Software programs for population genetics & population genomics.
Listed A to Z – annotated by method.
A
Abbababa – tests for ancient admixture by calculating the D-statistic
ABySS – de novo, parallel, paired-end sequence assembler for short reads
adegenet – R package for genome-wide SNP analysis (including PCA)
Admixture – estimates individual ancestries from multilocus SNP data (i.e., STRUCTURE)
ALLPATHS-LG – short-read genome assembler
AM Graham Pipeline on GitHub – customized scripts and pipelines
AMAS – fast tool for alignment manipulation and summary statistics
ANGSD – analysis of next generation sequencing data
ANNOVAR – for functional annotation of genetic variants
Archeopteryx – visualization, analysis, and editing of large highly annotated phylogenetic trees
Arlequin 3.5 – large set of methods/statistical tests for pop gen analyses
ASTRAL – estimates unrooted species tree from set of unrooted gene trees
ATGC: Montpellier Bioinformatics – bioinformatics platform
aTRAM – automated target restricted assembly method
B
BayesAss – inference of recent migrants
BayeScan – identifying candidate loci under natural selection
BayesFST – Bayesian estimation of the coancestry coefficient FST
BayPass – genome-wide scan of adaptive differentiation and association analysis
Bcftools – variant calling and manipulating VCF and BCF files
Beagle – phases haplotypes and imputes missing data
BEAST2 – Bayesian analysis of rooted phylogenies using MCMC
BEST – Bayesian estimation of species trees under coalescent model
bgc – identify introgression by Bayesian estimation of genomic clines
Bowtie – ultrafast, memory-efficient short read aligner
BRAKER – pipeline for fully automated prediction of protein coding gene structures
Buerkle Lab Software – population genetics softwares (e.g., bgc, introgress)
BWA – mapping similar sequences to a reference genome
C
Chimera – visualization and analysis of molecular structures
ClineFit – fits genotypic data to cline model
CLUMPP – aggregates multiple STRUCTURE runs
CMPG Lab – population genetics softwares
Cn3D – 3D molecular visualization/analysis
COANCESTRY – estimates pairwise relatedness
CrossMap – converts genome coordinates between assemblies
CView – tool for exploring sequence alignments using dynamic network
D
dadi – diffusion approximations to the allele frequency spectrum to fit population models
ddRAD-seq Pipeline – customized scripts and pipelines for RAD-Seq
Demerelate – pairwise relatedness within populations
DensiTree – graphical analyses of sets of trees
dfoil – ABBA-BABA tests for a symmetric tree
discoal – coalescent simulator for selective sweeps with recurrent mutation, recombination, and gene conversion
DnaSP – large set of methods/statistical tests for pop gen analyses
Dsuite – ABBA-BABA D-statistics
E
EAGLE – algorithm to identify tissue/cell-specific enhancer-gene interactions
easySFS – converts VCF files to dadi/fastsimcoal format
ecdf – R function to calculate the population branch statistic (PBS)
EEMS – visualization of spatial population structure from georeferenced samples
evobiR – R package for comparative analyses
Exonerate – generic tool for pairwise sequence comparison
F
fastsimcoal – coalescent simulation for population splitting, growth, migration/admixture, and recombination
FastSMC – identifies and estimate age of pairwise identical-by-descent (IBD) genomic regions
fastStructure – population structure inference from SNP genotypes
FASTX-Toolkit – command line tools for short-read FASTA/FASTQ files
Felsenstein Software List – list of phylogeny programs
FigTree – graphical viewer of phylogenetic trees
fineRADstructure – population structure inference from RAD-Seq data
FSTAT – computes F statistics
G
Galaxy – workflow system for bioinformatics
GBLOCKS – trims multiple sequence alignments to capture conserved blocks
GDA – methods/statistical tests for pop gen analyses
GenAlEx – genetic analysis in Microsoft Excel
GENESIS – analysis of data with population structure and relatedness (PC-Air & PC-Relate)
Genome Analysis Toolkit – tools for variant discovery and genotyping
Geneious – analysis of DNA sequence data
Geneland – statistical analysis of population structure
Genepop – methods/statistical tests for pop gen analyses
GEOPORTAL-SERNANP – web portal for Peru’s protected areas
