I regularly find myself with large edited alignments which contain identical sequences (as the N and C terminal parts have been trimmed). I would like a quick way to find these sequences and remove selected ones (I want to leave very similar ones which are of interest). Does anyone have a good way to do this in JalView. Building a crude tree works for smaller alignments…but for me this takes hours for a larger alignment. Having a distance matrix with identity values (or some better variant), which is linked in the GUI back to the original alignment would be ideal. Just highlighting sequences with >n% identity to at least one other sequence would also do the trick.
Many Thanks
Matthew Hindle