JWB - Links

•Arlequin3 (Laurent Excoffier, Guillaume Laval, and Stefan Schneider): an exploratory population genetics software environment with a Java graphical interface that can be implemented either at the intra-population or at the inter-population level. Windows only.
•BayesAss (Greg Wilson and Bruce Rannala): Bayesian estimation of recent migration rates. Similar to Structure, except doesn't assume Hardy-Weinberg, and so is useful in assigning recent (2-3 generations) migrants. Multiple platforms.
•BEAST (Alexei Drummond and Andrew Rambaut): Simultaneous Bayesian estimation of phylogeny and divergence time. Does not require the assumption of autocorrelated rates of substitution across a tree, and allows for arbitrarily complex partitioning strategies. Multiple platforms.
•BioEdit (Tom Hall): a biological sequence alignment editor involving several sequence manipulation and analysis options and fully-automated links to local and WWW-based anaylsis programs. The best alignment editor I have seen. Unfortunately only available for Windows machines, and development has been discontinued.
•Bio-Perl (various): an extremely powerful Perl 5 module used for bioinformatics. Available on any platform Perl can be installed.
•Bio-Phylo (Rutger Vos): Similar to Bio-Perl in structure and ease-of-use, but geared towards analyzing and manipulating phylogenetic trees. Available on any platform Perl can be installed.
•Bottleneck (Sylvain Piry, Jean-Marie Cornuet, and Gordon Luikart): a coalescent-based method for the detection of genetic bottleneck signatures. Tests for a transient elevated level of heterozygosity relative to what is expected under mutation-drift equilibrium. Requires only a single sample from a population. Informative for 2-4Ne generations. Available in french or english for PC.
•BottleSim (Chih-Horng Kuo): a very user-friendly application for the simulation of realistic bottleneck scenarios. In addition to specifying the magnitude and duration of bottleneck, allows input of many important parameters (life span, age of reproduction, generation overlap, mating system, sex ratio). Mac or PC.
•Convert (Jeff Glaubitz): the best format conversion program out there for diploid data. Outputs files for GDA, Genepop, Arlequin, Popgene, Microsat, Phylip, and Structure. PC only.
•GARLI (Derrick Zwickl):a genetic algorithm approach to maximum likelihood inference of phylogeny. Superior to rival MetaPIGA in terms of likelihood calculation and complexity of the models supported (GTR+I+G by default). The current incarnation supports only a single population of trees. Very fast. Can run in parallel.
•GeneClass (J.-M. Cornuet, D. Paetkau, L. Baudouin, A. Estoup, S. Piry, and A. Alapetite): in my eyes, the best assignment package out there for analyses with pre-defined populations (although this 'pre-definition' should reflect data, and not the assumptions of the investigator). Offers several different assignment methods (genetic distance, allele frequencies, Bayesian criteria), nice interface, and speedy analyses. PC or Linux platforms.
•HyPhy (S. L. Kosakovsky Pond and S. V. Muse): an enormously powerful ML package that allows the testing of myriad evolutionary hypotheses, and to this end includes tools for data simulation. Supports partitioned models of evolution. Multiple platforms supported.
•HP-RARE (Stephen Kalinowski): uses rarefaction to accomodate differences in sample sizes when estimating indices of diversity and private alleles. Allows hierarchical sampling. PC only.
•LAMARC (various): a coalescent-based package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of genetic data from populations. Includes the programs Migrate, Fluctuate, Recombine, Lamarc and Coalesce.
•MacClade (David Maddison and Wayne Maddison): a computer program that provides tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. MacClade reconstructs and displays character evolution on the phylogenetic tree and gives feedback via tree graphics, statistics, and charts. Also very useful in constructing PAUP blocks for use in PAUP*.
•MEGA4 (Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei): a program for phylogenetic reconstruction and tests of molecular evolution. Though lacking the likelihood analyses of PAUP*, it works quite well for distance, minimum evolution and parsimony analyses. Multiple platforms supported.
•Mesquite (Wayne Maddison and David Maddison): across-platform modular system for evolutionary analysis. I have not found the time to explore this fully, but it looks very promising.
•Modeltest (David Posada): used in conjunction with with PAUP*, Modeltest helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion.
•MrBayes3 (Fredrik Ronquist and John Huelsenbeck): the program for Bayesian inference of phylogeny. This represents the standard of phylogenetic analysis, particulary because of speed (via MCMCMC) and ease of interpretation. Multiple platforms supported.
•Multidivtime (Jeff Thorne): a Bayesian modelling of among-lineage rate variation for the purpose of phylogenetic dating. Assumes an autocorrelation of substitution rates from ancestor to descendent branches (although this autocorrelation can break down with long branch lengths. Supports multiple genes and multiple temporal constraints. Unix.
•PAML (Ziheng Yang): a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Of importance is it allows the ML analysis of amino acid sequences, which PAUP* does not currently do.
•PAUP* (David Swofford): if you are not familiar with PAUP*, you are not a molecular phylogeneticist.
•PHYCAS (Paul Lewis, Mark Holder, and David Swofford): a soon-to-be released open-source phylogenetic analysis package.
•PHYLIP (Joseph Felsenstein): a free package of programs for inferring phylogenies. Again, if you are not familiar with PHYLIP, you are not a molecular phylogeneticist.
•Phylogeny Programs: an amazing list of phylogeny packages cross-referenced by method, computer system, data type, etc. Compiled and maintained by Joseph Felsenstein.
•r8s (Michael Sanderson): a penalized likelihood rate-smoothing approach to phylogenetic dating in the face of rate heterogeneity. Single gene only, but multiple temporal calibrations. Offers sequence or fossil-based cross validation. Allows analysis of bootstrapped trees for the estimation of 95% confidence intervals on inferred dates. Unix.
•RAxML (Alexandros Stamatakis): a very fast maximum likelihood phylogeny reconstruction program, written explicitly for the analysis of large (several thousand taxon) data sets. Very nice options are partitioned substitution models, parallel implemention, and the use of constraint trees.
•Structure (Jonathan Pritchard): a Bayesian assignment software package. Identifies distinct populations and probable migrant history of all individuals. Most importantly, Structure does not require a priori definition of populations (in my eyes, the biggest problem in population genetics today).