SoftLinks
Maintained by Sergios-Orestis Kolokotronis. Email me if you think a program should be listed here.
© 2007-2020 Sergios-Orestis Kolokotronis.
Genomes | Alignment | Microsatellites | Molecular Evolution | Phylogeny | Population Genetics
Genomes
BLAST eukaryotic genomes @ NCBI
BLAST protozoan genomes @ NCBI
Alignment
OS: all
Webserver: No
Implements a joint Bayesian estimation of alignment and phylogeny. Instead of inferring trees based on a single fixed alignment, it considers near-optimal alignments when estimating the phylogeny. In addition, it can produce alignments colored to indicate uncertain areas of the alignment. Command-line interface.
OS: *nix
A probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Uses machine-learning techniques to estimate gap and substitution parameters on the fly. Can align 100s-1000s sequences using a randomized inference algorithm to reduce the computational cost of MSA, as well as very long sequences using the "anchor annealing" technique.
OS: *nix
Webserver: No
Uses the Marginalized Posterior Decoding algorithm which uses the posterior distribution of alignments to optimize the correct assignment of homology of individual nucleotides, instead of finding a single most probable alignment. Simulations show that the MPD algorithm has higher sensitivity and specificity than the Viterbi and Needleman-Wunsch algorithms.
OS: all
Webserver: No
Alignment viewer. Connects to a webserver to align with T-Coffee or MUSCLE. Visualizes alignment in PCA.
OS: all
Local & global alignments. To run it locally you must download the source code and compile it. It
uses anchoring schemes and VISTA visualization.
OS: all
Constrained ancestral alignment of multiple sequences. It is able to effectively align divergent sequences, as well as incomplete unfinished sequences.
OS: all
Webserver: No
Simultaneously estimates phylogeny and alignments via Direct Optimization. New version is faster.
OS: all
Webserver: No
Uses HMMs for probabilistic multiple alignment of nucleotide and amino-acid sequences by a stepwise progressive method.
OS: all
Multiple sequence alignment using partition function posterior probabilities. Both AA and DNA/RNA.
OS: all
Webserver: No
For Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.
OS: all
Webserver: No
An advanced alignment tool bringing together algorithmic alignment of molecular sequences, with human editing. Parts of the sequences can be realigned. Squint can align a nucleotide sequence by amino acid or codon.
OS: all
More accurate than ClustalW for sequences with less than 30% identity, but slower.
Microsatellites
Descriptive statistics, distances, miscellaneous
OS: all
Rarefaction for allelic richness, private allelic richness, and private allelic richness for combinations of populations.
OS: Windows
Estimates null allele frequencies via a EM algorithm and Fst when null alleles are present via the C2 method.
OS: all
Excel add-in for a variety of analyses (diversity stats, AMOVA, Mantel correlation, PCA, assignment, spatial autocorrelation).
OS: Windows
Analyzes genotypic data, tests for clonality, and describes spatial clonal organization.
OS: Windows
A very good program for all kinds of descriptive statistics and FCA. Uses a spreasdsheet entry format and exports in various input formats.
OS: Mac
All kinds of analyses, including AMOVA, PCA, k-means clustering, likelihood G-statistic for population differentation, diversity, clone assignment, HWE test, distances, Mantel correlation. Great for data manipulation and input file conversion.
OS: R
Hierarchical F-statistics in >2 levels using the method of moments. Also tests for population differentation using the likelihood G-statistic.
OS: all
Converts the output of Hudson's ms program into microsatellite data. The output could be directly analyzed by MSA.
compiled by David McDonald
OS: *nix
A Mathematica package for the analysis of deterministic multilocus population genetic models.
OS: R
Standardizes sample size before comparing allelic richness estimates. Plots allele distribution/frequency across populations/locus, and the relationship between allelic richness and genet/individual number in a population.
Population Assignment, Gene Flow, Landscape Genetics, Hybrid Zones
OS: all
Bayesian assignment of individuals to populations, admixture, and spatial genetics. DNA sequences also accepted as input. Fast!
OS: all
Bayesian method that makes inferences about recent proportions of immigrant genes in subdivided populations and that identifies the environmental factors that are responsible for observed gene flow patterns.
