align.seqs alignment width not flush

This is a basic question, but the forum search won’t let me search for it because the words I’m using are too common (surprise “alignment” is a common word here :shock: )

I am aligning a huge set of 454 amplicon sequences against a reference alignment and its possible that the candidate sequences will be longer (wider?) than the reference. Mothur doesn’t seem to have a problem with this in most cases and the alignment produced is flush. However, in some cases 45 sequences out of ~700,000 the output aligned sequence is wider than the reference which breaks downstream processes that expect a flush alignment. Any idea what’s going on? Perhaps a better question is what happens when candidate sequences extend beyond the region covered by the alignment… An example would be aligning a full length 16S sequence against a reference of just V1-V3 regions.

This might be helpful in the future, Searching

Gotta love Google. That’s a clever workaround…

This post would indicate that I should not be seeing aligned candidates that are wider than the template:

I’ve submitted an example to the mothur.bugs address to illustrate, although I’m not sure I’d call this a bug just yet…