polyploidy

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.

Robust identification of orthologous Synteny with the Orthology Index

Genetic maps in autopolyploids

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

An R package for predicting ploidal level from sequence data using site-based heterozygosity 

An R package for comparative transcriptomic analyses of hybrids and their progenitors

An Example of Subgenome Phasing for Complex Allopolyploidy

Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)

Manual

Scripts, information and data for publication in APPS.

An R package for flow cytometry histogram analysis

A dashboard to explore and download the duplicated gene repertoire in eukaryote species

github repository for R package mpQTL

AKRUP: ancestral karyotype reconstruction universal pipeline

R-based autopolyploid population and population genetic simulation

How does disturbance on a landscape affect the establishment of new polyploid plant species?

Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"