"in silico DNA, RNA, Protein Sequence,
and Structure Analysis:

Theory and Practice"

Wednesday, 8 January 1997

Morning Lectures

9:30 AM Phylogenetic Analysis and Molecular Clocks:

"Trees, Ladders, Chains: Reclassifying Life, Recalculating Time"

"Phylogenetic 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?


10:45 AM Break

11:15 AM Cladistics and Character Based Trees; Evolutionary getrics; Tree Statistics.

12:30PM - 2PM Lunch

Afternoon Laboratories

2-5 PM Phylogenetic Trees

SOFTWARE: MacClade (MacOS), Phylip (MacOS, Windows, Unix), Tree of Life (web), PAUP (MacOS), PAML (MacOS, Dos, Unix), Searching (web): Blast, Blitz, BioScan


MacClade 2.1

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

Phylip v3.5

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


Description: A new version will support both MS-Windows and the Macintosh, the old Mac only version is known as the most sophisticated parsimony program availible.

Written by: David Swofford (Smithsonian Instition)

For more information: Help using PAUP


Description: PAML (for Phylogentic Analysis by Maximum Likelihood) contains three main programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data. The software runs on the Macintosh and UNIX systems.

Written by: Ziheng Yang (University of California, Berkeley)

For more information: PAML readme


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

Bibliography - Phylogenetic Analysis and Molecular Clocks

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: Wed Jan 1 21:12:17 1997