Alignment step cuts bp off of some sequences

[susanrkennedy]

The Align Sequences button in the Sequence Data Tool cuts bp off of the end of some sequences in the alignment, and shifts reading frame by inserting gaps:

This does not happen with every dataset I have tried, but consistently happens to some of them.

[tokebe]

Apologies for the long delay to explaining this. This is caused by the trimming step, which occurs after the alignment. The trimming step shifts the reading frame to ensure there are no stop codons, and then trims to ensure the sequences are a multiple of 3 length.

This implementation is rather incomplete, and is currently being re-written to not remove base pairs, instead relying only on adding gaps. The rewrite will fix additional issues and hopefully make the whole thing a bit more reliable and more clear in the steps it's taking.

I'll mark the issue closed when the rewrite is out.