OS: Windows
Determines the composition of the newly colonised population and makes inferences about the factors that influenced individuals to establish a new population. Uses a hierarchical Bayesian model to combine multilocus genotype data with demographic and environmental data, and rjMCMC to get posterior densities.
OS: Windows
ML implementation of the classical STRUCTURE model without admixture and uncorrelated allele frequencies relying on expectation-maximization.
OS: all
Excel add-in for a variety of analyses (diversity stats, AMOVA, Mantel correlation, PCA, assignment).
OS: Windows
Infers spatial genetic structure by analyzing genotypes and geographic coordinates simultaneously through a 2D graphical representation.
OS: R
Bayesian assignment of individuals to populations using GPS coordinates; estimates the spatial organization on populations.
OS: Windows
A Bayesian method to evaluate the effect that biotic and abiotic environmental factors (geographic distance, language, temperature, altitude, local population sizes, etc.) have on the genetic structure of populations. Good for population processes, such as range expansions, by simply introducing longitude and latitude as the explanatory variables. Estimates Fst values for each local population and relates them to environmental factors using a GLM.
OS: Windows
ML estimates of Ne and migration rate from the observed temporal and spatial differences in marker allele frequencies.
OS: all
Detects the presence of subfamilies in batches of offspring. Written in Mathematica and R.
OS: Windows & OS9
Uses a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.
OS: Windows
Identifies population sub-division (barriers to gene flow) and assigns individuals to populations using a Bayesian method.
OS: Windows
Searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to populations of origin using a ML criterion.
OS: Windows
Designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.
OS: all
Bayesian assignment of individuals to populations allowing for the number of populations to vary following a Dirichlet prior.
OS: Windows & Linux
Bayesian clustering based on a hierarchical mixture model where cluster priors are defined as HMRF. Takes into account geographical coordinates. Compared to BAPS and STRUCTURE on its website.
OS: R
Analyzes individually georeferenced multilocus genotypes for the inference of genetic boundaries among populations.
Relatedness, Parentage
OS: Windows
Parentage analysis using allele frequencies and simulations in a ML framework.
OS: Windows
Implements a ML method that assigns individuals in a sample into full-sib families nested within half-sib families (colonies).
OS: all
Uses likelihood calculation and simulations to perform paternity and parentage studies with codominant, dominant, cytoplasmic markers or combinations of different marker types.
OS: Windows
Calculates the informativeness of markers in inferring pairwise relatedness or relationships.
OS: Windows
Looks for maternity, paternity, or simultaneously for both potential parents, using multilocus genotypes and birth and death dates of individuals (if available). Also calculates the probability of successfully allocating an individual offspring to its parents.
Selection
OS: Windows
Detects loci that might be under selection in samples from structured populations.
Population size [changes], Ne estimation
OS: Windows
Implements the method of Cornuet & Luikart (1996 Genetics) for detection of reduction in Ne using allele frequency data.
OS: Windows
Estimates population census size using various rarefaction methods. Outputs R scripts for plotting.
OS: Windows
Performs a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems.
OS: Mac
Estimates M, the ratio of the number of alleles to range in allele size, for a sample of microsatellite loci can be used to detect reductions in Ne.
Genome Scanning and Detection
OS: all
Webserver for the identification and extraction of SSRs from genomic libraries and primer design.
Webserver for STR detection and primer design.
Molecular Evolution
Information
OS: Windows
Webserver: No
All-time classic! Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
Information
OS: All
Webserver: No
A program package implementing a variety of sophisticated models of nucleotide and protein sequence evolution via ML. Allows to test alternative hypotheses using likelihood ratio tests. Not recommended for tree-building.
Information
OS: All
Webserver: No
A program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. It is not intended as a method of constructing phylogenies but rather testing evolutionary hypotheses without conditioning on a single tree topology. It uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
Information
OS: All
Webserver: Yes
Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language.
Information
OS: All
Webserver: No
Provides ML estimates of substitution model parameters of a phylogenetic tree and an alignment of homologous sequences. A broad range of Markov models of nucleotide and aminoacid substitutions are implemented. Coding sequences can also be analyzed under various codon-based substitution models. These models are especially useful as they accommodate site-specific switches between selection regimes.
Information
OS: All
Webserver: Yes
Server for the identification of site-specific positive selection and purifying selection.
Information
OS: *nix
Webserver: No
Simulates the evolution of nucleotide and aminoacid sequences along a phylogeny using a range of substitution models.
