MCB 372: Computer Methods in Molecular Evolution

Lectures, Demonstrations (in BPB 401), and Labs (in Chemistry T115)

Lecture 14: handouts, ppt, html
Clustering gene families based on phylogenetic information

Lecture 13: handouts, ppt, html
HyPhy -LRT on partitions, Detecting HGT

Lab J: Supertrees and Quartets2

Lecture 12: handouts, ppt, html
super matrix and - trees continued. LBA

Lab I: Supertrees and Quartets (files here)

Lecture 11: handouts, ppt, html
super matrix and - trees. HGT and the tree/web/dance of life

Lab H: MrBayes

Lecture 10: handouts, ppt, html
likelihood, Bayes, ...

Lab G: phylogenetic reconstruction (continued)

Lecture 9: handouts, ppt, html
likelihood, Bayes, ...

Midterm

Lecture 8: handouts, ppt, html
likelihood, Bayes, ...

Lab F: phylip, phyml, tree-puzzle

Lecture 7: handouts, ppt, html
Building trees

Lab E: clustal, muscle, and emboss

Lecture 6: handouts, ppt, html
sequence alignment

Lab D: Geneplot; PSIblastII

Lecture 5: handouts, ppt, html
loops, cluster etiquette, geneplot

Lab C: PSI BLAST

Lecture 4: handouts, ppt, html
scalars, psiblast, blastpgp, psitblastn

Lab B: Blastall searches using genomes

Lecture 3: handouts, ppt, html
blastall, perl, unix continued

Lab A: Databases and Blastall searches

Lecture 2: handouts, ppt, html
databank searches, blast, unix, Perl

Lecture 1: handout, ppt, html
Student projects, databanks, blast

DISCUSSION Your questions my answers. You might also get a few comments from me without anyone having asked a question. If you have questions or comments mail them to gogarten@uconn.edu