| Software |
OS |
Webserver |
Comments |
| BEAST |
all |
No |
A program for Bayesian MCMC analysis of molecular sequences. Orientated towards
molecular clock analyses. Not for constructing phylogenies but rather testing
evolutionary hypotheses without preconditioning on a single tree topology. Uses MCMC
to average over tree space, so that each tree is weighted proportionally to its
posterior probability. Implements a Bayesian generalized skyline plot. |
| DnaSP |
Windows |
No |
All-time classic! Performs a multitude of tests and analyses, including coalescent simulations.
Populations can be mouse-defined. |
| Arlequin |
all |
No |
Descriptive statistics, neutrality tests, mismatch distribution, AMOVA, Fst,
Minimum Spanning Trees, assignment test, (partial) Mantel test, gametic phase estimation;
handles sequence, RFLP, and microsatellite data. Latest version (3.x) runs only on Windows. |
| DMLE+ |
all |
No |
Allows multipoint LD mapping using an arbitrary number of SNPs or microsatellite markers.
Implements MCMC methods for Bayesian estimation of the posterior probability density of the
position of a disease mutation relative to a set of markers. |
| HabloBlock |
all |
No |
For haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution
or reconstruction) and LD mapping (or genetic association studies). For high-density
haplotype or genotype SNP data and is based on a statistical model accounting for
recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain in its core. |
| IM/IMa |
Windows & *nix |
Yes/Yes |
Fits an isolation model with migration to haplotype data drawn from two closely
related species or populations. Large numbers of loci can be studied simultaneously,
and different mutation models can be used. Uses check-pointing. |
| MDIV |
Windows |
Yes |
MDIV will simultaneously estimate divergence times and migration rates between two
populations under the infinite sites model or under a finite sites model. It assumes a
constant population size. |
| LAMARC |
all |
No |
A package of programs for computing population parameters, such as population size,
population growth rate and migration rates by using likelihoods for samples of data
(sequences, microsatellites, and electrophoretic polymorphisms) from populations. It
approximates the summation of likelihood over all possible gene genealogies that could
explain the observed sample. |
| LARD |
all |
No |
This is a program to detect the presence of recombination in a set of sequences by
looking at the set of sequences to discover which are the most plausible parents of a
potentially recombinant sequence, and performing a likelihood ratio test for each
possible breakpoint position of whether the three-species tree differs on the two sides
of the breakpoint. |
| LDhat |
all |
No |
A program for the analysis of recombination rates from population genetic data. |
| LIKEWIND |
*nix |
No |
ML-based method for detecting conflicting phylogenetic signal in nucleotide
sequence alignments. Detects recombination in divergent sequences. |
| MANVa |
All |
No |
Multilocus Analysis of Nucleotide Variability. Calculates descriptive statistics and
neutrality tests for observed data. Analysis on total/synonymous/nonsynonymous/silent/coding
and any other annotated regions given in GFF files. Coalescent simulations are enabled
and compared with observed results.
|
| ΜEAdmix |
Windows |
No |
ML estimates of admixture proportions and genetic drift using the coalescent. |
| Migrate |
*nix |
Yes |
estimates the effective population sizes and migration rates of n constant populations
using nonrecombining sequences, microsatellite data or enzyme electrophoretic data. It
can run multiple loci in parallel on computer clusters.
|
| MSVAR |
Windows |
Yes |
estimates by MCMC demographic parameters of a single population, such as current and
ancestral effective population size and time since Ne change. Flexible priors.
|
| omegaMap |
*nix |
Yes |
Detects natural selection and recombination in DNA or RNA sequences. Residues under
selection can be mapped and color-coded using
Protein Explorer and
MolScript. Distributed with a collection
of R scripts.
|
| RDP |
Windows |
No |
Recombination Detection Program applies a number of recombination detection and
analysis algorithms. It includes several methods, such as RDP, MaxChi, Chimaera,
Geneconv, Bootscan, and Siscan. |
| RECOMBINE |
all |
No |
This program fits a model which has a single population of constant size with a single
recombination rate across all sites. It can accomodate either plain DNA, RNA, or SNP data. |
| VariScan |
all |
No |
A software package for the analysis of DNA sequence polymorphisms at the whole
genome scale. Among other features, the software: (1) can conduct many population
genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that
allows capturing relevant information from DNA polymorphism data; and (3) it facilitates
the visualization of the results in the most commonly used genome browsers. |
Comprehensive
list of programs for recombination detection. |
| Software |
OS |
Webserver |
Comments |
| ms |
All |
No |
All-time classic engine for coalescent sequence simulations under a Wright-Fisher neutral model.
|
| msHOT |
All |
No |
Modified ms to account for crossover and gene conversion hotspots.
|
| SimCoal2 |
All |
No |
Simulates coalescent events, recombination, migration, demographic fluctuations. DNA, SNPs, microsatellites, RFLP.
|
| SerialSimCoal |
All |
No |
Simulates coalescent events under migration and demographic fluctuations applied to ancient DNA data.
|
| SPLATCHE |
Windows |
No |
Incorporates the influence of the environment in the simulation of migration of a given species from one origin.
|
| AquaSPLATCHE |
Windows |
No |
Simulate genetic diversity based on a realistic vectorized environment.
|
| EvolveAGene |
All |
No |
Simulates coding sequences given a substitution model and selection intensity along a phylogeny. Accomodates indels, too.
|
| Dawg |
All |
No |
Simulates sequences given a GTR substitution model and indel evolution.
|
| Seq-Gen |
All |
No |
Simulates sequences given a substitution model along a phylogeny.
|
| Indel-Seq-Gen |
*nix |
No |
Simulates protein sequences given a substitution model along a phylogeny incorporating info on domains, motifs and indels.
|
| Rose |
*nix |
No |
Simulates sequences given a substitution model along a phylogeny incorporating indels.
|
| mlcoalsim |
All |
No |
Multilocus analyses. Neutrality tests and other statistics, under several demographic
models and strong positive selection using the theory of the coalescent. Coalescent simulations
accounting for recombination. Simulations conditioned on S and/or Rm values using a
rejection algorithm are enabled.
|
| PopG |
All |
No |
One-locus Population genetics simulation program for teaching. |
Email me if you think a program should be listed here.
