Copyright (C) 2018 Arthur Zwaenepoel

VIB/UGent center for plant systems biology - Bioinformatics & evolutionary genomics group http://bioinformatics.psb.ugent.be/beg/

wgd - simple command line tools for the analysis of ancient whole genome duplications

Installation

Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). Tested with Python3.5 & Python3.6 on Linux Ubuntu. If you don't have python or pip installed a simple sudo apt-get install python3-pip should do.

To install: clone the repo, navigate to it and install it with pip

$ git clone https://github.com/arzwa/wgd.git
$ cd wgd
$ pip install .

For the command line interface, upon installation run

$ wgd

to get a list of the available commands. To get usage instructions for a command (e.g. ksd) run

$ wgd ksd --help

To use as a Python package as well as to find additional documentation and examples for the CLI, please consult the docs at http://wgd.readthedocs.io/en/latest/

Notes

Note on input data: while the input data is rather straightforward (a CDS fasta file will do for most analyses) it may be of interest that the wgd suite was extensively tested with data from the PLAZA platform, so for examples of the right input data formats (in particular CDS fasta files for sequence data and GFF files for structural annotation), please have a look there.

Note on virtualenv: you can install wgd in a virtual environment (using virtualenv). If you would however encounter problems with running the executable directly (e.g. wgd --help doesn't work) you can circumvent this by directly calling the CLI, using python3 ./wgd_cli.py --help (assuming you are currently in the directory where you cloned wgd).

Citation

Until this package is described in a formal publication, please cite this repository if you use the software in your research. For citation of the tools used in wgd, please consult the documentation at http://wgd.readthedocs.io/en/latest/.