PAUP: This user-friendly software performs neighbor-joining, parsimony, and likelihood searches. Use version 4.0b8 or later -- check its website frequently for updated versions. Also check for bug reports -- for example, 4.0b10 outputs the wrong format scores for ModelTest, though this can be fixed.

MacClade : An excellent program for tree drawing, character mapping, and file conversion. Also comes in a version for educators. Use version 4.05 or later.

Sequencher: Used for editing and assembling sequences. Must be purchased.

Staden package: An open source sequence editor, primer finder, etc. More difficult to use at first than Sequencher, but it's free. Free

MrBayes: A program, written by John Huelsenbeck, which uses Bayesian inference for phylogenetic reconstruction, including measuring clade support and computing error bars on divergence times. Use version 2.0 or later. Free.

ModelTest: This program by Posada and Crandall implements likelihood ratio tests for selecting the appropriate likelihood model. Also note the workaround for a bug in PAUP 4.0b10 at PAUP's website. Free.

ClustalX: Used to align sequences with many gaps. Uses a gap creation cost:gap extension cost method, not direct optimization. Use version 1.8.1 or later. Free.

PaupRat: Creates a batch file to make PAUP use the parsimony ratchet, a fast way of finding optimal trees. Free.

TreeRot: Creates a batch file to calculate Bremer support, including partitioned Bremer support, in PAUP. Free.

Mesquite: This is a modular, java-based program which has uses in coalescence, morphometrics, character mapping, and more. Can interact with PAUP. Beta.

Phylip: I tend to use PAUP, Phylip's main competitor, for most phylogenetic analyses. However, some of the software modules in Phylip have been useful. Free.

r8s: A program for estimating divergence times on a tree, among other uses. It implements some methods which do not require non-rejection of a molecular clock. Now available for OS X, as well as unix. Free.

Felsenstein's list of phylogeny programs: The most comprehensive list of phylogeny programs available.

UC Davis: Where I currently study.

Population Biology: My graduate group (Davis has "graduate groups" which span departments).

Entomology: UC Davis' entomology department website.

Bay Area Biosystematists: Monthly discussion group comprised of systematists/phylogeneticists of the San Francisco Bay area (which apparently includes Davis, >1.5 hr away from San Francisco).

David Baum: Evolution of Malvales, evolution of inflorescences, and phylogenetic theory.

Pete Cranston: Systematics, ecology, and biogeography of aquatic insects.

Michael Donoghue: Phylogenetic theory, plant evolution, and more.

Brian Farrell: Beetle (and other insects) systematics, plant-insect coevolution. My undergraduate adviser.

Joseph Felsenstein: Phylogenetic theory.

Penny Gullan: Scale insect systematics.

John Huelsenbeck: Models of evolution, tests of trees, and viral evolution. Home of MrBayes.

Dave Maddison: Beetle systematics, MacClade, and Tree of Life.

Emilia Martins: Phylogenetic comparative methods.

Nancy Moran: Group studying the aphid-Buchnera symbiosis.

Benjamin Normark: Evolution of genetic systems.

Oxford Evolutionary Biology Group: Useful software.

Mark Pagel: Especially useful for the software from the Pagel group. Note the scripts for using multiple trees (such as trees from a Bayesian analysis, sets of bootstrap trees, all equally parsimonious trees, etc.) in analyses of trait evolution.

Naomi Pierce: This group studies butterfly-ant interactions as well as other topics in ecology and evolution.

Mike Sanderson: Plant systematics, phylogenetic theory and methods.

Andrea Sequeira: Herbivorous insect evolution at several scales.

Derek Sikes: Nicrophorus (burying beetle) systematics.

Peter Wainwright: Evolution, biomechanics, etc. of fishes.

Phil Ward: Ant systematist and my adviser.

Ziheng Yang: Includes PAML and a program to estimate population sizes.

NCBI: The National Center for Biotechnology Information, hosts sites such as GenBank (sequences of many organisms), BLAST (you can search to see what sequences in the database are most similar to a sequence you have) and PopSet (sequences gathered for one phylogenetic or population-genetic project).

TreeBase: Aligned datasets and trees.

EvolDir: An email directory and mailing list for evolutionary biologists, maintained by Brian Golding. Includes job postings, lab protocols, upcoming conferences, and more.

Entomology index of internet resources: Maintained by Iowa State, a vast searchable database of websites with insect information. If you want information on the web about insects, start here. Includes mailing lists.

Travelocity: Find cheap airfares.

Travel tips: From American Express. Tipping, visas, etc.

US State Dept.: Includes information on state of health, crime, visa requirements, etc.

CDC travel info: What vaccinations you need, recent outbreaks, etc.

Molecular Systematics: This website has lecture notes on how to do molecular systematics, explanations of the techniques, and links to very useful papers. Great for people just starting in the field, useful for everyone else, too.

Intellicast.com: Weather, including local, national and international. See the local radar map.

Babelfish: Can translate from and to many languages. Somewhat useful for articles in other languages, but a limited scientific vocabulary.

NY Times Navigator: Developed for Times reporters, a compilation of information-rich websites.

Bibliography conversion : CGI made from the bp perl script to convert bibiliographies from one format to another, including the format used by bibtex.

Myrmecos.net : A website of insect (mostly ant) photos by my labmate, Alex Wild. Spectacular.

Site map