MCB 372 - Spring 2000
Computer Methods in Molecular
Evolution
Instructors: J.Peter
Gogarten (weeks 1 - 8, see below),
Paul
Lewis (weeks 9 -16: Introduction to
PAUP, etc.)
New Times: Mondays 12 –1 PM and Wednesdays 10 AM – 12 PM
The second part of the course is HERE.
Exam 1 (return by 3/29/00)
Examples of correct (or nearly correct) answers Histogram of results from exam1 and some explanations
Class
8: Discussion of problems. How to
design a ml-ratio test.
Class 7: PUZZLE, puzzle trees, ml-mapping and ml ratio
test
Assignments
#7, Comments #7
Class 6 Overview on methods of phylogenetic
reconstruction, X-windows, and phylo_win.
Assignment
#6
Class 5 Intro to alignment and trees continued,
Protein Structure
“Assignments
#5”
Class4 Sequence alignment, clustalw & clustalx,
treeview
Assignments
#4, Comments #4, some Unix commands
Class3 Types of homology, genome analyses
Assignments
#3, Comments #3
Class2 Blast, iterative blast, and genomes at NCBI
Assignments
#2, Comments #2
Class1 Databanks at NCBI,
Assignments
#1 , Comments
Recommended Textbooks:
Roderic D. M. Page, Edward
C. Holmes: Molecular Evolution: A Phylogenetic Approach
Blackwell
Science Inc; ISBN: 0865428891 - currently
on back order.
This book gives an excellent introduction to terms, methods, and problems in
molecular evolution. It does not
contain too many details on individual algorithm, but it provides a very
readable overview.
Li: Molecular Evolution – well written, gives good background,
especially with respects to the biological aspects of evolution.
Graur and Li: Fundamentals of Molecular Evolution,
Second Edition – more data on algorithms, but fewer examples
Hillis, Moritz, and Mable: Molecular Systematics, Second Edition – A lot of data and
information on how to make trees. It does not make for an easy reading
experience. Only recommended to look
things up in more detail.
“Bigwords.com” has a
list of these books. They might be
cheaper than other places – they might not. Their list is here. In case you get lost, the B-code is B-2BIXZP (gives
you another 5% discount).
Send an Email to Peter Gogarten or use this response page