Gephi – network visualization software
GERMLINE2 – identifies identical by descent segments in genomic data
GEVA – Genealogical Estimation of Variant Age
gghybrid – R package for analysis of hybrids and hybrid zones
gnomAD – Genome Aggregation Database for exome and genome sequencing
GOLD – graphical analysis of linkage disequilibrium
Gompert Lab Software – population genetics softwares (e.g,. bgc, introgress)
GOSemSim – semantic comparisons of Gene Ontology (GO) annotations
G-PhoCS – coalescent genealogy sampler suitable for genomic data
GPU MrBayes – implements MrBayes MC(3) on the GPU using CUDA
H
HaploBlock – haplotype block analysis and LD mapping
Haplogrep – mtDNA haplogroup classification
Haploview – haplotype block analysis and LD mapping
Hey Lab Software – population genetics softwares for coalescent analysis (e.g., IM, IMa2, HKA)
hierfstat – hierarchical F-statistics
HKA – Hudson, Kreitman, Aguade (HKA) test for natural selection
HmmCleaner – multiple sequence alignment filtering
Hudson Lab Software – population genetics softwares (e.g., ms)
Hybpiper – extracts target sequences from high-throughput DNA sequence capture reads
HybridCheck – for graphical analysis of recombination, introgression, and hybridization, including ABBA-BABA tests and the dating of recombination and introgression events
HyPhy – infers strength of selection from phylogenetic sequence data
HZAR – hybrid zone analysis using R
I
IBD Web Service – genetic Isolation By geographic Distance
IBS – Illustrator for Biological Sequences
iLASH – ultra-rapid detection of IBD tracts
IM/IMa/IMa2/IMa3 – coalsecent genealogy samplers with population divergence
ImageJ – image acquisition, analysis and processing software
IMgc – generates recombination-filtered DNA sequence data
INCA – analysis of codon usage bias
IQ-TREE – fast maximum likelihood algorithm for inferring phylogenetic trees
iSAFE – statistical method for pinpointing location of favored mutation in a large genomic region ~5 Mbp
L
LAMARC – coalescent genealogy sampler with recombination and population growth
Lat/Long GPS distance – measures distance between geographic points etc.
LDhat – analysis of recombination rates
LINTRE – tests for molecular clock and makes linearized trees
LocusZoom – tool for visualization of GWAS results
LOSITAN – selection detection using FST outliers
MAFFT – multiple sequence alignment
MaSuRCA – whole genome assembly
MEGA – large set of methods/statistical tests for pop gen analyses
Merlin – linkage analysis tool for pedigree analysis
Mesquite – phylogentics, population genetic, and multivariate analysis
MGLTools – 3D molecular visualization/analysis
MIGRATE – coalescent genealogy sampler to infer population genetic parameters
Mimicree2 – genome-wide forward simulations for evolve & resequencing studies
MITObim – for assembly of mitochondrial genomes from NGS reads
mlRho – estimates theta and recombination rate from single diploid genome
ModelTeller – machine learning algorithm for phylogenetic model selection
MOE – molecular visualization, modeling, and simulation
MP-EST – maximum pseudo-likelihood estimation of species trees
MrBayes – Bayesian inference of phylogeny
ms – generates simulated genealogies under Wright-Fisher model
msBayes – hierarchical Approximate Bayesian Computation (hABC) for phylogeography
msms – coalescent simulation with selection
MYcroarray (Arbor Biosciences) – customized NGS target enrichment
N
NeEstimator – estimates effective population size (Ne)
Network – drawing unrooted networks (similar to PopART)
NewHybrids – identification of hybrids
O
OligoCalc – oligonucleotide properties calculator
OrthoFinder – comparative genomics tool for finding orthogroups, rooted gene trees and species trees, and gene duplication events
P
PAML – Phylogenetic Analysis by Maximum Likelihood
ParallelStructure – R package to distribute parallel runs of STRUCTURE
PAUP* 4.0 – legendary software Phlogenetic Analysis Using PAUP
PCOC – tool for detecting convergent substitution
pegas – Population and Evolutionary Genetics Analysis System
PGDSpider – data conversion tool
PHASE – haplotype reconstruction and recombination rate estimation
PHAST – Phylogenetic Analysis with Space/Time models
phrapl – similar to Approximate Bayesian Computation (ABC) for phylogeography
