/usr/include/libphylo/mtREV24.dat is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | 23.18
26.95 13.24
17.67 1.90 794.38
59.93 103.33 58.94 1.90
1.90 220.99 173.56 55.28 75.24
9.77 1.90 63.05 583.55 1.90 313.56
120.71 23.03 53.30 56.77 30.71 6.75 28.28
13.90 165.23 496.13 113.99 141.49 582.40 49.12 1.90
96.49 1.90 27.10 4.34 62.73 8.34 3.31 5.98 12.26
25.46 15.58 15.16 1.90 25.65 39.70 1.90 2.41 11.49 329.09
8.36 141.40 608.70 2.31 1.90 465.58 313.86 22.73 127.67 19.57 14.88
141.88 1.90 65.41 1.90 6.18 47.37 1.90 1.90 11.97 517.98 537.53 91.37
6.37 4.69 15.20 4.98 70.80 19.11 2.67 1.90 48.16 84.67 216.06 6.44 90.82
54.31 23.64 73.31 13.43 31.26 137.29 12.83 1.90 60.97 20.63 40.10 50.10 18.84 17.31
387.86 6.04 494.39 69.02 277.05 54.11 54.71 125.93 77.46 47.70 73.61 105.79 111.16 64.29 169.90
480.72 2.08 238.46 28.01 179.97 94.93 14.82 11.17 44.78 368.43 126.40 136.33 528.17 33.85 128.22 597.21
1.90 21.95 10.68 19.86 33.60 1.90 1.90 10.92 7.08 1.90 32.44 24.00 21.71 7.84 4.21 38.58 9.99
6.48 1.90 191.36 21.21 254.77 38.82 13.12 3.21 670.14 25.01 44.15 51.17 39.96 465.58 16.21 64.92 38.73 26.25
195.06 7.64 1.90 1.90 1.90 19.00 21.14 2.53 1.90 1222.94 91.67 1.90 387.54 6.35 8.23 1.90 204.54 5.37 1.90
0.072 0.019 0.039 0.019 0.006 0.025 0.024 0.056 0.028 0.088 0.169
0.023 0.054 0.061 0.054 0.072 0.086 0.029 0.033 0.043
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
S_ij = S_ji and PI_i for the mtREV24 model (Adachi and Hasegawa 1996).
The PI's used to sum to 0.999 and I changed one of the freq from 0.168
into 0.169 so that the sum is 1. Prepared by Z. Yang according to
data sent by Dr M. Hasegawa. This matrix was obtained from the 12
mitochondrial proteins encoded by the same strand of the DNA from a
diverse range of species including bird, fish, frog, lamprey, as well
as mammals (see Adachi and Hasegawa 1996 for details). The other
matrix (mtmam.dat) included in the package is based on the same
proteins from mammals only.
Adachi, J. and Hasegawa, M. (1996) MOLPHY version 2.3: programs for
molecular phylogenetics based on maximum likelihood. Computer Science
Monographs of Institute of Statistical Mathematics 28:1-150.
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