Hello!

I've been trying to find a software that does what the post title describes, but without luck. I tried installing JalView but it won't install for some reason "Installer User Interface Mode Not Supported".

I have hundreds of images to generate so going to a browser MSA viewer and manually saving is not feasible. Am I out of luck or just bad at googling?

Big thanks in advance!
There’s a commandline version of `Espript` IIRC. That would probably work.

I also like the TeX package `texshade` for rendering MSAs, if you’re prepared to get your hands dirty with TeX.

<s>I’ll post an example when I’m at a proper computer.</s>

Finally at a computer, so here's an example of something you can do with TeXShade. You can of course run TeX from the commandline. It would probably be sufficient to write a wrapper script to inject the file names, or to actually write the source itself for you.


    \documentclass[a4paper, oneside, 11pt]{report} % Doc Setup
    \usepackage[left=1cm, right=1cm, top=1cm, bottom=1cm]{geometry}  % Doc Geometry
    \usepackage{texshade}
    \usepackage{lscape}
    
    \begin{document}
    \begin{landscape}
    
    \begin{texshade}{/path/to/your/alignment.ext}
      \seqtype{P}
      \setfont{numbering}{tt}{md}{sc}{small}
      \setfont{names}{tt}{md}{up}{tiny}
      \setfont{residues}{tt}{md}{sc}{tiny}
      \setfont{ruler}{tt}{bf}{sc}{tiny}
      \shadingmode[allmatchspecial]{similar}
      \feature{top}{1}{25..25}{fill:$\downarrow$}{Hi, I'm an annotation}
      \feature{bottom}{1}{70..76}{brace}{So am I!}
    \end{texshade}
    \end{landscape}
    
    \end{document}

This creates:

<a href="https://ibb.co/GRQg3PG"><img src="https://i.ibb.co/SBwq7vH/Screenshot-2019-06-17-at-10-39-39.png" alt="Screenshot-2019-06-17-at-10-39-39" border="0"></a>


It might not be a perfect solution, as you'd need to play with the sizing etc, or perhaps figure it out dynamically. I *think* `Espript` actually runs LaTeX behind the scenes anyway.