These have become available. They will be mostly in PDF format (one is in HTML format):
|Introduction, parsimony, distance (Mark Holder)|
|Topology searching (Mark Holder)|
|PAUP* (Mark Holder)|
|Nucleotide substitution models etc. (Jeff Thorne)|
|Likelihood (Joe Felsenstein)|
|PHYLIP lab materials (Joe Felsenstein)|
|PAUP* lab materials (Mark Holder)|
|Bootstraps (Joe Felsenstein)|
|More realistic models (Jeff Thorne)|
|Bayesian inference (Jeff Thorne)|
|MrBayes lab (Mark Holder)|
|BEAST demo materials (Mark Holder)|
|Divergence times (Jeff Thorne)|
|Comparative methods, the coalescent, and the future (Joe Felsenstein)|
These will each be posted in two formats: WMA and MP3. The links currently do not work; each will become active as that lecture's audio files are posted, on the same day as the lecture.
If you want to hear the corresponding talks from the 2014 course (the most recent time we gave it) look here.
|WMA format||MP3 format|
|Introduction, trees, parsimony (Mark Holder)||Lecture1.WMA||Lecture1.mp3|
|Distance methods, topology searching (Mark Holder)||Lecture2.WMA||Lecture2.mp3|
|PAUP* Lab (Mark Holder)||Lab1.WMA||Lab1.mp3|
|Nucleotide substitution models etc. (Jeff Thorne)||Lecture3.WMA||Lecture3.mp3|
|Likelihood (Joe Felsenstein)||Lecture4.WMA||Lecture4.mp3|
|PHYLIP Lab (Joe Felsenstein)||Lab2a.WMA||Lab2a.mp3|
|PAUP* Lab (Mark Holder)||Lab2b.WMA||Lab2b.mp3|
|Bootstraps (Joe Felsenstein)||Lecture5.WMA||Lecture5.mp3|
|PHYLIP and PAUP* bootstrap lab (Joe and Mark)||Lab2c.WMA||Lab2c.mp3|
|More realistic models (Jeff Thorne)||Lecture6.WMA||Lecture6.mp3|
|Tutorial (all three)||Tutorial.WMA||Tutorial.mp3|
|Bayesian inference (Jeff Thorne)||Lecture7.WMA||Lecture7.mp3|
|MrBayes lab (Mark Holder)||Lab3.WMA||Lab3.mp3|
|Divergence times (Jeff Thorne)||Lecture8.WMA||Lecture8.mp3|
|BEAST demonstration (Mark Holder)||Lab4.WMA||Lab4.mp3|
|The coalescent and comparative method and the future (Joe Felsenstein)||Lecture9.WMA||Lecture9.mp3|
We are continually revising the webpages for the programs used in the lab exercises. The main webpage for them is here.
In that webpage you will find information on the new PHYLIP programs which we are making available on a test basis.
For the PAUP* and MrBayes labs, Mark Holder has a web page It has links for PAUP* and for the data sets used in those labs. They are in the Nexus format. When saving those data sets from your browser using the Save As choice in the browser's File menu, make sure they end up with an extension of .nex
Mark has also put nearby Nexus versions of the data sets that Joe collected for his PHYLIP labs. They are here.
For learning about MCMC methods, two teaching programs are very helpful:
I have a web page here that describes using
PHYLIP as well as the R packages
which we will use in our labs.
A folder of data sets that can be used in the lab sessions will be found here.