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Tools for Evolutionary Genetic Analyses

Quick links to databases and programs

GenBank cross database query.
PhyLoTA: browse GenBank by phenetic clusters. alignment and tree building tools online.
BoLD: database for DNA Barcode of Life.

Analytical Protocols

I have posted two informal but potentially useful documents I have written. Below are some useful links as well. If you have any suggestions, comments, or questions, please drop me a line at andrew ∀ (replace ∀ with @, obviously).

Horribly detailed instructions to running a SOWH test

I wrote this horribly detailed instructions to running a parametric bootstrap test of phylogenetic tree topology, aka, a SOWH test, downloadable as a RTF document. Talk about doing things the hard way! Nowadays, I might recommend one try Mequite first.

You probably should also consult the definative but not-quite-as-detailed SOWH guideline written by the masters of the subject, Anderson, Goldman and Rodrigo, available here.

Thanks to Church et al. (2015) for citing this page and my horribly detailed instructions to running a parametric bootstrap test. These authors now offer a cleverly named automated version, SOWHAT. I was happy to see they tested their SOWHAT on the same data set we originally applied our SOWH test protocol to:
Wang IJ, Crawford AJ, Bermingham E (2008) Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland tropical forests of Isthmian Central America. Molecular Phylogenetics and Evolution 47, 992-1004. PDF here.

Horribly detailed instructions to running multidivtime

Jeff Thorne and colleagues have designed a brilliant piece of software, multidivtime (aka, "multidistribute" or "Thornian Time Traveler"), for estimating divergence times of samples on a given phylogeny based on DNA (or AA) sequences. This program required no molecular clock, but the user should input some form of temporal constraints based on fossil data or a robust biogeographic hypothesis. This program also allows (and encourages) simultaneous analysis of multiple loci. Polytomies or missing data are no problem. The only catch is that this program is definitely NOT "point 'n' click."

I provide a 9-page, step-by-step user's guide to multidistribute that will walk you through estbranches and multidivtime. Updated version (for 2008) now provides tips on the closely related Thornian Time Traveller by Ziheng Yang.
First time users should also consider BEAST as an alternative or a point of comparison.

Prospective first-time users of multidivtime should also consider the following aids and alternatives:
MULTIDIVTIME_HELPER and CONVERTER scripts from the biokubuntu webpage. (NB: Link busted last time I tried it!).

A plug for Brian O'Meara's old page

For some concise tips on using PAUP*, check out Brian O'Meara's old web page.


Software by Bailey Kessing

As a community service I am posting a copy of the program, Sequencer version 6.1.0 (not Sequencher!), a very handy DNA sequence analysis program written by Bailey Kessing, formerly of the Naos Marine Laboratories at STRI. The program runs in Mac OS9. In my Crawford (2003a) paper I cited this program as being available at which no longer exists due to a reorganization of STRI's webpages.


For my PhD thesis project I studied ecological genetics, phylogenetics, and molecular evolution in "dirt frogs" of the genus Craugastor (formerly Eleutherodactylus) in the family Brachycephalidae, or Strabomantidae, depending on whom you ask. For this work I designed original primers for PCR amplifying and sequencing a 1,300 base pair long portion of the c-myc gene, containing intron 2 and portions of the flanking exons. I also used mitochondrial DNA primers designed by Bob Macey for amplifying the "ND2-WANCY" region. I designed innumerable internal primers for this region, specific for my frogs. A list of all PCR and sequencing primers, with standardized location and a complete list of all the samples (by collector number) I used them on, is available for download here in PDF, copied from TABLE III.2 of my dissertation.


Published datasets are available on my CV page.

Useful papers

Various PDF's related to evolutionary genetics in general and phylogeography in particular are available on my Filogeografía course webpage.

Mine are available on my PDFs page.