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 http://evolution.gs.washington.edu/sisg/2016/2016_SISG_19_3.pdf.
The download site for test versions of PAUP is http://people.sc.fsu.edu/~dswofford/paup_test
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:
Instructions at http://evolution.gs.washington.edu/sisg/2016/2016_SISG_19_10.pdf.
We will be using Dr. Tracy Heath's excellent lab on divergence time estimation. Links:
A very nice tutorial by Mary Kuhner and Jon Yamato.