For Windows95 tools
Morning Lectures
9:00 AM Evolutionary Homology versus Sequence Similarity: Darwin to DNA; Combinatorics of Sequence Comparisons, Dot Plots, Two-way and Multiple Sequence Alignments; Gap penalties; Assumptions about mutations - transition versus transversion frequencies.
"Similarity is observed; Homology is inferred." How is sequence similarity measured? How do different kinds of "yardsticks" influence our inferences about similarity (parsimony, maximum likelihood, and tree assumptions? Do we employ chemical similarity of amino acyl residues or genetic similarity of notations as criteria? How much do we penalize for gaps? What can be inferred about function from sequence similarity?
10:45 AM Break
11:15 AMPhylogenetic Trees I: Analysis and Molecular Clocks
Theodosious Dobhansky said: "Nothing makes sense except in light of evolution." We will explore using a weaker corollary as a heuristic: "Everything in biology makes more sense in light of evolution." How do we draw evolutionary inferences? How do we test evolutionary hypotheses? How do inform traditional and industrial problems in biology?
12:30PM - 2PM Lunch
Afternoon Laboratories
2-5 PM Phylogenetic Trees
SOFTWARE:
MacClade (MacOS),
Phylip (MacOS, Windows, Unix),
Tree of Life (web),
Searching (web):
Blast,
Blitz,
BioScan
Software:
Description: An interactive, graphical program for analyzing phylogenies
and studying character evolution on the Macintosh.
Written by: Wayne Maddison and David Maddison (University of Arizona)
For more information: MacClade introduction
Description: A free package of programs for inferring phylogenies which runs
on DOS, MS-Windows, Macintosh, or UNIX operating systems.
Written by: Joe Felsenstein (University of Washington)
For more information: Descriptions of the programs within Phylip
How does your tree fit? Tree of Life
NCBI (Genbank) BLAST Sequence Searching
EBI (EMBL) BLITZ Sequence Searching
BioScan: Compare a DNA sequence
BioScan: Compare a PROTEIN sequence
Need a program to ....? Try:
For Windows95 tools
For general programs on all machines
For Netscape
or Microsoft Internet Explorer
Feng, D.F., Johnson, M.S., and Doolittle, R.F. 1985. "Aligning Amino Acid Sequences: Comparison of Commonly Used Methods." J. Mol. Evol. 21:12-125.
Feng, Da-Fei and Doolittle, Russell F. 1987. "Progressive Sequence Alignment as a Prerequisite to Correct Phylogenetic Trees." J. Mol. Evol. 25:351-360.
Doolittle, Russell F. and Feng, Da-Fei. 1990. "Nearest Neighbor Procedure for Relatinng Progressively Aligned Amino Acid Sequences." Methods in Enzymology, 183:659-669.
Feng, Da-Fei and Doolittle, Russell F. 1990. "Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences." Methods in Enzymology, 183:375-389.
Feng, Da-Fei and Doolittle, Russell F. 1996. "Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them." Methods in Enzymology, 66:368-381.
Programs available by Anonymous ftp: juno.ucsd.edu
Brown, James R. (1996). "Preparing for the flood: evolutionary biology in the age of genomics." Trends in Ecology ad Evolution (TREE) 11(12):510-513 (December).
Kumar, S., Tamura, K., and Nei, M. 1995. "MEGA: Molecular Evolutionary Genetics Analysis, Version 1.02." Syst. Bio. 44(4):576-577.
WEB Pages
Trueman, John. "Making Phylogenetic Estimates."
Maddison, Wayne P. and Maddison, David R. 1996. "MacClade Home Page."
Felsenstein, Joe. 1996. "Phylip." WEB Page. Department of Genetics, University of Washington, Box 357360, Seattle, WA 98195-7360.
Lyons-Weiler, James. 1996. "Software for the Mac that will perform 'Relative Apparent Synapomorphy Analysis' (RASA)". http://loco.biology.unr.edu/archives/rasa/rasa.html. or by anonymous ftp at loco-biology.unr.edu (pub) (rasa).
"Journey into Phylogenetic Systematics." WEB Page.
"A Comparison of the Schools of Taxonomy." WEB Page.
Trueman, John. "BioInformatics Workshops: Cladistic methods for phylogenetic analysis." WEB Page. Research School of Biological Sciences, Australian National University.
Last modified: Fri Dec 31 21:12:17 1997