Question: Emacs Bioinformatics - Ale Vs Biomode Vs Ralee
5
gravatar for Drj
7.2 years ago by
Drj60
Drj60 wrote:

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 • 2.6k views
ADD COMMENTlink written 7.2 years ago by Drj60

Ale and Ralee are not updated often.

ADD REPLYlink written 7.2 years ago by Gjain5.3k
2
gravatar for Andreas
7.2 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

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

Andreas

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Andreas2.4k
2
gravatar for Ian
7.2 years ago by
Ian5.3k
University of Manchester, UK
Ian5.3k wrote:

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

ADD COMMENTlink written 7.2 years ago by Ian5.3k

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

ADD REPLYlink written 7.2 years ago by Drj60
1
gravatar for Chris Penkett
7.2 years ago by
Chris Penkett470
Cambridge, UK
Chris Penkett470 wrote:

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

http://biostar.stackexchange.com/questions/14885/vim-highlighting-for-msa

ADD COMMENTlink written 7.2 years ago by Chris Penkett470
0
gravatar for Mdeng
7.2 years ago by
Mdeng520
Germany
Mdeng520 wrote:

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

ADD COMMENTlink written 7.2 years ago by Mdeng520
1

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)

ADD REPLYlink written 7.2 years ago by Drj60

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

ADD REPLYlink written 7.2 years ago by Mdeng520
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