MCB 5472

Computer Methods in Molecular Evolution

Textbooks:

None is required but the following are recommended.

	Unix and Perl Primer for Biologists Keith Bradnam & Ian Korf Version 2.3.3 - November 2009. Available at http://korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v2.3.3.pdf
	Beginning and Mastering Perl for Bioinformatics By: James Tisdall Available through via safari online - search for Perl for Bioinformatics
	BLAST By: Ian Korf; Mark Yandell; Joseph Bedell Publisher: O'Reilly Media, Inc. Available through via safari online - search for BLAST
	Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum Publisher: Garland Science; 1 edition (August 29, 2007) Language: English ISBN-10: 0815340249 Recommended by people in my lab Amazon.com
	Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition Edited by Andreas D. Baxevanis and B. F. Francis Ouellette The book covers many aspect of bioinformatics that we do not cover in class, but it is an excellent reference. The section on phylogenetics is rather weak, but you have your instructors to provide you with much more detail. Includes a very short Perl primer at the end Don't buy the 2nd edition by mistake! link to Amazon.com link to publisher
	Inferring Phylogenies by Joe Felsenstein ISBN: 0-87893-177-5;   $61.95 paper Excellent book on phylogenetics and many aspects of population genetics (e.g., gene coalescence in populations, a topic that is rather relevant to species phylogenies in microorganisms :)). For most MCBler this is not exactly bedtime reading, but if you need a well founded thorough explanation, this is a good book to consult. Link to publisher, link to amazon.com
	Bioinformatics And Molecular Evolution (Paperback) by Paul G. Higgs, Teresa K. Attwood The authors discuss in detail many applications in molecular evolution and bioinformatics. This book should be very useful to those who want to study some aspects of things covered in this course in more detail. Link to amazon.com
	Essential Bioinformatics (Paperback) by Jin Xiong Excellent book, it provides a very readable and concise overview of the most important tools and concepts in Bioinformatics Link to Amazon.com
	Learning Perl, Fourth Edition By Randal L. Schwartz, Tom Phoenix, brian d foy Fourth Edition July 2005 ISBN: 0-596-10105-8 This book is available via safari online - search for learning PERL
	Molecular Evolution : A Phylogenetic Approach by Roderic D. M. Page, Edward C. Holmes Paperback - 352 pages (October 1998) Blackwell Science Inc; ISBN: 0865428891 This book gives an excellent introduction to terms, methods, and problems in molecular evolution.  It does not contain details on individual algorithm, but it provides a very readable overview.  Rather expensive and outdated! (Borrow it to read, don't buy) Available in the Library, link to amazon.com