1
0 * 0,1:seqs or patters in paml format (mc.paml); 2:paup format (mc.nex)
2
13147 * random number seed (odd number)
3
4 10000 10 * <# seqs> <# codons> <# replicates>
5
1.5 * <tree length; see note below; use -1 if tree below has absolute branch lengths>
6
((1 :0.1, 2 :0.2) :0.12, 3 :0.3, 4 :0.4);
11
0.00983798 0.01745548 0.00222048 0.01443315
12
0.00844604 0.01498576 0.00190632 0.01239105
13
0.01064012 0.01887870 0 0
14
0.00469486 0.00833007 0 0.00688776
15
0.01592816 0.02826125 0.00359507 0.02336796
16
0.01367453 0.02426265 0.00308642 0.02006170
17
0.01722686 0.03056552 0.00388819 0.02527326
18
0.00760121 0.01348678 0.00171563 0.01115161
19
0.01574077 0.02792876 0.00355278 0.02309304
20
0.01351366 0.02397721 0.00305010 0.01982568
21
0.01702419 0.03020593 0.00384245 0.02497593
22
0.00751178 0.01332811 0.00169545 0.01102042
23
0.02525082 0.04480239 0.00569924 0.03704508
24
0.02167816 0.03846344 0.00489288 0.03180369
25
0.02730964 0.04845534 0.00616393 0.04006555
26
0.01205015 0.02138052 0.00271978 0.01767859
30
============================================================================
31
Change values of parameters, but do not delete them. You can add
32
empty lines, but do not break one line into several lines.
34
Note that tree length and branch lengths under the codon model are
35
measured by the expected number of nucleotide substitutions per codon
36
(see Goldman & Yang 1994). For amino acid models, they are defined as
37
the expected number of amino acid changes per amino acid site.
39
64 codon freqs are in fixed order TTT, TTC, TTA, TTG, TCT, TCC, ..., GGG,
40
from abglobin.nuc under the F3x4 table
42
=================!! Check screen output carefully!! ========================
46
mtCDNAape.nuc (7 apes):
47
position 1: T:0.20517 C:0.28293 A:0.30784 G:0.20406
48
position 2: T:0.40979 C:0.27911 A:0.18995 G:0.12116
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position 3: T:0.15105 C:0.43290 A:0.37123 G:0.04482
51
0.013116 0.037590 0.032235 0.003892
52
0.008933 0.025603 0.021955 0.002650
54
0.003878 0.011114 0.009530 0.001151
55
0.018086 0.051835 0.044451 0.005366
56
0.012319 0.035306 0.030276 0.003655
57
0.008384 0.024027 0.020604 0.002487
58
0.005347 0.015325 0.013142 0.001587
59
0.019679 0.056401 0.048366 0.005838
60
0.013404 0.038415 0.032942 0.003977
61
0.009122 0.026143 0.022419 0.002707
63
0.013045 0.037386 0.032060 0.003870
64
0.008885 0.025464 0.021836 0.002636
65
0.006047 0.017329 0.014861 0.001794
66
0.003857 0.011053 0.009479 0.001144
70
bglobin.nuc (17 vertebrates):
71
position 1: T:0.13930 C:0.23080 A:0.23652 G:0.39338
72
position 2: T:0.31005 C:0.20997 A:0.32802 G:0.15196
73
position 3: T:0.26675 C:0.34191 A:0.05923 G:0.33211
75
0.011746 0.015055 0.002608 0.014623
76
0.007954 0.010195 0.001766 0.009903
78
0.005758 0.007379 0 0.007167
79
0.019461 0.024944 0.004321 0.024229
80
0.013179 0.016892 0.002926 0.016408
81
0.020589 0.026390 0.004572 0.025634
82
0.009538 0.012226 0.002118 0.011875
83
0.019943 0.025562 0.004428 0.024829
84
0.013506 0.017311 0.002999 0.016815
85
0.021099 0.027044 0.004685 0.026269
86
0.009774 0.012529 0.002170 0.012169
87
0.033169 0.042516 0.007365 0.041297
88
0.022463 0.028792 0.004988 0.027966
89
0.035092 0.044980 0.007792 0.043691
90
0.016257 0.020838 0.003611 0.020240
added
removed
MCcodon.dat
