R scripts and data files to test the "instant speciation" hypothesis

Estimate the polyploidy

Manual

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

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.

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

An R package for flow cytometry histogram analysis

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

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.

AKRUP: ancestral karyotype reconstruction universal pipeline

Script and data supporting a Brassica network analysis manuscript submitted to Applications in Plant Sciences

Genetic maps in autopolyploids

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

Scripts, information and data for publication in APPS.

R-based autopolyploid population and population genetic simulation

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

github repository for R package mpQTL

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