/usr/lib/R/site-library/phangorn/extdata/cpREV.dat is in r-cran-phangorn 2.4.0-1.
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 | 105
227 357
175 43 4435
669 823 538 10
157 1745 768 400 10
499 152 1055 3691 10 3122
665 243 653 431 303 133 379
66 715 1405 331 441 1269 162 19
145 136 168 10 280 92 148 40 29
197 203 113 10 396 286 82 20 66 1745
236 4482 2430 412 48 3313 2629 263 305 345 218
185 125 61 47 159 202 113 21 10 1772 1351 193
68 53 97 22 726 10 145 25 127 454 1268 72 327
490 87 173 170 285 323 185 28 152 117 219 302 100 43
2440 385 2085 590 2331 396 568 691 303 216 516 868 93 487 1202
1340 314 1393 266 576 241 369 92 32 1040 156 918 645 148 260 2151
14 230 40 18 435 53 63 82 69 42 159 10 86 468 49 73 29
56 323 754 281 1466 391 142 10 1971 89 189 247 215 2370 97 522 71 346
968 92 83 75 592 54 200 91 25 4797 865 249 475 317 122 167 760 10 119
0.0755 0.0621 0.0410 0.0371 0.0091 0.0382 0.0495 0.0838 0.0246 0.0806 0.1011 0.0504 0.0220 0.0506 0.0431 0.0622 0.0543 0.0181 0.0307 0.0660
A R N D C Q E G H I L K M F P S T W Y V
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
Symmetrical part of the rate matrix and aa frequencies, estimated for
plant chloroplast proteins, under the REVaa model. The first part is
S_ij = S_ji, and the second part has the amino acid frequencies
(\pi_i). The substitution rate from amino acid i to j is Q_ij =
S_ij*PI_j. This is the cpREV model used in protml 2.3b6 (12/10/98),
described by
Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa. 2000. Plastid
genome phylogeny and a model of amino acid substitution for proteins
encoded by chloroplast DNA. Journal of Molecular Evolution 50:348-358.
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