MCB 5472: Computer Methods in Molecular Evolution

Lectures, Demonstrations (Mondays in BP201), and Labs (in BPB 201)

List of student presentations

Lab10: Comments on bipartitons, quartets and supertrees. Work on student projects

Lecture 13: Discussions of Problems, and Constructive Neutral Evolution, detecting HGTs (slides)

Lab9: Work on student projects

Lecture 12: Gene transfer and the tree of life (slides)

Lab8: Calculating trees and student projects Assignment 8

Lecture 11: Gene transfer and selection (slides)

Lab 7: Positive and Purifying Selection (HyPhy, PAML, MrBayes) Assignment 7

Lecture 10: Discussion midterm practical part and dN/dS ratios slides

Midterm Practical Portion

Lecture 9: Trees, terminology, ancestral state reconstruction, and selection (if time :))
                  SLIDES

Midterm postponed to Wednesday after Spring-break.
Please try to do assignment #5 and go through these rest of these slides.

Lecture 8: Review session for midterm / Sorting and sorting hashes by key / Slides

Lab 6: Instructions: Delineating pan-genomes, Pan-genome analysis.html_notebook, Pan-genome analysis.Rmd (slightly updated plots as compared to the instructions), Zip file of created images

Lecture 7: Pangenomes, the Black Queen Hypothesis and Division of Labor
                Slides

Lab 5: Intro to Rhtml_notebook, slides, example data matrix, intro.Rmd,
            intro2.Rmd updated version with interactiv vulcano plot .Rhistory, list of Dyanna's modules.Rmd

              if time: slides on trees, exercise on ml-tree and LRT

Lecture 6: Alignment - trees, discussion of lab4, if time tree -> web of life
                class06_2018.pptx (link to bootstrap)

Lab 4: Sequence alignment Assignment 4

Lecture 5: multiple sequence alignment, gene plots - discussion, system commands in perl
                class05_2018.pptx, class05.pl (input), class04_answrs.pl, evaluations.pl

Lab 3: Gene and mummer plots Assignment 3

Lecture 4: Within genome recombination, GC bias, and hashes
                  class04_2018.pptx, Scalar->array_example.pl, class03_answers.pl (input), class04.pl (input)

Lab 2:       Databank Searches and Commandline Blast: Assignment2
                 class02_answers.pl

Lecture 3: The BBC cluster, scalars and arrays in Perl, Blast and PSI blast
                Vijender Singh's slides, class03.pptx
                class03.pl (updated version strange characters removed !)

Lab 1: Getting to know Unix (possibly blast on the web): Assignment 1

Lecture 2: Homology / if time Blast searches
                 class02.pptx class02.pl
                 note .nanorc .vimrc

Lecture 1: Discussion of student projects, Getting to know Unix
                class01.pptx

Lab 0: Getting to know Unix: Assignment 0 (we will do a modified version of this next week)
                 

Discussion, hints and messages 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