GWideCodeML

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A Python package for testing evolutionary hypotheses in genome-wide approaches.

GWideCodeML 최신버젼 다운로드

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# GWideCodeML

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

## Installation
### Option 1:

1. Download GWideCodeML \
`git clone https://github.com/lauguma/GWideCodeML.git` \
`cd GWideCodeML`

2. Install \
`python setup.py install`

3. 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.

### Option 2: conda environment
(easier, recommended option)

0. 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

1. Download GWideCodeML \
`git clone https://github.com/lauguma/GWideCodeML.git` \
`cd GWideCodeML`

2. Create a conda environment from yml file \
`conda env create -f gwidecodeml_conda.yml`

3. Activate conda environment \
`conda activate gwcodeml`

4. Install and run GWideCodeML \
`python setup.py install` \
`gwidecodeml -h`

## Requirements

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/

## Citation

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

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