|• 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
• 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.
(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
• 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.
(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.
• 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.
• 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
• 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.
• 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
• PAUP* (David Swofford): if you are not familiar
with PAUP*, you are not a molecular phylogeneticist.
(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
• 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.
• 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
• 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