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:
#NEXUS begin data; dimensions ntax=10 nchar=10; format datatype=restriction interleave=no gap=-; matrix homer 1100000000 marge 1100000000 sheldon 0011000000 amy 0011000000 lily 0000110000 marshall 0000110000 wilma 0000001100 fred 0000001100 scooby 0000000011 shaggy 0000000011 ; end;
The input to MrBayes (for more information on the commands refer to the MrBayes manual).
set autoclose=yes nowarn=yes
mcmc Nchains=8 Ngen=1000000 Temp=0.100000
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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