How to extract sequences from tree based on bootstrap value

[Vivek Keshri]

Dear Group members, 

Good Morning !!

I am using FigTree v1.4.2, I want to extract only those sequnces or Taxa from phylogeteic tree which has >80% bootstrap value. Please let me know any easy way  ...

Waiting for favorable response... 

Sincerely 

Vivek Keshri 

[Ryan Ellingson]

Hi Vivek,

If I understand your question correctly, what you're trying to do is kind of impossible because support values refer to nodes on the tree, not to individual taxa. I'm not sure what your motivation is, but I would recommend not removing taxa with low support anyway. I think most people would agree that the proper way to present a tree with low support values is to collapse those particular nodes into polytomies so that any uncertainty in the topology is clearly shown, although I'd be interested to hear opposing arguments if they're out there.

Cheers,

Ryan

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[Rachel]

hi all-

my interest is related to this, so I'm posting here instead of de novo:

I want to export the node support for my tree, so that I can prep my tree for publication in a program that CAN collapse nodes with poor support (FigTree cannot last I checked).

I've explored the exporting features of FigTree, and so far things aren't working. I see that I can select annotations, and then chose to export annotations in the nexus file. the problem is that I don't see how internal nodes are named or designated in figtree. anyone?

Rachel

[Vivek Keshri]

Dear Ryan, 

Thank you very much for your reply. I would like to simplify my question. Actually I want to condense nodes based bootstrap values, like this image (http://openi.nlm.nih.gov/imgs/512/198/3407896/3407896_viruses-04-01093-g002.png).

Let me know whether it is possible or not in FigTree v1.4.2. 

Sincerely, 

Vivek Keshri 

[William Gearty]

I do not believe that functionality is included in FigTree, but there a number of other programs that can handle this.

I would suggest another tree viewer, Tree Graph: http://treegraph.bioinfweb.info/.

The documentation on the function you are interested in can be found here: http://treegraph.bioinfweb.info/Help/wiki/Collapsing_nodes_by_support.

Good luck,

Will

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William Gearty

people.stanford.edu/wgearty

[Vivek Keshri]

Thank you very much William. Yes it is interesting application. I will try for the same, 

Thanks a lot 

Vivek