_0
- nbformat=5.1.3=pyhd3eb1b0_0
- ncurses=6.3=h7f8727e_2
- nest-asyncio=1.5.1=pyhd3eb1b0_0
- nettle=3.7.3=hbbd107a_1
- networkx=2.8.8=pyhd8ed1ab_0
- notebook=6.4.8=py39h06a4308_0
- nspr=4.32=h9c3ff4c_1
- nss=3.69=hb5efdd6_1
- numexpr=2.8.1=py39h6abb31d_0
- numpy=1.21.2=py39h20f2e39_0
- numpy-base=1.21.2=py39h79a1101_0
- oauth2client=4.1.3=py_0
- openh264=2.1.1=h4ff587b_0
- openssl=1.1.1s=h166bdaf_0
- packaging=21.3=pyhd3eb1b0_0
- paml=4.8=h48adae2_0
- pandas=1.4.1=py39h295c915_1
- pandocfilters=1.5.0=pyhd3eb1b0_0
- pango=1.42.4=h7062337_4
- paramiko=2.11.0=pyhd8ed1ab_0
- parso=0.8.0=py_0
- pbzip2=1.1.13=0
- pcre=8.45=h295c915_0
- peppy=0.35.2=pyhd8ed1ab_0
- pexpect=4.8.0=pyhd3eb1b0_3
- phylobayes=4.1c=hac87e47_0
- phyml=20160115.patched=hee5dff1_0
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pigz=2.6=h27826a3_0
- pillow=9.0.1=py39h22f2fdc_0
- pip=21.2.4=py39h06a4308_0
- pixman=0.38.0=h516909a_1003
- plac=1.3.5=pyhd8ed1ab_0
- pluggy=0.12.0=py_0
- ply=3.11=py_1
- prettytable=3.4.1=pyhd8ed1ab_0
- prometheus_client=0.13.1=pyhd3eb1b0_0
- prompt-toolkit=3.0.20=pyhd3eb1b0_0
- prompt_toolkit=3.0.20=hd3eb1b0_0
- protobuf=3.17.2=py39he80948d_0
- psutil=5.8.0=py39h3811e60_1
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pulp=2.7.0=py39hf3d152e_0
- pure_eval=0.2.2=pyhd3eb1b0_0
- py=1.9.0=py_0
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.7=py_0
- pycosat=0.6.3=py39h3811e60_1006
- pycparser=2.21=pyhd3eb1b0_0
- pygments=2.7.1=py_0
- pynacl=1.4.0=py39h3811e60_2
- pyopenssl=22.0.0=pyhd3eb1b0_0
- pyparsing=3.0.4=pyhd3eb1b0_0
- pyqt=5.12.3=py39hf3d152e_8
- pyqt-impl=5.12.3=py39hde8b62d_8
- pyqt5-sip=4.19.18=py39he80948d_8
- pyqtchart=5.12=py39h0fcd23e_8
- pyqtwebengine=5.12.1=py39h0fcd23e_8
- pyrsistent=0.18.0=py39heee7806_0
- pysftp=0.2.9=py_1
- pysocks=1.7.1=py39h06a4308_0
- pytest=6.2.5=py39h06a4308_2
- python=3.9.11=h12debd9_2
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python-irodsclient=1.1.5=pyhd8ed1ab_0
- python-isal=1.1.0=py39hb9d737c_1
- python-lzo=1.14=py39h388aed1_2
- python_abi=3.9=2_cp39
- pytorch=1.13.0=py3.9_cpu_0
- pytorch-mutex=1.0=cpu
- pytz=2021.3=pyhd3eb1b0_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyyaml=6.0=py39h7f8727e_1
- pyzmq=22.3.0=py39h295c915_2
- qt=5.12.9=h763d07f_1
- qtconsole=5.3.0=pyhd3eb1b0_0
- qtpy=2.0.1=pyhd3eb1b0_0
- r-ape=5.5=r36h306847c_0
- r-base=3.6.3=hd272fe0_4
- r-fastmatch=1.1_0=r36hcdcec82_1005
- r-igraph=1.2.6=r36h084b37e_1