Information
OS: All
Webserver: Yes
Estimates the best-fitting model of DNA substitution among 56 models in conjunction with PAUP*. Uses AIC and also calculates model-averaged estimates and parameter importance. The FindModel webserver uses Weighbor, NJ, or MrBayes to generate the JC69 tree (does not allow for invariant sites). Also implemented in HyPhy.
Information
OS: All
Webserver: No
Carries out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies.
Information
OS: All
Webserver: No
Estimates the best-fitting model of DNA substitution among 56/24 models in conjunction with PHYML. It differs with Modeltest in that it does not evaluate all models on the same topology, but rather uses PHYML to maximize the likelihood function for each model, which is needed for calculating AIC/AICc/AICw/BIC.
Information
OS: All
Webserver: No
Estimates the best-fitting model of DNA substitution among 24 models that can be implemented in MrBayes in conjunction with PAUP*.
Information
OS: All
Webserver: Yes
Estimates the empirical model of aminoacid substitution fitting the data best among 64 models. Uses a BioNJ or user-defined starting tree. Can optimize parameters and the topology. Interacts with PHYML.
Information
OS: All
Webserver: Yes
Selects the best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. Interacts with PHYML.
Information
OS: *nix
Webserver: Yes
ML estimation of evolutionary rates using heterochronous dated sequences. Also implemented in HyPhy by allowing for clock relaxation.
Information
OS: OSX
Webserver: No
Evaluates the fit of a group of phylogenetic models to DNA sequence data. The model's predictive ability is evaluated through simulation under the model. Comparison of simulated (or predictive data sets) is evaluated using the multinomial test statistic.
Information
OS: All
Webserver: Yes
Evaluates the fit of a group of phylogenetic models to DNA sequence data. The model's predictive ability is evaluated through simulation under the model. Comparison of simulated (or predictive datasets) is evaluated using the multinomial test statistic.
Information
OS: Windows
Webserver: No
Estimates the number of synonymous and nonsynonymous substitutions per site and their confidence intervals by Monte Carlo simulations.
Information
OS: Windows and source
Webserver: No
Carries out the HKA statistical test for natural selection and can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulations, as well as by the conventional chi-square approximation. The simulations can also be used to conduct other tests of natural selection, including Tajima's D (1989) and Fu and Li's D (1993).
Information
OS: All
Webserver: Yes
Performs various tests of neutrality.
Information
OS: Linux and Windows
Webserver: No
RNA-based phylogenetic methods.
Information
OS: All
Webserver: No
Simulates coding DNA sequence evolution. Accounts for selective pressure and indels.
Information
OS: All
Webserver: No
A tool to detect functional lineage-specific genes by evolutionary simulations.
Information
OS: All
Webserver: Yes
Extracts and plots information (diversity, dn/ds, hydrophobicity, etc) from an alignment (nuc/aa).
Information
OS: All
Webserver: Yes
Generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.
Phylogeny
Information
OS: All
Webserver: No
All-time classic! GUI is available for OS9 and Windows.
Information
OS: Windows
Webserver: No
Distance and parsimony. Various statistical tests of selection. Great alignment editor with NCBI BLAST capacity.
Information
OS: All
Webserver: Yes
Genetic Algorithm for Rapid Likelihood Inference. Very fast!
Information
OS: All
Webserver: BlackBox & CIPRES
Randomized Axelerated Maximum Likelihood for High Performance Computing. For large matrices, etc. Outputs sitewise likelihoods in Tree-Puzzle format for use in CONSEL. Starts ML optimization from random or MP trees. Does ELW. Accepts multiple outgroups. Spectacular user support, awesome and very fast!
Information
OS: All
Webserver: Yes
Fast for large phylogenies. Has customized versions for download on its website.
Information
OS: All
Webserver: No
Phylogenetic inference using ML. A variety of special analysis tools including a test for compositional equilibrium, plotting of rate profiles along sequence alignments, and NPRS tree calibration. It is programmable in the functional and system-independent programming language, TL.
Information
OS: All
Webserver: No
ML phylogenetic inference using quartet puzzling tree search. Does nucleotide, protein, and binary data.
Information
OS: All
Pasteur and EBC
All-time classic! Distance, parsimony, and likelihood.
