Installation

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\muscle-win64.v5.3.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.