Topics Sorted by Type of Analysis:
Reconstructing Phylogenetic Trees w/PAUP*, RAxML, GARLI, MrBayes, and BEST Tutorials
Model Selection w/jModelTest
Divergence Time Estimation w/BEAST Tutorial
Delimiting Populations & Species w/Structure and Structurama Tutorials
Phylogenetic Comparative Methods w/Mesquite, R, and BayesTraits Tutorials
Morphological Diversification and Rates of Evolution in R or Brownie
Community Phylogenetics w/Phylocom Tutorial
Biogeography w/Lagrange Tutorial
Lineage Diversification in Symmetree & R
Phylogenomics
Topics Sorted by Software:
BEAST: Divergence Time Estimation
BEST: Generating Species Trees with BEST
Brownie: Morphological Diversification and Rates of Evolution 2009/2010, we are now using R!
Garli: Rapid ML analysis using GARLI 0.95 GUI version & 1.0 command line version
jModelTest: Model Selection
Lagrange: Biogeography
Mesquite: Phylogenetic Comparative Methods
MrBayes: Bayesian Analyses
PAUP*: Parsimony (PAUP*)
PHYLOCOM: Community Phylogenetics
R: Phylogenetic Comparative Methods, Morphological Evolution in R, Lineage Diversification in R
RaxML: Fast ML analysis using RAxML
Structure & Structurama: Delimiting Populations & Species
Symmetree: ["Diversification Rates (Moore)" Lineage Diversification
General advice on succeeding in applied phylogenetics:
Advice for Aspiring Phylogeneticists
Version Management
Becoming a programmer
Course webpages by year
2008 Workshop
2009 Workshop
2010 workshop
2011 Workshop
2012 Workshop
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