MCB 5472: Computer Methods in Molecular Evolution

Lectures, Demonstrations (Mondays in BPB 401), and Labs (in BPB 301)

Presentations of Student Projects 7-13 (Evaluation Form #2)

Presentations of Student Projects 1-6 (Evaluation Form #1)

Lab 11: Work on student project

Lecture 13: Presentation by Amanda Dick on Short Branch Attraction

Lab 10: Work on student project

Lecture 12: dN/dS, supertrees/supermatrix, gene families
                   class12.pptx, class12.pdf

Lab 9: Assigment 9 Extracting data from repetitive tasks

Lecture 11: Types of selection
                   class11.pptx, class11.pdf

Lab 8: Assignment 8 MrBayes Intro

Lecture 10: Bayesian approaches,
                 the bipartition paradox, spectral decomposition and

                 class10.pptx, class10.pdf,


Review Session sample questions

lab 7: Assignment 7 Intro to phylogenetic reconstruction (PHYLIP, phyml, treepuzzle, )

Lecture 8: Phylogenetics part 2
                class8.pptx, class8.pdf,

lab 6: Assignment 6 PyMOL and sequence conversation, Intro to phylogenetic reconstruction (PHYLIP, seqboot, protpars)

Lecture 7: Scripts on strandbias, Trees - approaches to phylogenetic reconstruction
                class7.pptx, class7.pdf,

Lab 5: Assignment 5 introduction to PyMOL

Lecture 6: Trees, terminology, and ways to calculate them - interplay with alignment
                class6.pptx, class6.pdf,

Lab 4: Assignment 4 Sequence alignment

Lecture 5: Sequence alignment, reading directories
                class5.pptx, class5.pdf,

Lab 3: Assignment 3 Command line blast, genome plots, PSI Blast, Mummer

Lecture 4: PSI-blast, commandline blast, E-values versus %identity
                 file input/output, arrays, loops, hashes

                class4.pptx, class4.pdf,

Lab 2: Assignment 2 Literature databank searches and command line blast.

Lecture 3: Types of homology, Blast, PSI-blast (arrays, loops)
                class3.pptx, class3.pdf,

Lab 1: Assignment 1 Intro to Unix and web-based blast

Lecture 2: Unix continued
                Perl: types of variables and operations
                Homology, databanks

                class2.pptx, class2.pdf,

Lecture 1: Getting to know Unix
Discussion of student projects, homology, databanks
                  class1.pptx, class1.pdf
                  Pascal_s_Slides.pptx, Pascal_s_Slides.pdf

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