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.

Genetic maps in autopolyploids

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

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

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

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

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

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

Manual

An R package for flow cytometry histogram analysis

R-based autopolyploid population and population genetic simulation

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

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

AKRUP: ancestral karyotype reconstruction universal pipeline

github repository for R package mpQTL

Bioinformatic methods used in McElroy et al. (2021). Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes. Molecular Biology and Evolution.

Scripts, information and data for publication in APPS.

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

Estimate the polyploidy