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
// this is the end of the file. The rest are notes.
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. 2001. A general empirical model of
protein evolution derived from multiple protein families using
a maximum likelihood approach. Molecular Biology and
Evolution 18, 691-699.
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.