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

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The actual contents of the file can be viewed below.

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"  "
" 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. "