- r-lattice=0.20_44=r36hcfec24a_0
- r-magrittr=2.0.1=r36hcfec24a_1
- r-matrix=1.3_3=r36he454529_0
- r-nlme=3.1_150=r36h31ca83e_0
- r-phangorn=2.7.0=r36h03ef668_0
- r-pkgconfig=2.0.3=r36h6115d3f_1
- r-quadprog=1.5_8=r36hed91ed1_3
- r-rcpp=1.0.6=r36h03ef668_0
- ratelimiter=1.2.0=py_1002
- raxml=8.2.11=h6db2ed4_0
- readline=8.1.2=h7f8727e_1
- reproc=14.2.1=h36c2ea0_0
- reproc-cpp=14.2.1=h58526e2_0
- requests=2.27.1=pyhd3eb1b0_0
- reretry=0.11.1=pyhd8ed1ab_0
- rich=12.6.0=pyhd8ed1ab_0
- rsa=4.9=pyhd8ed1ab_0
- ruamel_yaml=0.15.80=py39h3811e60_1004
- s3transfer=0.6.0=pyhd8ed1ab_0
- scikit-bio=0.5.6=py39h6323ea4_0
- scikit-learn=1.0.2=py39h51133e4_1
- scipy=1.7.3=py39hc147768_0
- seaborn=0.11.2=pyhd3eb1b0_0
- sed=4.8=he412f7d_0
- send2trash=1.8.0=pyhd3eb1b0_1
- seq-gen=1.3.4=h779adbc_4
- setuptools=58.0.4=py39h06a4308_0
- sip=4.19.13=py39h295c915_0
- six=1.16.0=pyhd3eb1b0_1
- slacker=0.14.0=py_0
- slr=1.4.3=h69822e3_0
- smart_open=6.2.0=pyha770c72_0
- smmap=3.0.5=pyh44b312d_0
- snakemake=7.18.1=hdfd78af_0
- snakemake-minimal=7.18.1=pyhdfd78af_0
- sqlite=3.38.2=hc218d9a_0
- stack_data=0.2.0=pyhd3eb1b0_0
- stone=3.3.1=pyhd8ed1ab_0
- stopit=1.1.2=py_0
- suitesparse=5.10.1=h9e50725_1
- sysroot_linux-64=2.12=he073ed8_15
- t_coffee=11.00=h99d273f_0
- tabulate=0.9.0=pyhd8ed1ab_1
- tbb=2021.6.0=h924138e_1
- terminado=0.13.1=py39h06a4308_0
- testpath=0.5.0=pyhd3eb1b0_0
- threadpoolctl=2.1.0=pyh5ca1d4c_0
- tk=8.6.11=h1ccaba5_0
- tktable=2.10=hb7b940f_3
- toml=0.10.1=py_0
- toposort=1.7=pyhd8ed1ab_0
- torchvision=0.14.0=py39_cpu
- tornado=6.1=py39h27cfd23_0
- tqdm=4.64.0=py39h06a4308_0
- traitlets=5.1.1=pyhd3eb1b0_0
- treetime=0.9.4=pyh7cba7a3_0
- trimal=1.4=h87cb4c3_0
- typing-extensions=4.1.1=hd3eb1b0_0
- typing_extensions=4.1.1=pyh06a4308_0
- tzdata=2022a=hda174b7_0
- ubiquerg=0.6.2=pyhd8ed1ab_0
- uritemplate=4.1.1=pyhd8ed1ab_0
- urllib3=1.26.8=pyhd3eb1b0_0
- vcftools=0.1.16=h9a82719_5
- veracitools=0.1.3=py_0
- wcwidth=0.2.5=py_0
- webencodings=0.5.1=py39h06a4308_1
- wheel=0.37.1=pyhd3eb1b0_0
- widgetsnbextension=3.5.2=py39h06a4308_0
- wrapt=1.12.1=py39h3811e60_3
- xopen=1.7.0=py39hf3d152e_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h7b6447c_0
- yaml=0.2.5=h7b6447c_0
- yarl=1.6.3=py39h3811e60_2
- yte=1.5.1=py39hf3d152e_0
- zeromq=4.3.4=h2531618_0
- zipp=3.3.1=py_0
- zlib=1.2.11=h7f8727e_4
- zstandard=0.19.0=py39hb9d737c_0
- zstd=1.4.9=haebb681_0
prefix: /home/aparker/mambaforge/envs/phylo