wgd v2 documentation

wgd v2 is a Python package for the inference and timing of polyploidization (WGD) events. It suits those researchers who want to identify and date the WGD with a (few) genome. In this documentation, we provided the Theory, comprehensive Usage and multiple Recipes for different needs. For the installation, Please refer to the Installation page for detailed information of installing.

Check out the Recipes section for a quick start of examplar analysis such as whole paranome inference, WGD dating and etc.

Note

This project is under active development.

Contents

• Theory
  • Model of gene family evolution
• Installation
  • PYPI
  • Source
  • Conda
  • Docker
• Usage
  • Whole paranome delineation
  • Global/Local MRBHs inference
  • Orthogroup inference
  • Collinear coalescence inference of phylogeny
  • Orthogroup assignment
    • cli.dmd()
  • K_S distribution construction
  • Corrected K_S distribution construction
  • K_S tree inference
    • cli.ksd()
  • Mixture model clustering of K_S distribution
    • cli.mix()
  • Synteny inference
    • cli.syn()
  • Search of anchor pairs for molecular dating
    • cli.peak()
  • Concatenation-/Coalescence-based phylogenetic inference
  • Functional annotation of gene families
  • WGD dating
    • cli.focus()
  • K_S distribution visualization
  • Corrected K_S distribution visualization
  • Synteny visualization
    • cli.viz()
• Recipes
  • Whole paranome inference
  • K_S distribution construction
  • Synteny inference
  • Mixture modeling
  • Substitution rate correction
  • Substitution rate correction with mixture modeling
  • Multiple orthologous K_S distribution
  • WGD dating
• Citation
  • External software