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).