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tree view and distance matrix (Read 2569 times)

wdeng YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 2	tree view and distance matrix Dec 28^th, 2006 at 11:02am Hi, I am a newbie of this field. I used PAUP before and applied PAUP block to view the tree, define the MRCA, retrieve sequence of MRCA and get the distance matrix. I am wondering if I can do these through Hyphy batch file and how to do? Thanks! wdeng
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: tree view and distance matrix Reply #1 - Dec 28^th, 2006 at 4:41pm Dear wdeng, All of these actions are possible to perform with HyPhy batch language scripts, but the syntax and logic are quite distinct from PAUP*. Could you describe, as precisely as possible, what it is that you would like the script to do, and I'll try to sketch out the relevant code for you. Cheers, Sergei
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wdeng YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 2	Re: tree view and distance matrix Reply #2 - Dec 28^th, 2006 at 5:24pm Hi Sergei, Thank you very much. What I would like to do is that taking nucleotide sequence alignment, newick tree and a list of ingroup sequence names as input and using REV model, outputs MRCA sequence of those ingroup sequences and pairwise distance matrix among sequences (including MRCA). Best, wdeng
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Sergei

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Re: tree view and distance matrix
Reply #3 - Jan 8^th, 2007 at 10:58pm

Dear wdeng,

You can find the script which does this, allowing you to specify the model and the ingroup sequences interactively at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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You can download and run it via the menu command 'File>Open>Open Batch File.bf'.

The MRCA sequences is output to the console, and the distance matrix - to a file.

There are some comments in the file about what the blocks do.

Cheers,
Sergei

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

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