SISG 2016 -- Module 19 -- Molecular Phylogenetics - Software

The Molecular Phylogenetics module at SISG will be taught by Joe Felsenstein, Jeff Thorne, and Mark Holder. See the module's page on the SISG site for details about timing and location of the module.

You probably want Joe's page for the module rather than this page.

You may also be interested in labs used in the Workshop on Molecular Evolution or Mark's phylogenetics widgets.


Instructions for the lab are at

The download site for test versions of PAUP is

All versions are developmental (not stable). They are expiring versions, but Dr. Swofford usually posts a new version before each version expires.

PAUP demo for Windows Note: On some versions of Windows, you must run the PAUP executable by right-clicking the icon for PAUP and choosing the "Run As Administrator" from the drop-down menu.

Day One (Short) PAUP lab

Datafiles for the in depth PAUP lab

other relevant links:

MrBayes labs

Instructions at


MrBayes Lab data files: Other links:

BEAST 2 lab

We will be using Dr. Tracy Heath's excellent lab on divergence time estimation. Links:

See also the Taming the BEAST workshop course materials.

Coalescent link

A very nice tutorial by Mary Kuhner and Jon Yamato.

Other software links

Correction to slides