WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
Author | Pengchuan Sun (sunpengchuan) |
[email protected] | |
License | BSD |
WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments.
WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research.
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.
conda install -c bioconda wgdi
pip3 install wgdi
Documentation for installation along with a user tutorial, a default parameter file, and test data are provided. please consult the docs at http://wgdi.readthedocs.io/en/latest/.
Here are some videos with simple examples of WGDI.
chatting group QQ : 966612552
If you use wgdi in your work, please cite:
Sun P., Jiao B., Yang Y., Shan L., Li T., Li X., Xi Z., Wang X., and Liu J. (2022). WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.10.018.