0 * 0,1:seqs or patters in paml format (mc.paml); 2:paup format (mc.nex)
13147 * random number seed (odd number)
4 10000 10 * <# seqs> <# codons> <# replicates>
1.5 * <tree length; see note below; use -1 if tree below has absolute branch lengths>
((1 :0.1, 2 :0.2) :0.12, 3 :0.3, 4 :0.4);
0.3 * omega
5 * kappa
0.00983798 0.01745548 0.00222048 0.01443315
0.00844604 0.01498576 0.00190632 0.01239105
0.01064012 0.01887870 0 0
0.00469486 0.00833007 0 0.00688776
0.01592816 0.02826125 0.00359507 0.02336796
0.01367453 0.02426265 0.00308642 0.02006170
0.01722686 0.03056552 0.00388819 0.02527326
0.00760121 0.01348678 0.00171563 0.01115161
0.01574077 0.02792876 0.00355278 0.02309304
0.01351366 0.02397721 0.00305010 0.01982568
0.01702419 0.03020593 0.00384245 0.02497593
0.00751178 0.01332811 0.00169545 0.01102042
0.02525082 0.04480239 0.00569924 0.03704508
0.02167816 0.03846344 0.00489288 0.03180369
0.02730964 0.04845534 0.00616393 0.04006555
0.01205015 0.02138052 0.00271978 0.01767859
0 * genetic code (0:universal; 1:mammalian mt; 2-10:see below)
// end of file.
============================================================================
Change values of parameters, but do not delete them. You can add
empty lines, but do not break one line into several lines.
Note that tree length and branch lengths under the codon model are
measured by the expected number of nucleotide substitutions per codon
(see Goldman & Yang 1994). For amino acid models, they are defined as
the expected number of amino acid changes per amino acid site.
64 codon freqs are in fixed order TTT, TTC, TTA, TTG, TCT, TCC, ..., GGG,
from abglobin.nuc under the F3x4 table
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
* 10: blepharisma nu., 11: Yang's regularized code
* These codes correspond to transl_table 1 to 11 of GenBank.
=================!! Check screen output carefully!! ========================
(1)
mtCDNAape.nuc (7 apes):
position 1: T:0.20517 C:0.28293 A:0.30784 G:0.20406
position 2: T:0.40979 C:0.27911 A:0.18995 G:0.12116
position 3: T:0.15105 C:0.43290 A:0.37123 G:0.04482
0.013116 0.037590 0.032235 0.003892
0.008933 0.025603 0.021955 0.002650
0.006080 0.017424 0 0
0.003878 0.011114 0.009530 0.001151
0.018086 0.051835 0.044451 0.005366
0.012319 0.035306 0.030276 0.003655
0.008384 0.024027 0.020604 0.002487
0.005347 0.015325 0.013142 0.001587
0.019679 0.056401 0.048366 0.005838
0.013404 0.038415 0.032942 0.003977
0.009122 0.026143 0.022419 0.002707
0.005818 0.016675 0 0
0.013045 0.037386 0.032060 0.003870
0.008885 0.025464 0.021836 0.002636
0.006047 0.017329 0.014861 0.001794
0.003857 0.011053 0.009479 0.001144
(2)
bglobin.nuc (17 vertebrates):
position 1: T:0.13930 C:0.23080 A:0.23652 G:0.39338
position 2: T:0.31005 C:0.20997 A:0.32802 G:0.15196
position 3: T:0.26675 C:0.34191 A:0.05923 G:0.33211
0.011746 0.015055 0.002608 0.014623
0.007954 0.010195 0.001766 0.009903
0.012426 0.015929 0 0
0.005758 0.007379 0 0.007167
0.019461 0.024944 0.004321 0.024229
0.013179 0.016892 0.002926 0.016408
0.020589 0.026390 0.004572 0.025634
0.009538 0.012226 0.002118 0.011875
0.019943 0.025562 0.004428 0.024829
0.013506 0.017311 0.002999 0.016815
0.021099 0.027044 0.004685 0.026269
0.009774 0.012529 0.002170 0.012169
0.033169 0.042516 0.007365 0.041297
0.022463 0.028792 0.004988 0.027966
0.035092 0.044980 0.007792 0.043691
0.016257 0.020838 0.003611 0.020240