This file is indexed.

/usr/include/libphylo/mtREV24.dat.q is in rate4site 3.0.0-5.

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. "