Population genetics Tools

GADMA (Genetic Algorithm for Demographic Model Analysis) is a Python command-line tool that uses genetic algorithms and Bayesian optimization to automatically infer the demographic history of multiple populations from allele frequency spectrum (AFS) or VCF data, supporting up to three populations and multiple inference engines including dadi and moments.

GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).

GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing genome-wide TR tools is that it can handle repeats that are longer than the read length. GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.

Hail is a scalable, cloud-native genomic analysis tool designed for large datasets. It provides a query language for genomic data and supports batch computing for efficient variant calling and other analyses.

IMPUTE2 is a genotype imputation and haplotype phasing tool that uses a multi-population reference panel to impute missing genotypes in genome-wide association studies (GWAS), enabling researchers to increase the density of genetic markers and improve statistical power for association analyses.

InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

Adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator.

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

LDsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

This is a tool to plot allele frequencies in VCF files.

Software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

fwdpy11 is a Python package for forward-time population genetic simulation, using a C++ back-end (fwdpp) for efficiency. It supports flexible modelling of selection, demography, and multiple populations, with custom temporal samplers for analyzing populations during simulation.

Interactive assembly and analysis of RADseq datasets. ipyrad: interactive assembly and analysis of RAD-seq data sets. Welcome to ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. Welcome to ipyrad — ipyrad documentation.