Welcome to WGDI’s Documentation!

Description

WGDI (Whole-Genome Duplication Integrated analysis) is a Python-based command-line tool designed to facilitate comprehensive analysis of recursive polyploidization events and cross-species genome alignments. It supports three main workflows:

• Polyploid inference

• Hierarchical inference of genomic homology

• Ancestral chromosome karyotyping

These workflows improve the detection of whole-genome duplications (WGD) and the characterization of WGD-related events based on high-quality chromosome-level genomes. Importantly, WGDI can extract complete synteny blocks and aid in the reconstruction of detailed karyotype evolution. The toolkit is freely available on GitHub: GitHub.

Table of Contents

• Introduction
• Installation
• Usage
  • Dotplot
  • Improved collinearity
  • Non-synonymous (Ka) and synonymous (Ks)
  • BlockInfo
  • Correspondence
  • BlockKs
  • KsPeaks
  • PeaksFit
  • KsFigure
  • Polyploid classification
  • Ancestral_karyotype
  • Ancestral_karyotype_repertoire
  • karyotype_mapping
  • Karyotype
  • Shared_fusions
  • Fusion_positions_database
  • Fusions_detection
  • Alignment
  • Alignmenttrees
  • Retain
  • P-index
  • Circos
• Examples
• Changelog

Citing WGDI

If you use WGDI in your work, please cite the following publication:

Sun, P., Jiao, B., Yang, Y., Shan, L., Li, T., Li, X., ... & Liu, J. (2022).
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes.
Molecular Plant, 15(12), 1841-1851. https://doi.org/10.1016/j.molp.2022.10.018

Contact

For any questions or suggestions, feel free to contact Pengchuan Sun via email: sunpengchuan@gmail.com or submit changes on our GitHub repository.