| 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.
WGDI outperforms similar tools in terms of efficiency, flexibility and scalability.
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.
If you use wgdi in your work, please cite:
Sun P, Jiao B, Yang Y, et al. WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes[J]. bioRxiv, 2021. doi: https://doi.org/10.1101/2021.04.29.441969
- Fixed legend issue with (-kf).
- Fixed calculate Ks issue with (-ks).
- Improved the karyotype_mapping (-km) effect.
- Improved the alignmenttrees (-at) effect.
- Fixed some bugs.
- Fixed the error of the command (-conf).
- Improved the karyotype_mapping (-km) effect.
- Added the available data set of alignmenttree (-at). Low copy data set (for example, single-copy_groups.tsv of sonicparanoid2 software).
- The latest version adds karyotype_mapping (-km) and karyotype (-k) display.
- The latest version changes the calculation of extracting pvalue from collinearity (-icl), making this parameter more sensitive. Therefore, it is recommended to set to 0.2 instead of 0.05.
- The latest version has also changed the drawing display of ksfigure (-kf) to make it more beautiful.
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