Emacs Bioinformatics - Ale Vs Biomode Vs Ralee
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12.5 years ago
Drj ▴ 60

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 • 4.5k views
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Ale and Ralee are not updated often.

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12.4 years ago
Andreas ★ 2.5k

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

Andreas

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12.4 years ago
Ian 6.0k

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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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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12.5 years ago
Chris Penkett ▴ 490

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

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12.5 years ago
Mdeng ▴ 520

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

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

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