Gene trees

Material for a ASBS course by Rod Page, June 2000

Lecture

The lecture will introduce reconciled trees and how they can be used to depict the evolution of gene families, as well as infer species trees from complex gene trees. The "one gene = one character" argument of Jeff Doyle will be reviewed in this light. A detailed example concerning vertebrate phylogeny will be presented.

Exercises

A series of exercises showing how GeneTree can be used to address a range of questions. In addition to simple made-up examples, there will be a chance to look at some of the zoological data sets covered in the lecture, as well as examine the recent analyses of angiosperm phytochromes by Donoghue and Matthews.

Downloads

Please obtain these before the course starts.

Software (GeneTree)

GeneTree for MacOS

GeneTree for Windows 95/98/NT

GeneTree comes with example files, and the Web site has a manual you can download. There is also a tutorial that describes how to create data files for GeneTree, should you want to create your own.

Example files

Macintosh format

PC format

Exercise notes

PDF format


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