Is it possible to display sequence identity info between selected sequences in given alignment? "Calculate > Pairwise Alignments" option recalculates the alignment and unfortunately doesn't do a good job for low sequence identity sequences - it outputs just a part of a sequence alignment and displays sequence identity for that region only.
Percent identity calculations for two or more sequences is an outstanding feature request (http://issues.jalview.org/browse/JAL-788). I was hoping to get around to this for the up-coming release, but haven't been able to fit it in. If you register, and hit the 'watch' button, you'll get an email when I get around to working on it.
The implementation of this feature isn't really hard - but as you can see from the feature request entry, there are a few variations on PID calculations that require a little bit of work. As usual - if you know of any java programmers with a spare few hours, I'd be happy to guide someone on adding a new item to the 'Calculations' menu!
sorry I couldn't be more help!
On 29/08/2012 18:15, Vladimir Yarov-Yarovoy wrote: