*contributor

It just a minor issue that has been described in the title.

When I upload a DNA alignment with the lowercases alphabet, neither color schemes were applied.
If I changed it to uppercases, it will work.

There should be a user manual with simple use case examples of the Javascript library. This is how MSAviewer works. The msa view module could then be used as a viewer for BLAST results.

Exampe: http://cpmb.lshtm.ac.uk/templates/showArch.php?cathcode=00003.00040.00050.00300&cathmethod=&cathcluster=&type=AS (?)

Heard this is already known, just putting here for reference:

Sometimes image view doesn't render unless one reduces the height/width pixels to 2 (Chrome) or 1 (Firefox). Not a problem with Safari, which renders which the default settings.

When uploading an empty MSA or one that contains only a single sequence, the website just stops during the loading/rendering process instead of providing any error/warning message. While such a MSA does not make much sense, this case can occur when the MSA and links to AlignmentViewer are generated programmatically.

In case of an empty alignment, the website just hangs at "reading MSA...", while a single-sequence MSA hangs at "rendering MSA .. 0%."

The sequence conservation – consensus sequence section does not use the same font size as the aligned sequences. The offset is visible when displaying ~500 columns and disturbing when displaying > 1000 columns.

Add example files necessary to run AlignmentViewer

I believe K should match R (red) but is currently green. Thank you in advance for fixing!

Misspelling in the the About text "multiple"

Please add alternative colouring schemes for viewing the alignments. It makes a surprisingly big difference for experienced users ability to interpret an alignment. I personally like the ClustalX colouring scheme that is widely adopted, but there are other popular schemes it would be nice to incorporate as options.

f1000

Maybe consider a ajax call instead of downloading the whole file

EVfold has been retired in favor of EVcouplings. The "load couplings" option on alignmentviewer uses the old csv file format of evfold. In evcouplings, a similar file to that provided by evfold exists, but the column names have been changed. Attached an example of such a file.

Note that I have changed the extension from csv to txt in order to upload it to GitHub, but the file will always come in .csv format: 7fc6a52079d9c810c14726423d724df5_b0.1_CouplingScores.csv.txt

In practice, from my understanding of how this used to be, this means changing the JS parser for the file to consider residue A as column "i", resudue B as column "j". The file is sorted; the first row needs to be ignored (headers).

@sacdallago Is it easily possible to change the EVCouplings div so that the markers look like circles? Why were ellipses chosen?

Is it possible to get example files for "upload annotations" and "load couplings" tabs for the existing example alignment "1bkr:A"? And link to them from somewhere in the example box that says: "Or use example alignment: 1bkr:A"

It may be useful to offer a ranking scheme that deliberately clusters sequences according to their local similarity to each other (ie maximising the clarity of these patterns), rather than comparing everything to the first sequence.

Change from sanderlab.org/alignmentviewer to alignmentviewer.org

Show EC pairs on the MSA. Show strength of pairs with line thickness.

For the top graph on the stats view the three colours used for max/average and min identity are hard to distinguish. Please use a broader colour palette. Please add axis legends for this graph and make it clearer what the title of this graph is. The title is very clear for the bottom plot.
F1000

Move site

@MercifulCode Are there limitations to the annotations that are displayed in the UMAP plot? I think HUMAN does not appear for these example files:

https://github.com/dfci/alignmentviewer/tree/master/example

These links: Or use example alignment: 1bkr:A, MYG, BLAT on main page

Merge MutationAssessor code specificity residue viewing

Add more info