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Emacs Bioinformatics - Ale Vs Biomode Vs Ralee

I use emacs a lot for coding bioinformatics work. I recently started looking into tools to help me look at my data in emacs as well. I'm mostly looking at fasta sequences, aligned and unaligned, although other other functionality is certainly welcome. Files can sometimes be large (>100mb)

A quick google search turned up the following:

ale
biomode
ralee

( http://en.wikipedia.org/wiki/List_of_alignment_visualization_software ).

Anyone have any experiences/recommendations as to which to use? Main concerns are whether the software is maintained (ie not software-rotting) and usability.

fasta
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updated by Ian Ian • written by Drj • Drj

Ale and Ralee are not updated often.

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written by Gjain Gjain

4 answers

You might want to check DNA mode (assuming you're working with nucleic acids).

Andreas

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written by Andreas Andreas

I realise this is another deviation from EMACS, but have you ever looked at SeaView? It is also available for Linux.

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written by Ian Ian

yeah, I've used seaview. I like it. It's my go-to sequence viewer when I'm not using a text editor.

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written by Drj • Drj

This post also suggests ralee with one comment saying it looked good.

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updated by Ram Ram • written by Chris Penkett • Chris Penkett

What About IGV? I am using it with ssh -X on the server, where our mappings are located.

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written by Mdeng Mdeng

IGV is unrelated to emacs, but it looks like a nice tool nonetheless. Surprisingly, it can't even load fasta alignments though! (it can only load fasta files as a reference sequence)

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written by Drj • Drj

Sorry my fault, IGV is only for BAM/SAM files.

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written by Mdeng Mdeng

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