MSA output of unequal length

[dgslos]

I often get an MSA output where at least one sequence is 1bp longer then the other sequences in the alignment. Other software expect an alignment of equal length. Can this bug be fixed?

[epruesse]

Can you give me as much example as you can? This is tested in the unit tests, so normally works.

[dgslos]

Sorry for my late reply. I didn't need SINA for a long time, but it seems to happen quite frequently. Currently using SINA v1.7.2. Can I send you example data by email?