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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> MEME output http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1368119957 Message started by matias on May 9^th, 2013 at 10:19am

Title: MEME output
Post by matias on May 9^th, 2013 at 10:19am

Hello, I am running hyphy localyon ubuntu, MEME option with user given tree and i got the two output files x.results and x.results.branches

In the x.results.branches file there is a tree included, but this tree is not equal to the one specified to be use during the input options.

I found no explanation to this, any idea about this tree?

Title: Re: MEME output
Post by Sergei on May 9^th, 2013 at 11:52am

Hi there,

This should be the same tree just rooted on a different branch. The .branches file is meant to be used for downstream processing to identify individual branches under selection.

Sergei

Title: Re: MEME output
Post by matias on May 9^th, 2013 at 12:22pm

Hi, thanks for your response.

So, if I am running MEME with an unique tree on 2 thousands diferent genes I will always get same root and what is more important same "Node number" asignation for each tree nodes of them. Is this correct?