Great work so far on UGENE! Here are a couple of features that would help my own workflow for sequencing data:

1) Add the ability to reverse-complement an entire alignment. Sometimes I sequence in the reverse direction, but would like to go scan the alignment and contig in the opposite direction to see which sequences are correct.

2) Make the alignments from CAP3 editable. For now, I can export the ".ace" file to an alignment and edit from there, but it would be nice to edit the ".ace" alignment generated by CAP3 directly.

Keep up the good work.