There is a problem (at least for me).
I analyse an incomplete sequence matrix when sequences for some genes have not been obtained for all the samples in analysis. For example, I've got Co-1 gene but failed to obtain CytB gene for a given sample. As a result, there are some sequences in my matrix that have no matches in nucleotides at all.
So my questions are:
If there any algorithms to calculate the distance between two sequences without matches and to reconstruct distance-based phylogeny using (for instance) availible information about distance between other sequences in the matrix?
If so, is it possible to evaluate the branch support for a given phylogeny?