/usr/include/libphylo/mtREV24.dat.q 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 | " "
" 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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