This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you should prepare is the phased vcf file containg the data o…

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.j…

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

feature-based deep learning for the identification of selective sweeps

modified version of Hudson's ms allowing for finer control and tracking of migrant genealogies

Software for detecting introgression using supervised machine learning

SMC++ infers population history from whole-genome sequence data.

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.

General tools for genomic analyses.

Data format based on dictionaries

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files