Useful Databases

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.

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