Welcome to WGDI’s documentation!

Description

WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi).

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
  • Alignment
  • Alignmenttrees
  • Retain
  • P-index
  • Circos
• Examples
• Changelog

Citating WGDI

If you use wgdi in your work, please cite:

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

If you have any questions or good suggestions , send email via Pengchuan Sun’s mailbox or submit changes on our GitHub.