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HYPHY Package >> Feature Additions >> [IMPLEMENTED REQUEST] Wong-Nielsen selection test
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Message started by ofedrigo on Sep 27th, 2005 at 7:02am

Title: [IMPLEMENTED REQUEST] Wong-Nielsen selection test
Post by ofedrigo on Sep 27th, 2005 at 7:02am
Hi,

I try to implement Wong and Nielsen selection test for non-coding sequences in hyphy. Briefly this method is a modification of Yang and Nielsen test on coding regions.The difference is that new method uses two parititions (coding and non-coding) under two models (codon model and HKY). The HKY model has an additonal parameter zeta that is the rate normalized by the sysnonymous rate of the coding partition.

I am a novice in hyphy and can't figure out how to set up this zeta parameter in hyphy.

any advice?

thanks a lot

Olivier

Duke university
Biology Department

Title: Re: Wong-Nielsen selection test
Post by Sergei on Sep 27th, 2005 at 11:29am
Dear Olivier,

To set up this test one needs to write a custom batch file, which I'll be happy to do since it might be of general interest and will take me very little time to write.

As input in can either take:

1). Two separate sequence files (coding and noncoding) but with the same tree and the same number of sequences

2). A joint NEXUS file where coding and noncoding parts are defined as NEXUS CHARSETS

Which is easier?

Cheers,
Sergei

Title: Re: Wong-Nielsen selection test
Post by ofedrigo on Sep 27th, 2005 at 11:39am
hi Sergei,

it would be great if you can do it. I tried to modify the Yang & Nielsen test batch file but there are quite a bit of functionalities of the code that I do not understand yet.

to answer your question, two separate sequence files (coding and noncoding) will be the best.
eventually I would like to modify it later in order to use an intron as a neutral proxy as well (using the rate of the intron instead of ds to normalize zeta). this will be certainly relatively straighforward from your code.

thanks a lot,

Olivier

Title: Re: Wong-Nielsen selection test
Post by Sergei on Sep 27th, 2005 at 2:37pm
Dear Olivier,

Would you mind e-mailing me (help.at.datamonkey.org) some sample data, so I can debug the analysis before I post it?

Cheers,
Sergei

Title: Re: [REQUEST] Wong-Nielsen selection test
Post by Sergei on Sep 29th, 2005 at 11:00pm
Dear Olivier,

Here's a barebones (but self-contained) Wong-Nielsen analysis. I can't really test it because the Genetics paper doesn't point to any alignments downloadable that I can try it on:(

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Cheers,
Sergei

Title: Re: [IMPLEMENTED REQUEST]Wong-Nielsen selection test
Post by nica on Dec 15th, 2012 at 2:56am
Hi!

Just to make sure I understood properly, I will need to download HyPhy and implement the batch file there. There is no way of doing this in the datamokey server, right?

I have a very slow computer  :-[

Title: Re: [IMPLEMENTED REQUEST]Wong-Nielsen selection test
Post by Sergei on Dec 18th, 2012 at 8:21am
Hi Nica,

You are correct -- these analyses must be run on your computer. On the positive side, they should not be TOO CPU intensive.

Sergei

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