Many of these can be used to kickstart independent data mining projects! Choose your fancy!
- Dryad: repository of many phylogenetic trees and large datasets that have been published
- Genbank: repository of most if not all genetic sequences referred to in publications
- PhyLoTa: an aggregator for sequences by taxonomic classification and locus
- Phytozome: full plant genomes
- TAIR: annotated Arabidopsis thaliana genes and information on biosynthetic pathways
Recommended (Free!) Tools
- BEAST: a tool for putting dates on/calibrating phylogenetic trees.
- Bioedit: a sequence editer/aligner. An oldie, but a goodie.
- FigTree: a phylogenetic tree viewer.
- MEGA: first pass alignment analysis. Can create trees using relatively simple methods and do sequence similarity analyses.
- Mesquite: first pass analysis of character states on phylogenetic trees.
- MrBayes: more advanced phylogenetic trees using Bayesian methods. Requires command line.