Demo's for testing lecture are at:

phylogenetics_intro_2018.pdfMark's intro to phylogenetics lecture slides.
huelsenbeck_programming_for_evo_biol.pdfHuelsenbeck programming for evolutionary biologists (draft)
msa-2015.pdfMark's MSA lecture slides.
convincing-arg-model-selection.pdfSome notes on model testing
Zwickl-WoodsHole2015-lecture.pdfDerrick Zwickl's Searching slides
HolderTestingLectureWoodsHole.pdfMark's 2014 Topology testing lecture slides
5-primates.nexdata used in testing demo with paup.
5-taxa-HCG.tre trees used in testing demo with paup.
HolderTestingLectureWoodsHole2013.pdfMark's Topology testing lecture slides
HolderTestingLectureNotesWH2012.pdfNotes on the testing lecture.
Repository on GitHubVersion control for lecture materials
annotated.pdfThe beginnings of an annotated bibliography about the literature on topology testing.
Zotero groupGroup for references about topology testing
pboot_flow_chart.pdfFlow chart for the parametric bootstrapping lab
mb-mac-i386.tar.gzMrBayes 3.2.1 compiled for Mac i386 (use "tar xfvz mb-mac-i386.tar.gz"in a Terminal to uncompress and tar).
simwithdice.nexA NEXUS file with the data patterns that the class generated using 10-sided dice
coin_flip_mcmc.pyA Python implementation of the MCMC algorithm that John coded in lecture (he did his version in C++).