Need a sequence viewer

hubertofliege · 07-25-2012, 10:27 AM

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.

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.

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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07-25-2012, 10:27 AM	#1
hubertofliege Junior Member Location: Los Angeles Join Date: Mar 2012 Posts: 4	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.

08-01-2012, 07:28 PM	#2
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	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.

08-02-2012, 03:47 AM	#3
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Artemis is good, but maybe MEGA is more similar to Jalview (can't be sure from your description).

08-06-2012, 09:02 PM	#4
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	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.

08-07-2012, 02:49 AM	#5
AndrewC Junior Member Location: UK Join Date: Jul 2012 Posts: 2	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/