Information
OS: OSX
Webserver: No
ML (GTR) and ME with general additive distances, very large-scale neighborhood, iterated local search, and ant colony optimization.
Information
OS: All
Webserver: Yes
Bayesian inference of phylogeny accomodating multiple partitions (DNA, protein, morphology/binary). If an outgroup is not defined a priori, it assumes the first taxon is the outgroup.
Information
UNIX and Windows
Webserver: Yes
Bayesian analysis of phylogenies.
Information
OS: All
Webserver: No
Bayesian analysis of phylogenies. Allows for a mixture model without partitioning and for multiple outgroups.
Information
OS: *nix
Webserver: No
Bayesian MCMC phylogenetic reconstruction for protein sequences using the CAT mixture model.
Information
OS: All
Webserver: No
Bayesian MCMC phylogenetic reconstruction for DNA sequences written in Python.
Information
OS: All
Webserver: Yes
Phylogenetic reconstruction using parsimony with a simulated annealing heuristic search. For moderately large data matrices.
Information
OS: All
Webserver: No
Phylogenetic reconstruction using parsimony. The fastest MP program so far!
Information
OS: All
Webserver: No
Phylogenetic reconstruction using parsimony and ML (POYML). It uses Direct Optimization.
Information
OS: All
Webserver: No
PAUP implementation of the parsimony ratchet. See also a program for likelihood ratchet.
Information
OS: All
Webserver: Yes
Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language.
Information
OS: Linux and Windows
Webserver: No
RNA-oriented phylogenetic methods.
Information
OS: *nix
Webserver: No
ML phylogeny under protein covarion models.
Information
OS: Windows
Webserver: No
For median-joining networks; estimates TMRCA.
Information
OS: All
Webserver: No
Estimates median networks, parsimony splits, spectral analysis, split decomposition, neighbor-net, recombination networks, hybridization networks, standard tree reconstruction methods and the (refined) Buneman tree.
Information
OS: Windows
Webserver: No
Estimates phylogenetic networks from DNA sequences or nucleotide distances using the statistical parsimony algorithm.
Information
OS: All
Webserver: No
Combines MP trees into a single (possibly reticulated) graph.
Information
OS: All
Webserver: No
Phylogenetic analysis in R. Trees and networks, distance, Hadamard conjugation, ML, MP.
Information
OS: All
Webserver: No
Reconstructs of reticulate relationships. Infers horizontal gene transfer from a pair of species/gene trees and detects interspecific recombination breakpoints. Reads/stores/compares networks.
Information
OS: All
Webserver: No
For Bayesian estimation of TMRCA (among other things) in a strict or relaxed clock framework and evolutionary rates.
Information
OS: *nix
Webserver: No
Estimates absolute rates of molecular evolution and divergence times on a phylogenetic tree.
Information
OS: *nix
Webserver: No
Studies rates of molecular evolution and estimates divergence times.
Information
OS: All
Webserver: No
Phylogenetic dating of large trees without a molecular clock.
Information
OS: All
Webserver: Yes
Detects significant punctuated molecular evolution from phylogenetic trees. Where the punctuational effect is present the program will report the proportion of evolution attributable to speciation events (nodes). It also reports the deviation from the molecular clock caused by punctuational effects.
Information
R
Webserver: No
Reads/writes/plots/manipulates trees; comparative data analyses in a phylogenetic framework; diversification rates and macroevolution; distances from allelic and nucleotide data; Mantel's test; minimum spanning tree; population parameter theta; nucleotide diversity; generalized skyline plot; estimation of absolute evolutionary rates and clock-like trees using NPRS and PL; classifies genes in trees using the Klastorin-Misawa-Tajima approach. NJ/ML phylogenies.
Information
OS: All
Webserver: No
Implements several tests of differential diversification rates that exploit information on the topological distribution of species diversity throughout entire trees.
Information
OS: R
Webserver: No
Implements ML methods based on the birth-death process to test whether diversification rates have changed over time.
Information
OS: All
Webserver: No
Analyzes rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using LRT/AIC.
Information
OS: All
Webserver: No
Highly optimized/parallel versions of ParaFit and DistPCoA.
Information
OS: All
Webserver: No
Tests cophylogenetic associations, wrapper for ParaFit.
Information
OS: *nix
Webserver: No
Gene/species tree reconciliation and gene tree parsimony.
