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
Download GWideCodeML \
git clone https://github.com/lauguma/GWideCodeML.git \
cd GWideCodeML
Install \
python setup.py install
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)
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
Create a conda environment from yml file \
conda env create -f gwidecodeml_conda.yml
Activate conda environment \
conda activate gwcodeml
Install and run GWideCodeML \
python setup.py install \
gwidecodeml -h
Python >= 3.5
Python libraries
Software
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