/usr/include/libphylo/wag.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 36 37 38 39 40 41 42 | " "
" 0.551571 "
" 0.509848 0.635346 "
" 0.738998 0.147304 5.429420 "
" 1.027040 0.528191 0.265256 0.0302949 "
" 0.908598 3.035500 1.543640 0.616783 0.0988179 "
" 1.582850 0.439157 0.947198 6.174160 0.021352 5.469470 "
" 1.416720 0.584665 1.125560 0.865584 0.306674 0.330052 0.567717 "
" 0.316954 2.137150 3.956290 0.930676 0.248972 4.294110 0.570025 0.249410 "
" 0.193335 0.186979 0.554236 0.039437 0.170135 0.113917 0.127395 0.0304501 0.138190 "
" 0.397915 0.497671 0.131528 0.0848047 0.384287 0.869489 0.154263 0.0613037 0.499462 3.170970 "
" 0.906265 5.351420 3.012010 0.479855 0.0740339 3.894900 2.584430 0.373558 0.890432 0.323832 0.257555 "
" 0.893496 0.683162 0.198221 0.103754 0.390482 1.545260 0.315124 0.174100 0.404141 4.257460 4.854020 0.934276 "
" 0.210494 0.102711 0.0961621 0.0467304 0.398020 0.0999208 0.0811339 0.049931 0.679371 1.059470 2.115170 0.088836 1.190630 "
" 1.438550 0.679489 0.195081 0.423984 0.109404 0.933372 0.682355 0.243570 0.696198 0.0999288 0.415844 0.556896 0.171329 0.161444 "
" 3.370790 1.224190 3.974230 1.071760 1.407660 1.028870 0.704939 1.341820 0.740169 0.319440 0.344739 0.967130 0.493905 0.545931 1.613280 "
" 2.121110 0.554413 2.030060 0.374866 0.512984 0.857928 0.822765 0.225833 0.473307 1.458160 0.326622 1.386980 1.516120 0.171903 0.795384 4.378020 "
" 0.113133 1.163920 0.0719167 0.129767 0.717070 0.215737 0.156557 0.336983 0.262569 0.212483 0.665309 0.137505 0.515706 1.529640 0.139405 0.523742 0.110864 "
" 0.240735 0.381533 1.086000 0.325711 0.543833 0.227710 0.196303 0.103604 3.873440 0.420170 0.398618 0.133264 0.428437 6.454280 0.216046 0.786993 0.291148 2.485390 "
" 2.006010 0.251849 0.196246 0.152335 1.002140 0.301281 0.588731 0.187247 0.118358 7.821300 1.800340 0.305434 2.058450 0.649892 0.314887 0.232739 1.388230 0.365369 0.314730 "
" 0.0866279 0.043972 0.0390894 0.0570451 0.0193078 0.0367281 0.0580589 0.0832518 0.0244313 0.048466 0.086209 0.0620286 0.0195027 0.0384319 0.0457631 0.0695179 0.0610127 0.0143859 0.0352742 0.0708956 "
" 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 from 3905 globular protein amino acid sequences forming 182 "
" protein families. "
" The first part above indicates the symmetric 'exchangeability' "
" parameters, where s_ij = s_ji. The s_ij above are not scaled, but the "
" PAML package will perform this scaling. "
" The second part gives the amino acid frequencies (pi_i) "
" estimated from the 3905 sequences. The net replacement rate from i to "
" j is Q_ij = s_ij*pi_j. "
" Prepared by Simon Whelan and Nick Goldman, September 2000. "
" Citation: "
" Whelan, S. and N. Goldman. In press. A general empirical model of "
" protein evolution derived from multiple protein families using "
" a maximum likelihood approach. Molecular Biology and "
" Evolution. "
" See the following reference for notation used here: "
" Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and "
" applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. "
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