International Conference on Microbial Genomes 2005 Phylogenetics Workshop
Supported by The Institute for Genome Research and Genome Atlantic
April 13-16, Halifax, Nova Scotia
Workshop materials
David Bryant, McGill University: Supertrees and SuperNets
Outline
T. Martin Embley, University of Newcastle: Phylogenomic Analyses to Detect Prokaryote to Eukaryotes HGT
Slides
Useful links:
PyPhy (phylogenomic tools to make all trees from all genes in a genome)
P4 (likelihood and Bayesian phylogenetics with heterogeneous models)
ClustalX (graphical multiple alignment)
Gblocks (selection of conserved blocks from multiple alignments)
MrBayes (Bayesian inference of phylogeny)
FastME (fast distance-based phylogenetic trees)
Robert L. Charlebois, NeuroGadgets Inc. and Genome Atlantic: Genomic phylogenies based on normalized BLASTP scores
References and further information
Useful links:
NeuroGadgets Inc. Bioinformatics Web Service
Matthew Spencer, Dalhousie University: Phylogenies based on gene content
Outline
Slides
Detailed notes
Useful links:
PAUP* (phylogenetic software)
Phylip (phylogenetic software)
SplitsTree (phylogenetic software)
SHOT (Shared Ortholog and gene order Tree reconstruction tool)
GeneContent 1.0.2 (phylogenetic software for gene content data)
COG (database, Clusters of Orthologous Groups of proteins)
Elisabeth R. M. Tillier, University of Toronto: Dependency and Co-dependency: Predicting amino acid interactions within
and between proteins using co-variation
Outline
Useful links:
dependency paper and software
Tillier lab