Phylogeny from protein domain composition ?

Arlin Stoltzfus arlin at carb.nist.gov
Wed Jul 18 13:59:08 EST 2001

Guy Bottu wrote:
> Than this information could be given to programs that make phylogenetic
> trees from binary data, like the PHYLIP programs mix and dollop. Anyone
> a comment ?

This approach has been applied by 

  Snel B, Bork P, Huynen MA.
  Genome phylogeny based on gene content.
  Nat Genet. 1999 Jan;21(1):108-10.

using presence/absence of whole genes rather than presence/absence
of segments.  There is nothing wrong with doing this, though it 
is perhaps not the most sensitive or robust approach available. 
Presence or absence of a gene is a binary presence/absence character 
and can be subjected to analysis just the same as any other binary 
character one might use in systematics.

Patterns of presence/absence of genes are also used in methods 
that genomicists call "phylogenetic profiles" (though there is 
nothing phylogenetic about them).  



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