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Old 07-25-2012, 09:27 AM   #1
hubertofliege
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Location: Los Angeles

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Default Need a sequence viewer

I need a sequence viewer to do basic alignments of functional genes, but for some reason, MEGA has stopped working. It crashes whenever I try to open files or old sessions. It happens on both my Ubuntu machine and on a Mac my lab has.

I did a google search, but most of these viewers are rather old. Can anyone recommend a reliable sequence viewer?

Thanks.
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Old 08-01-2012, 06:28 PM   #2
A_Morozov
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Artemis - a java-based viewer with ability to search for ORFs and do other simple analyses. Interface is not so great, though.
Unipro Ugene - a real awesome software, including seq viewer, workflow designer and nearly any tool people often use (blast, bunch of alignment tools, etc). Can't be sure, but I think it can even read assemblies.
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Old 08-02-2012, 02:47 AM   #3
colindaven
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Artemis is good, but maybe MEGA is more similar to Jalview (can't be sure from your description).
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Old 08-06-2012, 08:02 PM   #4
A_Morozov
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BtW, why do you need a viewer for basic alignments? If they are for further analysis (ie phylogenies, building some sort of models, etc) command-line tools like clustalw or muscle should be ok.
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Old 08-07-2012, 01:49 AM   #5
AndrewC
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For desktop viewing/simple manual alignment editing you could use Jalview or GeneDoc. If you want to perform more demanding alignments and don't want to use the command line then there are a number of web based multiple sequence alignment tools available for example Clustal Omega or MUSCLE.

Jalview: http://www.jalview.org/overview.html
GeneDoc: http://www.nrbsc.org/gfx/genedoc/
Clustal Omega, MUSCLE etc: http://www.ebi.ac.uk/Tools/msa/
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