*Please note that all links open in new windows.

Software

There are many other programs available, most of these are Macintosh based. A good place to start is Felsenstein's list of phylogeny programs, the most comprehensive list of phylogeny programs available. Another excellent resource is the Phylogenetics Software Resources page maintained by the Museum of paleontology, at the University of California Berkeley

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 4.03 or later.

Sequencher: Used for editing and assembling sequences. We use version 4.1.

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. 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. We have found this especially useful on hundred-taxon datasets. 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.

Arlequin: Software for population genetics data analysis. Free.

Phylip: We tend to use PAUP, for most phylogenetic analyses. However, some of the software modules in Phylip have been useful. Free.

LAMARC: Used to estimate population parameters, such as effective population size, migration rate, and recombination rate. Free.

Databases

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.

Scientific societies' websites

A few relevant scientific societies are listed below:

Entomological Society of America (ESA)

Society for the study of evolution (SSE)

American Society of Naturalists (ASN)

Miscellaneous

Molecular Systematics: This website has lecture notes on how to do molecular systematics, explanations of the techniques, and links to very useful papers. To access lecture notes, click on "member labs " and then various members have lecture notes on their individual sites.

Technology Product Center: Reduced prices on computers and software for Harvard staff and students (Harvard link).

Harvard College: Includes information on courses, counseling, clubs, etc.

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.

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