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Phylogenetics course and tutorial May 31st-3rd June 2005

Aidan Budd, Toby Gibson, Carolin Kosiol, Lisa Mullan and Ari Loytynoja

Usage guide to phylogenetics programmes used in these tutorials

Brief guide to commands used during the course

Day 1, 31st May: Introduction to phylogenetic trees and phylogenetic estimation algorithms

Day 2, 1st June: Amino acid substitution models

Day 3, 2nd June: Estimating precision of phylogeny estimates

Day 4, 3rd June: Preparing alignments for phylogenetic analysis

Links

Groups and institutions of teachers

Centre for Computational Biology

Sites describing current ideas of species phylogenies

UCMP Phylogeny Exhibit

Tree of Life project

Both links are to the root of the tree of life on the respective sites - follow links down through the trees to reach your group of interest e.g. this page links to the vertebrates page at UCMP

Phylogenetic software used in the course

Overview (nearly all phylogeny programmes around)

Building and assessment of trees

PHYLIP Including neighbor, protml, consense, seqboot

PAML Including codeml

Visualiation of trees

GENETREE Used to reconcile gene and species trees

Working with alignments