5 * Part of TREE-PUZZLE 5.0 (June 2000)
7 * (c) 1999-2000 by Heiko A. Schmidt, Korbinian Strimmer,
8 * M. Vingron, and Arndt von Haeseler
9 * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
11 * All parts of the source except where indicated are distributed under
12 * the GNU public licence. See http://www.opensource.org for details.
25 void jttdata(dmatrix q, double *f)
28 * JTT model for amino acid evolution
29 * D.T. Jones, W.R. Taylor, and J.M. Thornton
30 * "The rapid generation of mutation data matrices from protein sequences"
31 * CABIOS vol. 8 no. 3 1992 pp. 275-282
34 q[0][1]=3.1628651460584e+00; q[0][2]=3.2804935927860e+00;
35 q[0][3]=4.8477237048666e+00; q[0][4]=3.4612244897959e+00;
36 q[0][5]=3.3130910900946e+00; q[0][6]=6.3199473337722e+00;
37 q[0][7]=1.0440154440154e+01; q[0][8]=1.3061224489796e+00;
38 q[0][9]=2.1726844583987e+00; q[0][10]=1.8443597219107e+00;
39 q[0][11]=2.2137668626773e+00; q[0][12]=2.7210884353741e+00;
40 q[0][13]=8.3265306122449e-01; q[0][14]=1.1537414965986e+01;
41 q[0][15]=2.2838213546288e+01; q[0][16]=2.7007955724663e+01;
42 q[0][17]=5.1311953352770e-01; q[0][18]=8.3673469387755e-01;
43 q[0][19]=1.7474335188621e+01;
45 q[1][2]=2.6598918637222e+00; q[1][3]=9.1014867485456e-01;
46 q[1][4]=6.1624649859944e+00; q[1][5]=1.8036482885837e+01;
47 q[1][6]=1.8924731182796e+00; q[1][7]=8.1810886516769e+00;
48 q[1][8]=1.9119717452198e+01; q[1][9]=1.4410687351864e+00;
49 q[1][10]=2.2211961707760e+00; q[1][11]=3.9239234676922e+01;
50 q[1][12]=2.5060690943044e+00; q[1][13]=3.9439775910364e-01;
51 q[1][14]=4.1953094963476e+00; q[1][15]=5.9016766126741e+00;
52 q[1][16]=3.8437069743152e+00; q[1][17]=7.6766706682673e+00;
53 q[1][18]=1.4173669467787e+00; q[1][19]=1.0308123249300e+00;
55 q[2][3]=3.2226935854843e+01; q[2][4]=1.8710963455150e+00;
56 q[2][5]=4.5351268130622e+00; q[2][6]=3.3951344979102e+00;
57 q[2][7]=4.5987249708180e+00; q[2][8]=2.3693774375271e+01;
58 q[2][9]=2.9235880398671e+00; q[2][10]=8.0960899565551e-01;
59 q[2][11]=1.5024269384537e+01; q[2][12]=1.9003322259136e+00;
60 q[2][13]=4.3853820598007e-01; q[2][14]=7.1083317047749e-01;
61 q[2][15]=2.9456208772690e+01; q[2][16]=1.3735908553410e+01;
62 q[2][17]=1.6706217370669e-01; q[2][18]=4.1661129568106e+00;
63 q[2][19]=9.7452934662237e-01;
65 q[3][4]=6.2857142857143e-01; q[3][5]=3.0662020905923e+00;
66 q[3][6]=4.5450549450549e+01; q[3][7]=7.5402435402435e+00;
67 q[3][8]=6.0544672718586e+00; q[3][9]=6.8808114961961e-01;
68 q[3][10]=3.6130902064968e-01; q[3][11]=1.6718197057180e+00;
69 q[3][12]=1.0879120879121e+00; q[3][13]=1.9340659340659e-01;
70 q[3][14]=7.3949579831933e-01; q[3][15]=3.4196528109572e+00;
71 q[3][16]=2.4749487800335e+00; q[3][17]=3.4536891679749e-01;
