Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
REL analysis (Read 1616 times)
jbragg
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 1
REL analysis
May 8th, 2014 at 8:23pm
 
Hello,

I'd be grateful for some assistance with troubleshooting. I've been running REL though hyphy (HYPHY 2.220140504 beta (MP) for Linux on x86_64) on my desktop ubuntu machine. However, I cannot reproduce the results of running  datamonkey on the same dataset. I expect there would be slight discrepancies, owing to the use of different models, etc, but the results seem to be strongly opposing. That is, on my desktop, I find 5 positively selected codons (BF cutoff = 20), and on datamonkey (Job ID:upload.45868464055980.1), four of these codon sites are found to be negatively selected.

A little more detail on the analyses on my desktop.

I started by estimating marginals. (Note, I made parameter files, and handed them to HYHYMP with system calls in perl, ie HYPHYMP < locus.params > std.out). The contents of the param file is below...

HYPHYMP
2
1
/home/jd/aln/ENSACAP00000021654_exon1_ambig.fa.macse.aln
1
/home/jd/hy/ENSACAP00000021654_exon1_ambig.fa.MG.tree
1
3
2
4
d
3
1
3
3
/home/jd/hy/ENSACAP00000021654_exon1_ambig.fa.rel.out

Then, I used Find Positively Selected Sites, as follows:

HYPHYMP
2
5
7
2
2
2
/home/jd/hy/ENSACAP00000021654_exon1_ambig.fa.rel.out.Dual.marginals
20
/home/jd/hy/ENSACAP00000021654_exon1_ambig.fa.ppr.out

This was the output
Counter Site Index      Log[BF{NS/S>1|s}]
1       84      2.671011887589512
2       167     2.757271429667007
3       185     2.780031678533128
4       257     2.673318104062748
5       283     2.73764052687031


But the datamonkey output looks like this:
Found 5 negatively selected sites (20 significance level)
Codon      E[dS]      E[dN]      Normalized E[dN-dS]      Posterior Probability      Bayes Factor
84      3.261      0.0792843      -3.18172      0.996993      34.7178
167      3.30716      0.0814483      -3.22571      0.997872      49.1188
185      3.27759      0.0796184      -3.19797      0.997315      38.9029
257      3.25518      0.0641413      -3.19104      0.997583      43.2157
283      3.27584      0.0764917      -3.19935      0.997411      40.341

I would be grateful for assistance in finding either 1. the source of my error, or 2. the source of my misunderstanding in interpreting the results.

thanks,
j.
Back to top
 
 
IP Logged