Many thanks for reading my question.
Recently, I want to align multiple sequences from different genomic regions with the whole genome sequences for subsequent phylogenetic study, but I found none of my known tools can fulfill my requirement. Can any fellows give me some suggestion. Thanks a lot.
For example, let's say that the whole genome consists of 3 regions, A,B,C. I have some complete genome sequences, and some sequences of A regions, some sequences of B regions, also some sequences of C regions. I want to get alignment on all those 4 kinds of sequences simultaneously, in one alignment operation (I do not want to align A,B,C to the whole genome sequences separately). And I have used many multiple alignment tools but found none can do this. So I wonder if anyone can help me solve this question.