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Software
The software that I've grown to love - and where to find it:
Phase - http://www.stat.washington.edu/stephens/software.html
For reconstructing haplotypes from diplotype data. Can also be used to estimate recombination rates and to identify recombination hotspots. From Matthew Stephens (University of Washington).
BAli-Phy - http://www.biomath.medsch.ucla.edu/~msuchard/bali-phy/index.php
A Bayesian method for simultaneously calculating sequence alignments and phylogenies. From Marc Suchard (UCLA).
PAUP* - http://paup.csit.fsu.edu
For phylogenetic reconstruction, using distance, parsimony, or likelihood criteria From David Swofford (Florida State University).
MrBayes - http://mrbayes.csit.fsu.edu/index.php
For phylogenetic reconstruction using Bayesian criteria. From John Huelsenbeck (UCSD), Bret Larget (University of Wisconsin), Paul van der Mark (Florida State), and Frederik Ronquist (Florida State).
MacClade - http://macclade.org/macclade.html
For phylogenetic analysis, especially in studies of character evolution. Also useful for data and tree manipulation. I often use it to manually align sequence data. From David Maddison (University of Arizona) and Wayne Maddison (University of British Columbia).
Tracer - http://evolve.zoo.ox.ac.uk/software.html?id=tracer
For visualizing parameter estimates through search time. Very useful for estimating when a Bayesian run has reached stationarity. From Andrew Rambaut (Oxford) and Alexei Drummond (University of Auckland).
TreeView - http://darwin.zoology.gla.ac.uk/~rpage/treeviewx
For tree manipulation. Produces publication-quality tree images, by Rod Page (University of Glasgow).
ModelTest - http://darwin.uvigo.es/software/modeltest.html)
Uses likelihood ratio tests to determine which model of evolution best describes your sequence data. Use with PAUP*. From David Posada (U. Vigo) and Keith Crandall (Brigham Young).
r8s - http://ginger.ucdavis.edu/r8s/)
For estimating absolute rates of molecular evolution and divergence times. From Mike Sanderson (UC-Davis).
MCMCcoal - http://abacus.gene.ucl.ac.uk/software/MCMCcoal.html
Uses a coalescent framework to estimate current and ancestral population sizes and divergence times for multiple species, given a fixed phylogeny. From Ziheng Yang (University College London).
mdiv - http://www.binf.ku.dk/users/rasmus/webpage/programs.html#MDIV
Uses a coalescent framework to estimate current population sizes and divergence times for pairs of species. Assumes no recombination and equal population sizes in all populations. Updated as IM. From Rasmus Nielsen (Cornell) and John Wakeley (Harvard).
ms - http://home.uchicago.edu/~rhudson1/source/mksamples.html
A program to generate samples under a variety of neutral models. From Richard Hudson (University of Chicago).
Seq-Gen - http://evolve.zoo.ox.ac.uk/software.html?name=Seq-Gen
Simulates the evolution of sequences along a phylogeny. From Andrew Rambaut (Oxford) and Nick Grassly (Imperial College, London).
Mesquite - http://mesquiteproject.org/mesquite/mesquite.html
For analyzing comparative data about organisms. Emphasis on phylogenetic analysis, but modules also concern population genetics, geographic distributions, multivariate analyses, parametric bootstrapping, coalescence, etc. From David Maddison (University of Arizona) and Wayne Maddison (University of British Columbia).
Beast - http://evolve.zoo.ox.ac.uk/beast/
For Bayesian MCMC analysis of molecular sequences. Not intended for phylogenetic reconstruction, rather for testing evolutionary hypotheses without conditioning on a single tree. From Alexei Drummond (University of Auckland) and Andrew Rambaut (Oxford).
IM - http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM
Fits an isolation with migration model to sequence data from two closely related populations or species. Estimates current and ancestral population sizes, migration rates, and divergence time. From Jody Hey (Rutgers) and Rasmus Nielsen (Cornell).
Lamarc - http://evolution.gs.washington.edu/lamarc/
For estimating population size, population growth rates, migration rates, recombination rates. Encompasses the previously independent programs Fluctuate, Migrate, Coalesce, and Recombine. From Peter Beerli (Florida State University), Mary Kuhner (University of Washington), and Joe Felsenstein (University of Washington).
TCS - http://darwin.uvigo.es/software/tcs.html
Creates networks from sequence data using statistical parsimony. From Mark Clement (Brigham Young), David Posada (Vigo), and Keith Crandall (Brigham Young).
GeoDis - http://darwin.uvigo.es/software/geodis.html
Implementation of the nested clade analysis. From David Posada (Vigo), Keith Crandall (Brigham Young), and Alan Templeton (Washington University of St. Louis).
Arlequin - http://anthro.unige.ch/arlequin/
For population genetic analyses, including AMOVA, Mantel test, neutrality tests, mismatch distribution, etc. From Stefan Schneider (Deram S.A.), David Roessli (U. Geneva), and Laurent Excoffier (U. Berne).
DnaSP - http://www.ub.es/dnasp/
For population genetic analyses, including neutrality tests, mismatch distribution, coalescent simulations, linkage disequilibrium, gene flow, etc. From Julio Rozas, J.C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas (U. Barcelona).
SNAP workbench - http://www.cals.ncsu.edu/plantpath/people/faculty/carbone/snap.html
A single interface for multiple population genetic programs. Includes clustalW, PHYLIP, genetree, seq2tr, treepic, mdiv, Migrate, RecPars, recom58, RecMin, gnuplot, TreeView, among others. From Eric Price and Ignazio Carbone (North Carolina State University).
GenePop - http://wbiomed.curtin.edu.au/genepop/
An online interface for population genetic analyses using microsatellite data. From Michel Raymond and Francois Rousset (U. Montpelier).
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