I can happen that proteins cannot be aligned properly over their whole
length. Now I have had an idea, but I do not know how scientifically
valid it is. There exist programs that can find local multiple sequence
alignments, like MACAW, MKDOM, Gibbs, dialign, MatchBox, etc. These
aligments are not suited to make a phylogeny for all the sequences, but
what if you recode the information into binary data, so that the presence
or absence of an aligned segment or domain is coded as 1 respectively 0.
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 ?