> Unfortunately, the files in question are under NDA - does it work with > other fasta files? I could not get it to work with the files I tried.
I just wrote a junit test for DNA alignments and it works for me. DNA alignments by default are using the nuc-4_4 substitution matrix for the alignment. It contains the following columns. A T G C S W R Y K M B V H D N Does your FASTA file contain any characters that are not in this list? Andreas _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
