introgression

DFOIL: Introgression Testing for Five Taxa

Detects Outliers and plots genomic clines from BGC output, and extends the plotting functionality of INTROGRESS to Correlate genomic clines and hybrid indices with Environmental Variables

Detecting Archaic Introgression from Population Genetic Data with S*

Script for detecting signals of introgression in large set of gene trees from unlinked markers

Statistics for Adaptive Introgression

An expert-guided workflow integrating D-statistic screening and BPP-based Bayesian model testing to reconstruct reticulate evolutionary histories.

Discordant attachment frequency tool

R package for introgression detection using coverage depth in GBS sequencing data

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

Introgression Simulation using ms and seq-gen

Genomic Analysis of Introgressed-Site and -Haplotype Identification

Repository with all scripts for Sarabia, Salado et al. (2024) Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus)

Haplotype marker based on 3,000 Rice Genomes for subpopulation inference

Revealing the Interspecific Breeding History of Hawaiian Macadamia through Transcriptome Sequencing and Analysis 

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

A modified version of FILET (software for detecting introgression using supervised machine learning), to use for introgression detection between Gonioctena intermedia and Gonioctena quinquepunctata

Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.

Snakemake Workflow for Investigating Genomic Landscapes of Introgression

Validated AADR pipeline for credibility-aware Neanderthal ancestry and Denisovan-affinity analyses.

ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.