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
- Installation
- Usage
- Whole paranome delineation
- Global/Local MRBHs inference
- Orthogroup inference
- Collinear coalescence inference of phylogeny
- Orthogroup assignment
- KS distribution construction
- Corrected KS distribution construction
- KS tree inference
- Mixture model clustering of KS distribution
- Synteny inference
- Search of anchor pairs for molecular dating
- Concatenation-/Coalescence-based phylogenetic inference
- Functional annotation of gene families
- WGD dating
- KS distribution visualization
- Corrected KS distribution visualization
- Synteny visualization
- Recipes
- Citation