Align.seqs is segfaulting for me on 1.31.1 when using flip=t. No problem without it. I’m aligning my sequences to a pcr.seqs processed version of the silva reference database, and the segfault happens nearly immediately.
If this is difficult to reproduce, I will try and come up with a small test case.
From log (I compiled from source):
Running 64Bit Version
Last updated: 5/29/2013”