Thanks very much for getting back to me so quickly. First, let me thank you for providing such a well-designed and extraordinarily useful tool. I very much appreciate the efforts of your group.
Yes, I was aware of the ability to control zoom by adjusting the font, but this is kind of kludgy and also doesn’t allow changes to the spacing between alignment columns (or compression of the columns - not sure what is actually happening). I agree that Ctrl+/- would likely work extremely well, and believe this would also enable zooming by mouse scroll wheel. I also really like the alignment overview, and think zooming could be controlled by adjusting the size of the red box in that view.
I actually use Jalview for teaching (CSB472 Computational Genomics & Bioinformatics), so there are a few features I would love that may not be frequently requested, but which would be particularly useful when trying to illustrate different alignment principles. For example, it would be very nice to be able to extract basic distribution stats and total alignment score from the conservation and quality related annotation tracks. This would enable comparison between different alignment. It would also be helpful to have some other output options for the tract data. For me the easiest would be if the data were listed vertically (each alignment column on a separate row). This would make it completely painless to paste into Excel. Right now it is pretty painful to do this, particularly with a long alignment.
I think one of the biggest mistakes I make (and certainly my students make) is when they try to scroll along the sequence using the arrow keys. It was a real shock to realize that doing this actually shifts the selected sequence and destroys the alignment. I would very much prefer if this were not the default behavior. I can’t tell you how many alignments I have screwed up because of this. Can the arrow keys simply move you along the sequence. Perhaps make shifting the sequence require Shift+arrow. Maybe there is a simple way to change this behavior that I am not aware of.
Is there a toggle to enable a fixed codon size. IOW, count gaps as position in the alignment, so a gap in a codon results in a untranslatable amino acid. This is useful for illustrating the utility of codon-based alignments (back-translating protein alignments to DNA) as well as why natural selection generally culls frameshift mutations out of populations.
Is there a way to count the number of stop codons in a sequence or alignment. Again, not only useful “in the real world”, but also useful for teaching.
When using the Translate to cDNA option, can you please either put the translation in a tab of the original sequence or put the original sequence name in the title of the window.
Can the phylogenetic tree be re-rooted or at least default to mid-point root.
I very often have alignments stall when “Collecting job results”. For example, I have a Muscle alignment stalled right now. It is not particularly big (60 proteins, ~800aa in length), so I can’t understand where the problem might be. Is there any way to increase the verbosity of the log data to track these issue better?
That’s probably more than you wanted to hear from me. I appreciate your consideration.
All the best,
David S. Guttman
Professor & Associate Chair for Research, Department of Cell & Systems Biology
Director, Centre for the Analysis of Genome Evolution & Function
University of Toronto
Toronto, Ontario, Canada
On Fri, Nov 30, 2018 at 3:21 AM Jim Procter <email@example.com> wrote:
THanks for the email, David.
On 29/11/2018 20:10, David Guttman wrote:
Is there an alternative means to zoom in and out of alignments that
doesn’t require the middle mouse button? Not all mice have a middle
buttons, and the control on this is poor. This seems like such a
fundamental task that it should be available by other means.
For the moment, you can ‘zoom’ via the font size menu - since the zoom
is simply implemented as a change in the alignment layout grid size (and
font size change).
We can certainly improve this: it could also be triggered by CTRL/CMD
+/-, as in browsers, or hooked up to mouse clicks via ALT and SHIFT/ALT.
We’ve also found that a pan/zoom mode is pretty essential when working
with big alignments, including support for trackpad/screen pinch-zoom
gestures. That is planned for a later release in the 2.11 series.
Are there any key combinations you’ve encountered that would be good for
Jalview to support ?
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