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|
name: gubbins_env
channels:
- conda-forge
- bioconda
- defaults
- r
dependencies:
# python
- python>=3.8,<3.11
# installation
- autoconf
- automake
- autoconf-archive
- pytest
- pytest-cov
- lcov
- check
- libtool
- cppunit
- pkg-config
- wheel
- pillow
- llvm
# algorithm
- scipy
- dendropy
- biopython
- multiprocess
- numpy<=1.23.0
- numba
# phylogenetics
- raxml=8.2.12
- iqtree>=2.2
- rapidnj
- raxml-ng=1.0.1
- fasttree=2.1.10
# Scripts
- ska2>=0.3.0
# R
- r-argparser
- r-magrittr
- r-tidyverse
- bioconductor-treeio
- bioconductor-ggtree
- r-aplot
- r-patchwork
- r-cowplot
- r-rcolorbrewer
|
