How to get image of mutliple alignment sequence that is labeled by row?

Question

[dec986]

I have been looking at many, many different multiple sequence alignment software packages. There's a post that I was using earlier from BioStars, but I can't find it anymore.

1. ADOMA doesn’t produce anything. There is no error message, just blank HTML
2. ESPript, which requires faxing or snail-mailing a license request, and waiting for a reply. Their download page is 404.
3. alv, which only prints to a terminal and cannot be saved to an output file
4. clustalo, which cannot print colored output, only through the web server, and cannot be scripted, which is unacceptable
5. texshade, which doesn’t work at all
6. CIAlign is the best so far, but cannot label rows or columns
7. alan would be nice, but again is terminal-only. When attempting to save to a file, the text becomes mangled
8. msa which does not label the rows, and does not have multiple coloring
9. ggmsa in R, which can't install on my version of R (ugh), and won't install with bioconductor either
10. ggtree in R, which can't install on my version of R, and won't install with bioconductor either
11. pymsaploter, which can't handle proteins
12. Wasabi, which cannot run at the command line
13. rMSA, which cannot work with my version of bioconductor or R
14. gmsa, which makes very poor quality images of large alignments

The best so far, though still lacking, is CIAlign,

the above is a low-resolution image of a SVG file.

I've opened an issue on CIAlign's GitHub page https://github.com/KatyBrown/CIAlign/issues/55, but guessing by many older, unanswered issues being there, I think my issue getting resolved that way is unlikely, so I'm posting here.

I'd like to be able to add x axis labels, titles, y axis labels especially, making interpreting these figures much easier.

Jalview seemed to work, but doesn't visualize very well for 2000 amino acid residues.

I'd like SVG or even EPS output, which looks much better than PNG or JPG.

How can I add row labels automatically using any multiple alignment visualization software?

[cmdcolin]

not sure if any exact tool might fit your needs but i have a list of many MSA tools here :) https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=MSA

[dec986]

thanks, I'm encountering problems with all of the programs there, unfortunately. By the way, most links for Boxshade are either 403 or 404

[cmdcolin]

dang, kudos for trying the many options available though! ill try to find a better boxshade link but the description recommends e.g. trying apt install boxshade, the link that is there was a webserver that helped automate it but command line is possible too. and indeed, sometimes it can end up that coding your own is the best way to go. though it can be tedious, hand generating SVG is possible, or maybe using R is possible too with e.g. ggplot geoms or something

Answer 1

[dec986]

I solved the problem by making my own, greatly-reduced, version of CIAlign's code.

[GenoMax]

You can put the code in a GitHub gist and the simply paste the link here. Biostars will render the code inline.

[dec986]

thanks, I've learned how to do a gitHub gist and have pasted the code into my original answer.