Thanks for posting to the list again, John.
John Taylor wrote:
(so it didn't arrive). I asked about a toggle translation option in
addition to the reverse complement. These are tools I use a lot in
BioEdit. They are very handy for research and teaching. Toggle
I can imagine. I think BioEdit still has a lot of fans out there because it's got some really practical features.
translate allows one to get sequences in the proper reading frame. It
also allows one to switch to amino acids for alignment and then back so
you end up with a codon alignment.
Does it preserve the variable sites in the third position from the original DNA at the end of all this ?
A few months ago there was a feature request concerning something like this, but in that case the idea would be to either have one view which showed the codon alignment, and the other would be the corresponding protein alignment. Scrolling would be tied between both alignment views, so moving the focus in one would also move the other. I'm afraid that kind of manipulation is not yet implemented either, but I'm just trying to get an idea of what would be most useful to everyone.
The back-translation function is really the most significant missing feature in Jalview at the moment. If the sequence is in Uniprot and has an EMBL cross reference then it can retrieve that sequence and propagate annotation from the protein back onto it, but not much more. Going from DNA to protein is better supported (ie an aligned set of coding regions are properly translated to an aligned set of proteins), but for a protein alignment there's curently no way of reconstructing the aligned cDNA from it. All the basic mechanisms are available to do this, but we have to find (someone's) time to actually write the routine to do it.
The reverse complement option is
also handy. My aim is to convert my lab to Linux. BioEdit is the main
thing holding us back (it's only available for Windows).
Wine may be the only way forward at the moment 
perhaps this'll change in a few months, though.
When might we expect Jalview 2.4?
There is a paper being drafted at the moment, and so the official release of 2.4 has been delayed until this is complete. However, you can get at a webstart version of the application from here:
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp
Jim.