72 q[3][18]=2.6895604395604e+00; q[3][19]=1.8608058608059e+00;
74 q[4][5]=5.5191637630662e-01; q[4][6]=3.2442396313364e-01;
75 q[4][7]=3.3297297297297e+00; q[4][8]=4.3726708074534e+00;
76 q[4][9]=9.1868131868132e-01; q[4][10]=9.9466248037677e-01;
77 q[4][11]=2.9830508474576e-01; q[4][12]=2.4095238095238e+00;
78 q[4][13]=4.1485714285714e+00; q[4][14]=7.3949579831933e-01;
79 q[4][15]=1.2862939958592e+01; q[4][16]=2.8125907990315e+00;
80 q[4][17]=6.8244897959184e+00; q[4][18]=1.2885714285714e+01;
81 q[4][19]=3.7714285714286e+00;
83 q[5][6]=2.0316061593796e+01; q[5][7]=1.3922214897825e+00;
84 q[5][8]=3.3861536130889e+01; q[5][9]=4.7172339855267e-01;
85 q[5][10]=4.2320327755868e+00; q[5][11]=1.7835941652395e+01;
86 q[5][12]=2.6573751451800e+00; q[5][13]=2.7595818815331e-01;
87 q[5][14]=9.4992143198743e+00; q[5][15]=3.2350653941322e+00;
88 q[5][16]=3.0973838067678e+00; q[5][17]=1.0512692882031e+00;
89 q[5][18]=1.5331010452962e+00; q[5][19]=1.0778164924506e+00;
91 q[6][7]=6.6857641051189e+00; q[6][8]=1.4458024443999e+00;
92 q[6][9]=6.7068415455512e-01; q[6][10]=5.7932850559579e-01;
93 q[6][11]=1.0365070686558e+01; q[6][12]=1.0138248847926e+00;
94 q[6][13]=2.6359447004608e-01; q[6][14]=1.1291226167887e+00;
95 q[6][15]=1.8337006611901e+00; q[6][16]=1.9520424900414e+00;
96 q[6][17]=6.9519420671494e-01; q[6][18]=3.8018433179723e-01;
97 q[6][19]=2.7772657450077e+00;
99 q[7][8]=1.2113479939567e+00; q[7][9]=3.2670032670033e-01;
100 q[7][10]=4.1817641817642e-01; q[7][11]=1.6354950592239e+00;
101 q[7][12]=7.6447876447876e-01; q[7][13]=3.0579150579151e-01;
102 q[7][14]=1.2391551215081e+00; q[7][15]=1.1138492529797e+01;
103 q[7][16]=1.8888816176952e+00; q[7][17]=3.3491450634308e+00;
104 q[7][18]=3.1853281853282e-01; q[7][19]=2.8416988416988e+00;
106 q[8][9]=1.0931677018634e+00; q[8][10]=3.2194389461470e+00;
107 q[8][11]=3.1498052426571e+00; q[8][12]=1.9130434782609e+00;
108 q[8][13]=2.7329192546584e+00; q[8][14]=6.7304834977469e+00;
109 q[8][15]=4.3726708074534e+00; q[8][16]=2.8162964522581e+00;
110 q[8][17]=7.8083407275954e-01; q[8][18]=3.5118012422360e+01;
111 q[8][19]=7.2877846790890e-01;
113 q[9][10]=1.4069798333535e+01; q[9][11]=1.2292791953809e+00;
114 q[9][12]=2.8366300366300e+01; q[9][13]=4.7384615384615e+00;
115 q[9][14]=5.8780435251023e-01; q[9][15]=2.4105749323141e+00;
116 q[9][16]=1.5243062022723e+01; q[9][17]=8.2888540031397e-01;
117 q[9][18]=1.8434065934066e+00; q[9][19]=5.7699633699634e+01;
119 q[10][11]=8.8039805231089e-01; q[10][12]=2.2425954997384e+01;
120 q[10][13]=1.5099529042386e+01; q[10][14]=6.2626896912611e+00;
121 q[10][15]=3.4917298022888e+00; q[10][16]=1.6109411169944e+00;
