kevintz wrote on Jan 18
th, 2009 at 10:41am:
Dear Sergei,
Sorry to bother you again.
I read your article on journal Gene 397 (2007) 38-50, entitled "Evolution of the interferon alpha gene family in eutherian mammals", and found Table 1 refered to KH tesing with all the P-value <0.01. While in my data set, the KH testing resluts show the p-value much smaller as far as 0.001. As you said, Bonferroni correction might be performed. So, my question is does the KH test doing Bonferroni correction automatically? if not, how? if yes, why not to refer in the article?
Thanks a million.
Best regards,
Tu Zeng
Dear Sergei,
I am very interested in the table 1 of above paper, and I also several basice questions aobut it.
1. Where can I find the AICc improvement in my KH test result file? for example from my attached file. Is it
Delta AIC = 280.92?2. Where can I find the LHS vs. RHS and RHS vs LHS. For example from my attached file.
Thank you very much!!
Sundy
Due to the character limitation, I deleted the "Tree aTree=[...]" and attached the entire file.
****************
Loaded 5 partitions
Sequences :10
Sites :3666
Variable :539
f(A) = 0.285291
f(C) = 0.227325
f(G) = 0.205476
f(T) = 0.281908
c-AIC = 17279.5
Log Likelihood = -8614.56089283971;
Shared Parameters:
GT=0.221445=0.221445
CT=1.90112=1.90112
CG=0.10546=0.10546
AT=0.471935=0.471935
AC=0.281374=0.281374
alpha=0.0102205=0.0102205
betaQ=3.72107=3.72107
betaP=4.31789=4.31789
Tree givenTree=(((Bat_SARS_273_DQ648856:0.0496989,((Bat_SARS_279_DQ648857:0.0282901,B
at_SARS_Rp_DQ071615:0.0244375)Node5:0.00575514,Bat_SARS_HKU3_DQ022305:0.0359314)
Node4:0.0267917)Node2:0.0374558,3_HP03E_GZ02:0.000232858)Node1:0.000864494,(130_
PC03_SZ13:0.000540745,(110_PC04_PC4_136:0.00192447,106_HP04_GZ0402:0.00137285)No
de12:0.0016568)Node10:0.00110442,(15_HP03M_BJ02:0.000823405,31_HP03L_Tor2:0.0002
70703)Node15:0.000270703);
Mean divergence : 6.49111%
Fitting a single-tree, multiple partition model
Log Likelihood = -8578.32862962121;
Shared Parameters:
S_1=0.92014
S_2=0.382852
S_3=0.560115
S_4=0.375399
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree tree_0=
Fitting a mutilple tree, multiple partition model
Log Likelihood = -8403.83189116324;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree tree_0=
Versus the single partition model: c-AIC = 16998.6
Delta AIC = 280.92
Versus the single tree/multiple partition model: Delta AIC = 216.577
Partition 1 : 381 sites
Partition 2 : 343 sites
Partition 3 : 1080 sites
Partition 4 : 722 sites
Partition 5 : 1140 sites
Fitting tree 1 to partition 1
Log Likelihood = -1181.64638188419;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 2 to partition 1
Log Likelihood = -1195.56564111684;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
KH Testing partition 1
Tree 2 base LRT = 27.8385. p-value = 0.025
Fitting tree 1 to partition 2
Log Likelihood = -977.448251979626;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 2 to partition 2
Log Likelihood = -968.982471135205;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 3 to partition 2
Log Likelihood = -972.312843728842;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
KH Testing partition 2
Tree 1 base LRT = 16.9316. p-value = 0.0001
Tree 3 base LRT = 6.66075. p-value = 0.0001
Fitting tree 2 to partition 3
Log Likelihood = -2258.19915763715;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 3 to partition 3
Log Likelihood = -2244.90399830231;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 4 to partition 3
Log Likelihood = -2285.99836857422;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
KH Testing partition 3
Tree 2 base LRT = 26.5903. p-value = 0.0001
Tree 4 base LRT = 82.1887. p-value = 0.0001
Fitting tree 3 to partition 4
Log Likelihood = -1640.47340028827;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 4 to partition 4
Log Likelihood = -1632.78789828693;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 5 to partition 4
Log Likelihood = -1639.94300504171;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
KH Testing partition 4
Tree 3 base LRT = 15.371. p-value = 0.0001
Tree 5 base LRT = 14.3102. p-value = 0.0001
Fitting tree 4 to partition 5
Log Likelihood = -2375.98828232171;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
Fitting tree 5 to partition 5
Log Likelihood = -2375.51119382618;
Shared Parameters:
betaP=4.31789=4.31789
betaQ=3.72107=3.72107
alpha=0.0102205=0.0102205
AC=0.281374=0.281374
AT=0.471935=0.471935
CG=0.10546=0.10546
CT=1.90112=1.90112
GT=0.221445=0.221445
Tree aTree=
KH Testing partition 5
Tree 4 base LRT = 0.954177. p-value = 0.0001
A total of 3/4 significant couplings
Mean splits identify: 0.26
***********************