Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy, including implementation of an ancestry complement model.

 

 

 

 

 

R package that provides a wrapper and STAN code for Dirichlet-multinomial modeling of count data. This is particularly useful for compositional analyses of taxa in ecology and could also be applied to differential gene expression.

 

 

 

 

 

This program calculates a hybrid index for individuals of unknown ancestry. The index is based on information from molecular markers and uses maximum-likelihood to estimate the proportion of alleles that were inherited from one of two hybridizing parental species.

 

 

 

This software implements Bayesian estimation of genomic clines between divergent lineages. Estimates are based on genotypes that are known or are estimated from DNA sequence reads. For most applications this software replaces introgress and bgc will continue to receive further development and enhancements.

 

 

 

This software implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

 

 

 

 

This is a software package that was used to illustrate variation in locus-specific introgression in hybrids. It was an R-package that is now archived. If you are looking for a replacement, consider gghybrid or bgc.

 

 

 

 

dfuse and simadmix are programs for the simulation of hybridization and admixture. They are variants of the same model and implement forward-in-time simulations of populations of diploid individuals, ancestry of their complete genomes based on modeling junctions, and the effects of finite population size, migration, and selection on genomic composition.