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Infer tree for each partition (Read 2987 times)

Miguel Junior Member Offline Hi Hyphy! Posts: 53 CBMSO, CSIC (Spain) Gender:	Infer tree for each partition Sep 28^th, 2006 at 8:27am Hi, In several sequences with several partitions, I'd like infer one tree for each partition, with for example NeighborJoining, so finally we can obtain several trees with diferent topology (each tree from each partition). Is it possible? What can I do for that?. I'm starting to use Hyphy, I like it. Thanks you! Miguel
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Sergei

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Re: Infer tree for each partition
Reply #1 - Sep 28^th, 2006 at 9:38am

Dear Miguel,

Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login for a general guide on how to infer trees using the GUI.

If you want to use only a part of the data, you can define the partition you are inferring the tree from to include only that part.

HTH,
Sergei

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Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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David

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Re: Infer tree for each partition
Reply #2 - Sep 29^th, 2006 at 3:06am

Dear Sergei,

Actually the tutorial above does not use several partitions. Basically we want to infer a tree independently for each partition. Basically we specify the partitions, select "infer tree" and then go to inference. What we are getting is 3 trees with a common topology (that for the whole alignment) with branches optimized for each partition. We want to obtain independent topologies also. I guess this can be done deleting and saving, but is it possible to do this automatically?

Best,

D.

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Sergei

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Re: Infer tree for each partition
Reply #3 - Sep 29^th, 2006 at 7:27am

Dear David,

That's right - when you select 'Infer Tree' from multiple partitions, it is actually inferred jointly from all of them. Doesn't make much sense for NJ, because you get the same tree as you would from the entire alignment, but it does for ML, where you search the tree space using joint LF from all partitions.

I can add the option of reconstructing each tree independently in the GUI, but the easiest way to do this with existing codebase (especially if you want to do this many times), would be to put together a little batch file.

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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