News: Hoopes Prize!

bioblitz shieldFarrell Lab undergraduate Adam Clark wins the Hoopes Prize!

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News

Prof. Farrell co-authors new paper which answers longstanding scientific question about cause of tropics' stunning biodiversity. More

Current research

News pictureCurrent research extends the evolution of insect-plant interactions to other trophic levels through a broad collaboration in the beetle Tree of Life project.

A new research dimension in the lab concerns the acoustic signals produced for mating and territory defense. More

Software links


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

Arlequin: Software for population genetics data analysis. Free.

Beast: "BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models."

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.

Garli: "GARLI is a program that performs phylogenetic inference using the maximum-likelihood criteron. Several sequence types are supported, including nucleotide, amino acid and codon. It is usable on all operating systems."

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

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.

MAFFT: MAFFT is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc"

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

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.

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.

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.

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.

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

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

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