[Biojava-l] NullPointerException when using Alignments.getMultipleSequenceAlignment

[Andreas Prlic]

> 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