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 10: Bayesian approaches,
the bipartition paradox, spectral decomposition and
class10.pptx, class10.pdf,
Midterm
lab 7: Assignment 7 Intro to phylogenetic reconstruction (PHYLIP, phyml, treepuzzle, )
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
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, class4.pl
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, class3.pl
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, class2.pl
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
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