Question

Emacs Bioinformatics - Ale Vs Biomode Vs Ralee

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12.3 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 • 4.4k views

ADD COMMENT • link updated 12.3 years ago by Ian 6.0k • written 12.3 years ago by Drj ▴ 60

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Ale and Ralee are not updated often.

ADD REPLY • link 12.3 years ago by Gjain 5.8k

score 2 · Answer 1 · 2012-01-04

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12.3 years ago

Andreas ★ 2.5k

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

Andreas

ADD COMMENT • link 12.3 years ago by Andreas ★ 2.5k

score 2 · Answer 2 · 2012-01-04

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12.3 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.

ADD COMMENT • link 12.3 years ago by Ian 6.0k

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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.

ADD REPLY • link 12.3 years ago by Drj ▴ 60

Ram · Answer 3 · 2012-01-03

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12.3 years ago

Chris Penkett ▴ 490

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

ADD COMMENT • link updated 4.6 years ago by Ram 43k • written 12.3 years ago by Chris Penkett ▴ 490

score 0 · Answer 4 · 2012-01-03

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12.3 years ago

Mdeng ▴ 520

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

ADD COMMENT • link 12.3 years ago by Mdeng ▴ 520

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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)