Analysis software

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camembert
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Analysis software

Is there somebody who knows another program which compares alligments and trees all in one?

joaquin939
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What type of trees?

What type of trees?

camembert
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joaquin939 wrote:What type of

joaquin939 wrote:

What type of trees?

genomic trees

albinpaul
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Ocimum Biosolutions offers

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

bgood
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camembert wrote:Is there

camembert wrote:

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.

bgood
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You might have a look at http

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.

camembert
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bgood wrote:camembert wrote

bgood wrote:

camembert wrote:
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

Scot E. DOwd Ph.D.
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DNAstar's megalign has this

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.

ryan_m
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Scot E. DOwd Ph.D. wrote

Scot E. DOwd Ph.D. wrote:

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.