VIB/UGent center for plant systems biology - Bioinformatics & evolutionary genomics group https://www.vandepeerlab.org/
wgd - simple command line tools for the analysis of ancient whole-genome duplications
Note: If you are interested in the methods implemented in wgd, you may also want to
consider the ksrates tool by Sensalari et al.
which can be used to carefully compare multiple Ks distributions and model them (ksrates
uses wgd under the hood).
Installation
Python package and command line interface (CLI) for the analysis of
whole-genome duplications (WGDs). Tested with Python3 on Linux. If you don't have
python or pip installed a simple sudo apt-get install python3-pip should do.
To install, simply run
git clone https://github.com/arzwa/wgd.git
cd wgd
pip install --user .
Note that depending on your python installation and whether you're in a
virtualenv, pip may default either to pip2 or pip3. If the
above installation step fails, please try to use pip3 instead of
pip.
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
For external software requirements: please consult the relevant section in the docs
Note: if you encounter issues, do verify you have the latest
PAML version.
To install the latest version, you best not rely on apt-get or any other
package manager but install from source. Something like this should work
(from within the directory where you want to install paml)
wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz
tar -xzf paml4.9j.tgz
pushd paml4.9j/src && make -f Makefile && popd
export PATH=$PATH:$PWD/paml4.9j/src/
Quick start
The main aim of wgd is computing whole-paranome and one-vs.-one ortholog Ks
distributions. For a whole-paranome distribution of a CDS sequence fasta file,
the minimal commands are:
$ wgd dmd ath.cds.fasta
$ wgd ksd wgd_dmd/ath.cds.fasta.mcl ath.cds.fasta
For one-vs.one orthologs the minimal commands are
$ wgd dmd ath.cds.fasta vvi.cds.fasta
$ wgd ksd wgd_dmd/ath1000.fasta_vvi1000.fasta.rbh ath.cds.fasta vvi.cds.fasta
For more information and these methods and other tools implemented in wgd,
please consult the docs.
Singularity container
A Singularity container is available for wgd, allowing to use
all tools in wgd without having to install all
required software on your system. To install Singularity follow
the instructions here.
Once you have Singularity installed (and you're in the virtual machine when running on Windows or Mac), you can build the container image locally (requires root privileges). To do so, first get the Singularity definition file from wgd GitHub repository and then run the build command:
git clone https://github.com/arzwa/wgd.git
cd wgd
sudo singularity build wgd.sif Singularity
Then you can use wgd as follows:
singularity exec wgd.sif wgd <command>
Alternatively, if you don't have root privileges, you can pull an older container
from Singularity Hub, which however doesn't support the syn (collinearity via i-ADHoRe) and dmd (diamond aligner) commands:
singularity pull --name wgd.simg shub://arzwa/wgd
Notes
Bug tracking: If the program crashes, exits unexpectedly or some
unexpected results are obtained, please run it again with the
--verbosity debug flag before the subcommand of interest (e.g.
wgd --verbosity debug ksd gf.mcl cds.fasta). If the anomaly persists,
please open an issue on this GitHub site.
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.
It is generally advised not to include pipe characters (|) in your gene
IDs, since these can have special meanings in certain parts of wgd.
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
Please cite us at https://doi.org/10.1093/bioinformatics/bty915
Zwaenepoel, A., and Van de Peer, Y.
wgd - simple command line tools for the analysis of ancient whole genome duplications.
Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915
For citation of the tools used in wgd, please consult the documentation at https://wgd.readthedocs.io/en/latest/index.html#citation.