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hubertofliege 07-25-2012 10:27 AM

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?


A_Morozov 08-01-2012 07:28 PM

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.

colindaven 08-02-2012 03:47 AM

Artemis is good, but maybe MEGA is more similar to Jalview (can't be sure from your description).

A_Morozov 08-06-2012 09:02 PM

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.

AndrewC 08-07-2012 02:49 AM

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.

Clustal Omega, MUSCLE etc:

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