BioInfo 4U

Steve's Quick Links

Steve's Home page

Steve's SGCEP Courses: Introductory Biology I and Biology II, and Environmental Science

Steve's VSU nonmajors introductory General Biology courses: I and II

Steve's VSU graduate level Molecular Phylogenetics course

Steve's FSU Introduction to Bioinformatics Laboratory course

Steve's FSU Comparative Genomics Outline

Steve's FSU GCG Workshops

Florida State University Department of Scientific Computing

High Performance Computing at Florida State University

Florida State University Biology Department

Guide to Online Higher Education in the United States

Special Topics Cell/Molecular: Molecular Phylogenetics

The syllabus can be foound here.

Course lectures and assigned readings

Lecture 1: In the beginning . . . the basics

Ubuntu -- read all you can stand.

Lecture 2: Similarity searching and homology

The Statistics of Sequence Similarity Scores Altschul, NCBI.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, et al. 1997.
Improved tools for biological sequence comparison Pearson and Lipman, 1988.
Protein sequence comparison and protein evolution Pearson, 2001.
Pearson's FastA server page Pearson, Univ. Virginia.

Lecture 3: Sequence alignment and how it matters!

Multiple sequence alignment Edgar and Batzoglou, 2006.
Upcoming challenges for multiple sequence alignment methods in the high-throughput era Kemena and Notredame, 2009.
Multiple sequence alignment for phylogenetic purposes Morrison, 2006.

Lecture 4: How to infer phylogenies

Maximum Likelihood in Phylogenetics Lewis, 2009.
Bayesian Phylogenetics Lewis, 2009.
Likelihoods and Phylogenies Felsenstein, 2009.
All references from 2009 Workshop on Molecular Evolution at the Marine Biological Laboratory (most with complete PDFs).

Lecture 5: Coalescence Peter Beerli's Coalescence lecture.

© 2013 Steven M. Thompson, acknowledgements and thanks to the Florida State University Biology Department for generously extending Web hosting and e-mail services beyond my FSU tenure.
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