Phylogenetic programs

Listed here are programs that have been discussed throughout the class with some basic instructions to get you started. If you are running a Linux or MacOSX, there should be no problem getting anything installed. If you are running Windows, it depends on the specific program.

Pairwise alignments
  • BLAST: the de facto standard for comparing sequences to a database of sequences. You can use the website version to search against the database that NCBI manages. You can use the standalone version to compare your own sequences. If there is desire for more extensive BLAST tutorials, just let me know (comment here, send an email, etc.)
  • SWIPE: (found here) is a very fast implementation of the Smith-Waterman algorithm. It rivals BLAST for speed (and is faster in many cases).
Multiple sequence alignments
  • MUSCLE: (found here). MUSCLE, like Mafft below, has replaced Clustal as the de facto standard alignment program.
  • Mafft: (found here). Mafft uses a variety of algorithms, depending on the size of the dataset, to align multiple sequences.
  • PRANK: (found here). PRANK is a phylogeny aware multiple sequence alignment program.
Distance-based phylogeny reconstruction
  • NINJA: (found here). NINJA is a great neighbor joining program that can take distance matrices or sequences. It is very fast and can handle very large number of species.
Parsimony phylogeny reconstruction
  • Parsimonator: (information found here and you can download from here). Parsimonator is a very fast parsimony tree builder. Here is a little tutorial on running it.
Likelihood phylogeny reconstruction
  • RAxML:
Bayesian phylogeny reconstruction
  • BEAST:
  • MrBayes:
  • phylobayes:
Phylogenetic visualization
  • Figtree: (found here)
  • . Figtree is a very user friendly tree viewer that should be able to read the ouput of any of the phylogenetic reconstruction programs above.

Divergence-time analysis programs
  • BEAST:
  • phylobayes:
  • r8s:
  • treePL:

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