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
.