Phylogenetic profiling

On my wiki I have a short summary of phylogenetic profiling. The program MrBayes is used for Bayesian inference for phylogeny and can be used for inferring relationships using binary type data such as phylogenetic profiles.

The input to MrBayes is a NEXUS file and here is the example I will use:

begin data;
  dimensions ntax=10 nchar=10;
  format datatype=restriction interleave=no gap=-;
  homer 1100000000
  marge 1100000000
  sheldon 0011000000
  amy 0011000000
  lily 0000110000
  marshall 0000110000
  wilma 0000001100
  fred 0000001100
  scooby 0000000011
  shaggy 0000000011

The input to MrBayes (for more information on the commands refer to the MrBayes manual).

set autoclose=yes nowarn=yes
execute test.nex
mcmc Nchains=8 Ngen=1000000 Temp=0.100000
sump burnin=5000
sumt burnin=5000

MrBayes outputs consensus trees (*.con) in the Newick format that can be visualised using TreeView.

This may be useful for converting large datasets into binary, although losing information, to observe whether any relationships exist.

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