int n1d = 4, M2a = 1, ternary = 1, trianglePriorM8 = 0, ip[4] = { 0 };
int n1d = 10, M2a = 1, ternary = 1, trianglePriorM8 = 0, ip[4] = { 0 };
Dear Ziheng,
I hope this message finds you well. I am revisiting results from an older codeml run (v4.9, model M8) and noticed significant differences and higher omega values when I reran it with a different version. Could you please clarify if there were any changes to codeml that might have caused this discrepancy? I encountered the same issue as the original poster, where I received 'nan' values, but this problem was resolved when I used the newer version. For version 4.9, I ran the analysis twice and obtained similar results and 'nan' values both times. The inputs for both versions were exactly the same.
Version 4.10.0
Snippet of output file
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: ref)
Pr(w>1) post mean +- SE for w
32 G 0.861 8.839 +- 3.410
70 G 0.897 9.191 +- 3.005
174 D 0.857 8.803 +- 3.445
Snippet of rst file
Bayes Empirical Bayes (BEB) probabilities for 11 classes (class) & postmean_w
(amino acids refer to 1st sequence: ref)
1 M 0.53875 0.08336 0.05745 0.04458 0.03627 0.03014 0.02521 0.02101 0.01735 0.01778 0.12812 ( 1) 1.468 +- 3.348
2 G 0.55965 0.08617 0.05894 0.04540 0.03667 0.03026 0.02514 0.02081 0.01708 0.01739 0.10250 ( 1) 1.209 +- 3.040
3 G 0.55965 0.08617 0.05894 0.04540 0.03667 0.03026 0.02514 0.02081 0.01708 0.01739 0.10250 ( 1) 1.209 +- 3.040
4 N 0.59409 0.09124 0.06217 0.04768 0.03834 0.03148 0.02602 0.02143 0.01749 0.01772 0.05233 ( 1) 0.705 +- 2.231
5 G 0.55965 0.08617 0.05894 0.04540 0.03667 0.03026 0.02514 0.02081 0.01708 0.01739 0.10250 ( 1) 1.209 +- 3.040
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32 G 0.02437 0.01086 0.01227 0.01315 0.01358 0.01364 0.01334 0.01270 0.01177 0.01333 0.86099 (11) 8.839 +- 3.410
Version 4.9, March 2015 (first run)
Snippet of output file
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: ref)
Pr(w>1) post mean +- SE for w
23 A 0.969* 1.554 +- 0.000
32 G 0.959* 1.500 +- 0.000
70 G 0.958* 1.497 +- 0.000
133 A 0.969* 1.554 +- 0.000
174 D 0.958* 1.498 +- 0.000
217 G 0.958* 1.503 +- 0.000
219 G 0.958* 1.470 +- 0.141
Snippet of rst file
1 M 0.00000 nan nan nan nan nan nan nan nan 0.00000 nan(1) 0.000+-0.000
2 G 0.00000 nan nan nan nan nan nan nan nan 0.00000 nan(1) 0.000+-0.000
3 G 0.00000 nan nan nan nan nan nan nan nan 0.00000 nan(1) 0.000+-0.000
4 N 0.00000 nan nan nan nan nan nan nan nan 0.00000 nan(1) 0.000+-0.000
5 G 0.00000 nan nan nan nan nan nan nan nan 0.00000 nan(1) 0.000+-0.000
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32 G 0.00000 0.00051 0.00126 0.00245 0.00425 0.00702 0.01152 0.01971 0.03898 0.00000 0.95851(11) 1.500+-0.000