122 q[10][17]=3.2366001345593e+00; q[10][18]=1.4505494505495e+00;
123 q[10][19]=1.0557823129252e+01;
125 q[11][12]=3.6577885391445e+00; q[11][13]=1.4915254237288e-01;
126 q[11][14]=1.2868062479229e+00; q[11][15]=2.8162964522581e+00;
127 q[11][16]=5.7494151926786e+00; q[11][17]=5.4790729851263e-01;
128 q[11][18]=5.3268765133172e-01; q[11][19]=7.4899112187248e-01;
130 q[12][13]=2.5666666666667e+00; q[12][14]=9.4491129785247e-01;
131 q[12][15]=1.6397515527950e+00; q[12][16]=1.2180790960452e+01;
132 q[12][17]=1.1972789115646e+00; q[12][18]=1.1130952380952e+00;
133 q[12][19]=1.7746031746032e+01;
135 q[13][14]=8.8739495798319e-01; q[13][15]=5.6298136645963e+00;
136 q[13][16]=8.3099273607748e-01; q[13][17]=3.3224489795918e+00;
137 q[13][18]=3.3392857142857e+01; q[13][19]=3.6000000000000e+00;
139 q[14][15]=1.6261762676085e+01; q[14][16]=6.8852490148602e+00;
140 q[14][17]=4.2256902761104e-01; q[14][18]=6.7787114845938e-01;
141 q[14][19]=1.2549019607843e+00;
143 q[15][16]=2.7891216619293e+01; q[15][17]=1.8740017746229e+00;
144 q[15][18]=3.7349896480331e+00; q[15][19]=2.4182194616977e+00;
146 q[16][17]=4.8702870978900e-01; q[16][18]=1.1985472154964e+00;
147 q[16][19]=6.7925746569814e+00;
149 q[17][18]=4.6020408163265e+00; q[17][19]=1.4693877551020e+00;
151 q[18][19]=1.0000000000000e+00;
154 f[0] = 0.077; f[1] = 0.051; f[2] = 0.043; f[3] = 0.052;
155 f[4] = 0.02; f[5] = 0.041; f[6] = 0.062; f[7] = 0.074;
156 f[8] = 0.023; f[9] = 0.052; f[10] = 0.091; f[11] = 0.059;
157 f[12] = 0.024; f[13] = 0.04; f[14] = 0.051; f[15] = 0.069;
158 f[16] = 0.059; f[17] = 0.014; f[18] = 0.032; f[19] = 0.066;
161 void dyhfdata(dmatrix q, double *f)
164 * Dayhoff model for amino acid evolution
165 * Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978)
166 * "A model of evolutionary change in proteins."
167 * Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3,
168 * National Biomedical Research Foundation, Washington DC, pp. 345-352.
171 q[0][1]=9.6472567159749e-01; q[0][2]=3.5927991886410e+00;
172 q[0][3]=4.3200552414656e+00; q[0][4]=1.3184584178499e+00;
173 q[0][5]=3.2267534963169e+00; q[0][6]=7.0141987829615e+00;
174 q[0][7]=8.5773867857875e+00; q[0][8]=8.1434196396611e-01;
175 q[0][9]=2.3518447453539e+00; q[0][10]=1.4735711728911e+00;
176 q[0][11]=9.3940162271805e-01; q[0][12]=2.5490196078431e+00;
177 q[0][13]=6.5922920892495e-01; q[0][14]=8.9189834148670e+00;
178 q[0][15]=1.4540712836859e+01; q[0][16]=1.3411904595370e+01;
179 q[0][17]=3.8517964118027e-02; q[0][18]=8.7897227856660e-01;
180 q[0][19]=7.4036511156187e+00;
182 q[1][2]=1.1890243902439e+00; q[1][3]=5.9525626545377e-02;
183 q[1][4]=8.4778922655537e-01; q[1][5]=8.8348561504191e+00;
184 q[1][6]=5.5954088952654e-02; q[1][7]=3.1434881434075e-01;
