Installation

Python package and command line interface (IDLE) for the analysis of whole genome duplications (WGDI). WGDI can be deployed in Windows, Linux, and Mac OS operating systems and can be installed via pip and conda.

Bioconda

conda install -c bioconda  wgdi

Pypi

pip install wgdi

Github

git clone https://github.com/SunPengChuan/wgdi.git
cd wgdi
python setup.py install

Dependencies

Some parts of WGDI use the following third-party softwares:

PAML | MAFFT | MUSCLE | PAL2NAL IQTREE

After you download and install the above packages. You can run wgdi -conf help > conf.ini to configure the path of the existing software.

[ini]
mafft_path = C:\bio\mafft-win\mafft.bat
pal2nal_path = C:\bio\[pal2nal.v14\pal2nal.pl
yn00_path = C:\bio\paml4.9j\bin\yn00.exe
muscle_path = C:\bio\muscle3.8.31_i86win32.exe

Add the directory of your software to the conf.ini file, and then execute wgdi -conf conf.ini to complete the configuration path.

[ini]
mafft_path = /usr/bin/mafft
pal2nal_path = /usr/local/bin/pal2nal.v14/pal2nal.pl
yn00_path = /usr/bin/yn00
muscle_path = /usr/bin/muscle
iqtree_path = /usr/bin/iqtree

Uninstall

If you don’t need wgdi, you can uninstall with pip uninstall wgdi or conda remove wgdi.