Analysis software [View Printable]
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camembert
Group: Member
Posts: 31
Joined: Dec 21, 2004
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Is there somebody who knows another program which compares alligments and trees all in one? |
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 Posted Feb 02, 2005, 16:51 PM |
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joaquin939
Group: Member
Posts: 44
Joined: Feb 06, 2005
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| Posted Feb 28, 2005, 0:16 AM |
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camembert
Group: Member
Posts: 31
Joined: Dec 21, 2004
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| joaquin939 said: | | What type of trees? |
genomic trees |
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| Posted Feb 28, 2005, 16:11 PM |
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albinpaul
Group: Member
Posts: 2
Joined: Aug 28, 2006
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Ocimum Biosolutions offers two software Genowiz and Genchek that offers tree view and many more feaures all in one. for details visit www.coimumbio.com
thanks
Albin Paul
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| Posted Aug 28, 2006, 9:07 AM |
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bgood
Group: Moderators
Posts: 154
Joined: Apr 12, 2006
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| camembert said: | | Is there somebody who knows another program which compares alligments and trees all in one? |
Do you mean phylogenetic trees? I'm not sure exactly what "genomic trees" means. |
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| Posted Aug 28, 2006, 16:02 PM |
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bgood
Group: Moderators
Posts: 154
Joined: Apr 12, 2006
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You might have a look at http://hyphy.org/ for creating phylogenetic trees using pretty much any method you like. I don't think that it incorporates the multiple alignment step inside it, but this may be a developing feature. For multiple alignments you could of course use ClustalW - which did have some minimal tree-building components in it the last time I checked. You might also have a look at Multalign. I'd be curious to hear your experiences with these. |
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| Posted Aug 28, 2006, 18:51 PM |
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camembert
Group: Member
Posts: 31
Joined: Dec 21, 2004
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| bgood said: | | camembert said: | | Is there somebody who knows another program which compares alligments and trees all in one? |
Do you mean phylogenetic trees? I'm not sure exactly what "genomic trees" means. |
Yes I mean phylogenetic trees |
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| Posted Aug 29, 2006, 15:48 PM |
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Scot E. DOwd Ph.D.
Group: Member
Posts: 119
Joined: Dec 28, 2004
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DNAstar's megalign has this type of functionality based upon clustalX or W. This would allow for generation of a multiple alignment and viewing of the associated tree.
It sounded at first like you want to compare one tree to another? This would be a differnt type of beast to conquer. |
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ryan_m
Group: Moderators
Posts: 279
Joined: May 06, 2006
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| Scot E. DOwd Ph.D. said: | DNAstar's megalign has this type of functionality based upon clustalX or W. This would allow for generation of a multiple alignment and viewing of the associated tree.
It sounded at first like you want to compare one tree to another? This would be a differnt type of beast to conquer. |
If you wanted to go this route you could simply use ClustalX as well. It has an implementation of the Neighbor-joining algorithm and does bootstrapping. It really depends on what you want to accomplish. |
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| Posted Jan 03, 2007, 20:22 PM |
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