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How do I interpret the results of TestBranchDNDS? (Read 964 times)
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How do I interpret the results of TestBranchDNDS?
Feb 16th, 2010 at 12:16pm
 
I ran TestBranchDNDS.bf and got a significant result.  I conclude that p < 0.05 means that there is a different dN/dS ratio on the branch that I selected.  But I'd also like to know the direction and magnitude of that difference.  Is there a way to collect that information?
Code:
1. Working on the null hypothesis.
Log Likelihood = -22513.0448697087;
Shared Parameters:
SharedNS1=0.820031
AC=0.936292
beta=0.764526
betaNSQ=7.38625
betaNSP=0.665395

Tree givenTree=((((ADEH_3064:633.747,((GBEM_1131:263.999,GSU2501:22.2845)Node6:17.0548,((GBEM_2680:158.449,GEOB_3155:0)Node10:77.767,(GURA_2004:13.3738,((GURA_1989:1.29475,GEOB_3166:0.353959)Node16:22.4046,(GBEM_1117:203.425,GBEM_1116:0)Node19:0)Node15:70.1522)Node13:49.4068)Node9:18.7198)Node5:0)Node3:0,GBEM_2659:223.044)Node2:0,GSU0701:58.5615)Node1:24.9835,GSU2503_OMCT_:0.520083,GSU2504_OMCS_:1.03642);

2. Working on the alternative hypothesis.
Log Likelihood = -22503.4438398671;
Shared Parameters:
SharedNS1=0.822401
betaNSP=0.416705
betaNSQ=3.5276
beta=0.752277
AC=0.892497

Tree givenTree=((((ADEH_3064:1566.79,((GBEM_1131:175.701,GSU2501:24.8875)Node6:0,((GBEM_2680:269.673,GEOB_3155:14.6207)Node10:58.3737,(GURA_2004:56.1702,((GURA_1989:1.16252,GEOB_3166:0.525991)Node16:16.4449,(GBEM_1117:303.635,GBEM_1116:0)Node19:0)Node15:35.7743)Node13:73.809)Node9:0)Node5:0.0670826)Node3:1.64666,GBEM_2659:196.4)Node2:0,GSU0701:47.0546)Node1:53.1492,GSU2503_OMCT_:0,GSU2504_OMCS_:1.57966);
Branch parameter estimates

givenTree.GSU2504_OMCS_.nsClass1 = 0.8497, 95% CI: 0.683963-1.11124


-2(Ln Likelihood Difference)=19.2021
Difference in number of parameters:1
p-value:1.17586e-05
 

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