Phylogenomics Lab Software – phylogenomics softwares (e.g., ModelTest, TCS)
phyloP – measures evolutionary conservation at individual alignment sites
phyluce – pipeline for UCEs
PhyML – phylogenetic analysis using maximum likelihood for large data sets
PhyParts – for examining clade support for trees including duplications and incomplete taxon sampling
PLINK – whole genome association analysis toolset
PLINK/SEQ – toolset for working with human genetic data
PopART – unrooted networks (similar to Network)
Popgenome – population genetics statistics for genomic data sets
Popgen Pipeline Platform – workflow platform for population genomic analyses
Pophelper – R package/web app to visualize population structure
PopLDdecay – linkage disequilibrium decay analysis for variant call format files
Poppr – R package similar to adegenet for analysis of populations with mixed modes of clonal and sexual reproduction
PRINSEQ @ SourceForge.net – filtering, reformatting, or trimming genomic data
Pritchard Lab Software – population genetics and other softwares (e.g., STRUCTURE)
PROVEAN – Protein Variation Effect Analyzer
PSMC – infers population size history from whole-genome diploid consensus sequence
PyMOL – 3D molecular visualization/analysis
PyPop – python for population genomics
Q
qqman – Manhattan plots for GWAS data
R
Rambaut Lab Software – phylogenetics softwares (e.g., BEAST, Tracer, FigTree)
Rarefaction Calculator – used for calculating allelic richness standardized to sample size
RAxML – Randomized Axelerated Maximum Likelihood
RAxML BlackBox – RAxML web-server
REDItools – python scripts for detecting RNA editing using RNA-seq
Relatedness – calculates relatedness
RevBayes – interactive computational environment for phylogenetics
RFMix – models ancestry along an admixed chromosome
RNA-Seq De novo Assembly Using Trinity – de novo assembly of RNA-Seq data
rna-star – ultrafast RNA-seq aligner
S
Salmon – quantification of RNA-Seq transcripts
SAMtools – Sequence Alignment/Map Tools
SeqKit – toolkit for FASTA/Q file manipulation
SHAPEIT – fast phasing of whole chromosome scale datasets
SNAPP – infers species trees and demographics from SNPs
SNaQ – species networks applying quartets
SOAPdenovo – short-read genome assembly
SPAGeDi – spatial genetic structure of mapped individuals/populations
SplitsTree4 – network oriented tool for quantifying tree uncertainty
SnpEff – variant annotation and functional effect prediction
Stacks – RAD-Seq pipeline
Stairway plot – infers demographic history using site frequency spectrum (SFS)
StatAlign – joint Bayesian estimation of alignments and evolutionary trees
STRING – functional enrichment analysis for protein-protein interaction networks
Stephens Lab Software – population genetics and other softwares (e.g., PHASE, HOTSPOTTER)
STRUCTURE – individual assignment to populations to infer populations structure
Structure Harvester – processes STRUCTURE results
SVDquartets – quartet inference from SNP data under the coalescent
SweeD – composite likelihood ratio test for detecting selective sweeps
SweepFinder – locates selective sweeps using SNP data
SWISS-MODEL Workspace – 3D molecular visualization/analysis
T
TASSEL – traits associations, evolutionary patterns, and linkage disequilibrium
TCS – reconstruction of networks using statistical parsimony
TempNet – temporal networks from heterochronus data
Tomahawk – fast calculation of LD for large cohorts
topGO – enrichment analysis tools for gene ontology
Treemmer – python tool to reduce size and redundancy of phylogenetic datasets
TreeMix – infers population splits with admixture for many SNPs
treePL – calculates divergence time using penalized likelihood
TreeRot – calculates decay indices
T-Rex – tool for reconstructing/visualizing trees and reticulation networks
U
Ultraconserved Elements (UCEs) – website devoted to Ultra Conserved Elements
USEARCH – ultrafast search and clustering algorithms
V
VCFtools – package for manipulating VCF files and pop gen analyses
VCF2Arlequin – python tool to convert vcf files to Arlequin format
vcf2dadiSNPs – R tool to convert a vcf file to dadi format
VolcanoFinder – genomic scan for adaptive introgression using a likelihood-ratio test
W
WebGestalt – web tool for gene ontology (GO) functional enrichment analysis
Published Lists of Pop Gen Softwares