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New plugin request: Usearch (Read 7830 times)
Jul 13th, 2013 at 6:04am

Ron   Offline
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The Usearch program provides a very useful set of commands for high throughput searching and clustering.  I think it would be useful to include it as a plugin for Ugene.  The program is available (32-bit version is free) from the same web site as MUSCLE (drive5).
 
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Reply #1 - Jul 15th, 2013 at 1:45pm

Yuriy Vaskin   Offline
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Thanks for the suggestion!
Actually we thought of integrating usearch. Your request is a good reason to consider it more carefully (https://ugene.unipro.ru/tracker/browse/UGENE-1805).
You might find useful our clustering feature with phylogenetic trees. Just build a tree and switch on the clustering mode.
 
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Reply #2 - Jul 20th, 2013 at 6:27am

Ron   Offline
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> Just build a tree and switch on the clustering mode

Thanks Yuriy!  I will try it.  Could you tell me how to switch on the clustering mode?   I built a tree from an alignment, but I didn't see any option to switch on clustering mode (I'm using the latest UGENE).
 
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Reply #3 - Aug 8th, 2013 at 6:21pm

German   Offline
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Ron, if you want to try clustering mode in UGENE, you need to open the tree and the alignment synchronized.

For example, you could open an alignment and run the "Build tree" dialog. If you use the default settings (see the attached screenshot "tree 1.png") then the built tree will be opened synchronized with the alignment.

On the screenshot "tree 2.png" you can see the blue vertical line. Drag and drop the line to the left or to the right, and the sequences of tree's nodes which are on the right side of the line will be grouped into the clusters.

Also, you can open an existing tree but not build the new one (the screenshot "tree 3.png").
 

tree_1.png (156 KB | )
tree_1.png
tree_2.png (104 KB | )
tree_2.png
tree_3.png (140 KB | )
tree_3.png
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