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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Batch file for the MEME model http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1358521111 Message started by pixel on Jan 18^th, 2013 at 6:58am

Title: Batch file for the MEME model
Post by pixel on Jan 18^th, 2013 at 6:58am

Hello!
Is there any batch file for the MEME model and if not how could I use it througth the command lines?
Thanks in advance!

Title: Re: Batch file for the MEME model
Post by Sergei on Jan 18^th, 2013 at 9:11am

Hi Pixel,

MEME is an option for QuickSelectionDetection.bf.

Follow the steps you would for SLAC (e.g. Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login) until you get the dialog for "ANCESTOR COUNTING OPTIONS" (badly named, I agree). Then select MEME, the p-value, and decline to save individual fit files to disk.

Sergei

Title: Re: Batch file for the MEME model
Post by pixel on Jan 21^st, 2013 at 8:48am

Thank you very much! So after the running I have two outputs (attached files). In the file meme1.out, I have the values givenTree.XXX.t . Are those values the significant probabilities for each branch being under positive selection or is it something else? In the meme2.out file, the tree that is given is with the estimated branch lengths. Isn't it?

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=meme.zip (93 KB | 4 )

Title: Re: Batch file for the MEME model
Post by Sergei on Jan 21^st, 2013 at 3:30pm

Hi there,

There should also be a CSV file with p-values for positive selection and other parameter estimates for each site. Your 1st file is the nucleotide model fit (not to be interpreted as anything in particular), and the second file is more detailed branch-site information. It can either be read directly, or visualized with the help of the attached batch file.

Sergei

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=MEME_plotter.bf (4 KB | 16 )

Title: Re: Batch file for the MEME model
Post by pixel on Jan 22^nd, 2013 at 2:39am

Thank you! I am runnîng it on Ubuntu so I don't have the csv file. Is it possible to have on Ubuntu too? Is there any information about the significant probabilities for each branch being under positive selection?

Title: Re: Batch file for the MEME model
Post by Sergei on Jan 23^rd, 2013 at 10:55am

Hi there,

There should definitely be a final CSV output (the one you specify in response to "Save site-by-site LRT results to"), regardless of the platform.
This file will give you p-values for having each SITE subject to diversifying selection (BranchSiteREL will give you the same for BRANCHES).

Sergei

pixel wrote on Jan 22^nd, 2013 at 2:39am:

Thank you! I am runnîng it on Ubuntu so
I don't have the csv file. Is it possible to have on Ubuntu too? Is there any information about the
significant probabilities for each branch being under positive selection?

Title: Re: Batch file for the MEME model
Post by pixel on Feb 27^th, 2013 at 7:48am

Thank you! I will try to keep the CSV file!