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

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

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

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