MCB 5472: Computer Methods in Molecular Evolution

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

Lab 10: Branchclust continued / Coalescence

Lecture 12: Gene families / Super Trees and Super Matrices
                pptx ppt pdf

Lab 9: Branchclust
           Assignment 9

Lecture 11: Types of selection #2 -- How to assemble gene families.
                pptx ppt pdf

Lab 8: dN/dS ratios
           Assignment 8

Lecture 10: Types of selection
                pptx ppt pdf

Lab 7: Handling genome size data sets
           Assignment 7

Lecture 9: Phylogenetic reconstruction and positive selection / the queue
                pptx ppt pdf

Lab 6: Inferring Phylogenies
           Assignment 6

Lecture 8: Phylogenetic reconstruction - part 2
                pptx ppt pdf

Lab 5: Inferring Phylogenies
           Assignment 5

Lecture 7: Phylogenetic reconstruction - part 1
                pptx ppt pdf

Midterm with answers

Lecture 6: Intro to Trees
                pptx ppt pdf

Lab 4: Sequence alignment
           Assignment 4

Lecture 5: Sequence alignment, sytem(), sort {} ()
                pptx ppt pdf

Lab 3: PSI Blast
           Assignment 3

Lecture 4: arrays, loops, hashes
                 pptx ppt pdf

Lab 3: snow-day cancellation

Lecture 3: PSI Blast, arrays, loops.
                 pptx ppt pdf - class3.pl gi_list.txt

Lab 2: Blastall, genome plots, mummer:
           Assignment 2

Lecture 2: Blast, scalar variables and context, interpolation.
                   pptx ppt pdf - class2.pl

Lab 1: Entrez, blink, Blast, blastall
           Assignment 1

Lecture 1: Discussion of student projects, blast, blastall, and formatdb
                   pptx ppt pdf (what we actually went through is at pptx, ppt, pdf)

Lab 0: Getting to know Unix: Assignment 0

 

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