GWideCodeML is a Python package that provides support for testing evolutionary hypothesis using codeml (from the PAML package) in a genome-wide framework.
For further information on installation and usage, please visit https://github.com/lauguma/GWideCodeML/wiki
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Download GWideCodeML
git clone https://github.com/lauguma/GWideCodeML.git
cd GWideCodeML
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Install
python setup.py install
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Run GWideCodeML: if succesfull installation, gwidecodeml executable is created. You can check it by writing in your console:
gwidecodeml -h
Note: if you choose this option, all requirements must be satisfaied before running GWideCodeML (e.g. codeml must be installed and available from the working directory), see Requirements section.
(easier, recommended option)
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Install and initialize miniconda
(skip in case you already have a conda env and know how it works)
https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
close and open a new console before continue -
Download GWideCodeML
git clone https://github.com/lauguma/GWideCodeML.git
cd GWideCodeML
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Create a conda environment from yml file
conda env create -f gwidecodeml_conda.yml
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Activate conda environment
conda activate gwcodeml
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Install and run GWideCodeML
python setup.py install
gwidecodeml -h
Python >= 3.5
Python libraries
- Biopython
- Scipy
- ete3
Software
- codeml from the PAML package (Phylogenetics Analysis by Maximum Likelihood). http://abacus.gene.ucl.ac.uk/software/paml.html \
- fastTree: http://www.microbesonline.org/fasttree/
Macías L. G., Barrio E. and Toft. C. "GWideCodeML: a Python package for testing evolutionary hypothesis at the genome-wide level" G3: Genes, Genomes, Genetics (2020) doi:10.1534/g3.120.401874.
Our pipeline uses third-party software:
Yang, Z. "PAML 4: a program package for phylogenetic analysis by maximum likelihood." Mol Biol Evol (2017) doi: 10.1093/molbev/msm088
Huerta-Cepas, J., Serra, F and Bork, P. "ETE 3: Reconstruction, analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi: 10.1093/molbev/msw046