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Software

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).

More useful and interesting stuff:

  • How to test for the molecular clock

  • How to run a parametric bootstrap. From Boris Igic (UCSD)

  • Joe Felsenstein's big list of phylogenetics programs - A big list of phylogenetics programs. From... Joe Felsenstein...

  • Genetic software forum - Questions and answers about the use of software for genetic analysis. Hosted by Bruce Rannala (U. Alberta).

  • PhyCom - News, how-tos, and advice for the phylogenetics community. Hosted by Stephen Smith (Yale)

  • Evoldir - A listserv for evolutionary biologists. Includes job, conference, and workshop announcements, as well as analytical advice. Hosted by Brian Golding (McMaster).

  • Bat Conservation International - An organization dedicated to funding and promoting bat conservation through education and research.

  • Lubee Bat Conservancy -An organization working to conserve fruit bat populations through education and research.

  • The National Genographic Project - A landmark study aiming to genetically characterize human populations worldwide, and to reconstruct ancestral human migration patterns and demographic trends.

  • Genetic Identification Services - Develops microsatellite-enriched genomic libraries for academic, commercial, and government clients. I normally don't like to give out free commercials to private companies, but GIS went above and beyond the call of duty in constructing a library for my free-tailed bats. It's an expensive service, but they provide a quality product. You get what you pay for.

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Research Associate
Arizona Research Laboratories
Ecology and Evolutionary Biology
University of Arizona
Tucson, AZ 85721
Tel: (520) 626-0404
FAX: (520) 626-8050

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