Information
OS: All
Webserver: No
Provides a unified framework for incorporating duplication/loss parsimony in phylogenetic tasks. Gene/species trees reconciliation; gene duplication times in terms of speciation events; rearrange regions of a gene tree with weak support in the data to obtain alternate hypotheses
Information
OS: Windows & OS9
Webserver: No
Tests cophylogenetic associations.
Information
OS: Linux
Webserver: Yes
Visualizes tree-within-tree phenomena such as gene/species tree reconciliations.
Information
OS: All
Webserver: No
Maps gene trees onto species trees based on the soft parsimony method.
Information
OS: All
Webserver: No
Fits genetrees into species trees as well as combines trees in coevolutionary and biogeographic studies within an event-based parsimony context.
Information
OS: All
Webserver: No
Parsimony-based cophylogeny mapping of host and parasite trees.
Information
OS: All
Webserver: No
Mesquite module to plot the geographic location of taxa onto a calibrated map.
Information
OS: All
Webserver: No
ARCGIS extension for creating 'geophylogenies.'
Information
OS: All
Webserver: No
Test phylogeographic hypotheses (maps & genetic distances).
Information
OS: All
Webserver: No
Assesses the confidence of phylogenetic tree selection. Approximately Unbiased, SH, weighted SH, KH test and their CIs.
Information
OS: All
Webserver: No
For trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. Discrete and continuous characters.
Information
OS: All
Webserver: No
Uses BayesTraits to predict functional links among genes, on the basis of correlated gain and loss of genes from species' genomes.
Information
OS: OSX
Webserver: No
A post-tree analysis program for making inferences based on sampling character histories from the posterior distribution of character histories on a phylogeny(ies).
Information
OS: All
Webserver: No
Tests for significant phylogeny-trait correlations taking into account uncertainty arising from phylogenetic error by integrating over the credible set of topologies produced by a bayesian estimation method such as BEAST or MrBayes.
OS: All
Webserver: Maybe
See Joe Felsenstein's website
Population Genetics
Information
OS: All
Webserver: 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.
Information
OS: Windows
Webserver: No
All-time classic! Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: 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.
Information
OS: Windows and *nix
Webserver: 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.
Information
OS: Windows
Webserver: 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.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: No
A program for the analysis of recombination rates from population genetic data.
Information
OS: *nix
Webserver: No
ML-based method for detecting conflicting phylogenetic signal in nucleotide sequence alignments. Detects recombination in divergent sequences.
Information
OS: All
Webserver: 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.
Information
OS: Windows
Webserver: No
ML estimates of admixture proportions and genetic drift using the coalescent.
Information
OS: *nix
Webserver: 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.
Information
OS: Windows
Webserver: 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.
Information
OS: *nix
Webserver: 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.
Information
OS: Windows
Webserver: 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.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: 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.
Simulations
Information
OS: All
Webserver: No
All-time classic engine for coalescent sequence simulations under a Wright-Fisher neutral model.
Information
OS: All
Webserver: No
Modified ms to account for crossover and gene conversion hotspots.
Information
OS: All
Webserver: No
Simulates coalescent events, recombination, migration, demographic fluctuations. DNA, SNPs, microsatellites, RFLP.
Information
OS: All
Webserver: No
Simulates coalescent events under migration and demographic fluctuations applied to ancient DNA data.
Information
OS: Windows
Webserver: No
Incorporates the influence of the environment in the simulation of migration of a given species from one origin.
Information
OS: Windows
Webserver: No
Simulate genetic diversity based on a realistic vectorized environment.
Information
OS: All
Webserver: No
Simulates coding sequences given a substitution model and selection intensity along a phylogeny. Accomodates indels, too.
Information
OS: All
Webserver: No
Simulates sequences given a GTR substitution model and indel evolution.
Information
OS: All
Webserver: No
Simulates sequences given a substitution model along a phylogeny.
Information
OS: *nix
Webserver: No
Simulates protein sequences given a substitution model along a phylogeny incorporating info on domains, motifs and indels.
Information
OS: *nix
Webserver: No
Simulates sequences given a substitution model along a phylogeny incorporating indels.
Information
OS: All
Webserver: 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.
Information
OS: All
Webserver: No
One-locus Population genetics simulation program for teaching.