Note – this is pretty out of date!

For a more recent list of recommended tools posted more recently (Feb 2015), see my lab website.

Short read alignment


Annotation & browsing

Genome alignment

  • MUMmer
  • Mauve

Phylogenetics & population genetics

  • BEAST – Bayesian inference, divergence date estimation
  • RAxML – fast maximum likelihood inference, great for large datasets
  • phylip – Parsimony, likelihood, minimum evolution, etc etc… the grandaddy of phylo software, best for small data sets
  • PAML – maximum likelihood phylogenetic & evolutionary inference
  • PhyML – maximum likelihood, run online here
  • SplitsTree4 – brilliant Java-based app from Daniel Huson, builds phylogenetic networks and trees of nearly every kind
  • Dendroscope – Java-based tree viewer app from Daniel Huson, lots of alternative views available and can build consensus tree or network from sets of trees
  • FigTree – tree viewer app, radial or dendrogram, can load annotations, great for viewing BEAST trees
  • iTOL (interactive tree of life) – online tool, load up your tree file and associated data for an amazing array of visualisation options. great for overlaying data (eg gene content, protein domain structures, etc) on a tree
  • Hal – phylogenetic analysis of whole genomes
  • PhyloGeoViz – visualize haplotype frequencies (as pie charts) over an interactive map (google maps/google earth)

16S & Metagenomics


2 thoughts on “Software

    • Yes! Excellent point. I know this group well and they have some great stuff going. I should be using BRIG more, thanks for the reminder.

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