MCB_372

MCB 372 - Spring 1998

Computer Methods in Molecular Evolution

Instructors: J.Peter Gogarten (class 1-15, see below),
Don Les and Chris Simon (class 16-24: Introduction to PAUP)

Overview on pages accessible from this page

Class #1, #2, #3, #4, #5, #6, #7, #8, #9, #10, #11, #12, #13, #14, #15
Assignments #1, #2, #3, #4, #5, #6
Other class related stuff: Intro to X-windows
Some Unix commands

Course Outline and description of pages:

Notes on class 1 (Wednesday, January 21):

Databank Searches using the WWW (Entrez, Medline, Blast)

1^stHomework Assignment (Sequence Search and Retrieval)

Notes in class 2 (Monday, January 26):

Overview on Phylogenetic Reconstruction:

From Databank Searches to Tree Building

Notes on class 3 (Wednesday, January 28):

When are two sequences homologous?

If you want to use a PC for your analyses, you can download a ZIP compressed file by clicking here (contains the programs prdf and prss, help files and the three test files). The original of these programs and many other programs by Bill Pearson are also available from his web page at ftp://ftp.virginia.edu/pub/fasta/.

2^nd Homework Assignment (Quantifying Sequence Similarity)

Notes on class 4 (Monday, February 2):

Multiple Sequence Alignments

3^rd Homework Assignment (clustalw & co)

Notes on class 5 (Wednesday, February 4)

Multiple Sequence Alignments and
Introduction to Unix: telnet and FTP

Notes in class 6 (Monday, February 9th)

Building distance trees with clustalw
Neighbor Joining, Bootstrapping

4^th Homework Assignment (clustalw & co)

Notes in class 7 (Wednesday, February 11th)

Notes in class 8 (Monday, February 16th)

Bootstrapping: informative and non-informative sites