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*

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

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

Discordant attachment frequency tool

Statistics for Adaptive Introgression

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

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

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

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

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

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

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

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

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

Snakemake Workflow for Investigating Genomic Landscapes of Introgression