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Methodology Questions >> How to >> tree view and distance matrix http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1167332536 Message started by wdeng on Dec 28th, 2006 at 11:02am |
Title: tree view and distance matrix Post by wdeng on Dec 28th, 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 |
Title: Re: tree view and distance matrix Post by Sergei on Dec 28th, 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 |
Title: Re: tree view and distance matrix Post by wdeng on Dec 28th, 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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