185 q[1][8]=8.4753987678285e+00; q[1][9]=2.2684090115941e+00;
186 q[1][10]=5.5954088952654e-01; q[1][11]=1.6681312769010e+01;
187 q[1][12]=3.1707317073171e+00; q[1][13]=4.8959827833572e-01;
188 q[1][14]=3.6754156468900e+00; q[1][15]=5.4755072760812e+00;
189 q[1][16]=9.6472567159749e-01; q[1][17]=7.5538020086083e+00;
190 q[1][18]=2.7977044476327e-01; q[1][19]=8.6083213773314e-01;
192 q[2][3]=3.2459324155194e+01; q[2][4]=7.3852625416383e-02;
193 q[2][5]=3.7732198142415e+00; q[2][6]=5.3911764705882e+00;
194 q[2][7]=5.0264375413087e+00; q[2][8]=1.9061418685121e+01;
195 q[2][9]=2.7901430842607e+00; q[2][10]=1.2482698961938e+00;
196 q[2][11]=1.1542279411765e+01; q[2][12]=1.9117647058824e-01;
197 q[2][13]=5.0183823529412e-01; q[2][14]=1.5181660899654e+00;
198 q[2][15]=1.7697478991597e+01; q[2][16]=8.3557302231237e+00;
199 q[2][17]=8.6029411764706e-01; q[2][18]=3.4411764705882e+00;
200 q[2][19]=5.7352941176471e-01;
202 q[3][4]=2.5534152404601e-02; q[3][5]=4.8811013767209e+00;
203 q[3][6]=4.0561952440551e+01; q[3][7]=4.4423506911730e+00;
204 q[3][8]=3.0865788117500e+00; q[3][9]=8.5749078239692e-01;
205 q[3][10]=2.5926985518518e-02; q[3][11]=2.5930851063830e+00;
206 q[3][12]=1.1667143483333e-01; q[3][13]=1.2963492759259e-02;
207 q[3][14]=4.7853935065891e-01; q[3][15]=3.4167709637046e+00;
208 q[3][16]=2.3984722282163e+00; q[3][17]=3.2408731898147e-02;
209 q[3][18]=8.1351689612015e-02; q[3][19]=6.3829787234043e-01;
211 q[4][5]=2.1864264103535e-02; q[4][6]=1.4770525083277e-02;
212 q[4][7]=3.9055458751427e-01; q[4][8]=1.0223340673168e+00;
213 q[4][9]=1.5970515970516e+00; q[4][10]=3.9098448749850e-02;
214 q[4][11]=8.0776309049169e-03; q[4][12]=1.4155086538140e-01;
215 q[4][13]=8.6898395721925e-02; q[4][14]=6.8155604487784e-01;
216 q[4][15]=5.8097784568373e+00; q[4][16]=5.9929928084086e-01;
217 q[4][17]=3.4759358288770e-01; q[4][18]=3.4759358288770e+00;
218 q[4][19]=1.7647058823529e+00;
220 q[5][6]=2.5476780185759e+01; q[5][7]=1.0174974779977e+00;
221 q[5][8]=2.1573939173192e+01; q[5][9]=6.5266504894988e-01;
222 q[5][10]=2.6634492806410e+00; q[5][11]=5.5466331269350e+00;
223 q[5][12]=4.0247678018576e+00; q[5][13]=1.8038017885416e-02;
224 q[5][14]=5.5044618466582e+00; q[5][15]=2.0267580716497e+00;
225 q[5][16]=1.9256432155439e+00; q[5][17]=9.6202762055552e-02;
226 q[5][18]=1.0061919504644e-01; q[5][19]=1.2538699690402e+00;
228 q[6][7]=2.8869795109055e+00; q[6][8]=1.5519031141869e+00;
229 q[6][9]=2.1701112877583e+00; q[6][10]=4.0484429065744e-01;
230 q[6][11]=2.9823529411765e+00; q[6][12]=1.0705882352941e+00;
231 q[6][13]=1.9801735189768e-02; q[6][14]=1.7993079584775e+00;
232 q[6][15]=2.8184873949580e+00; q[6][16]=1.2261663286004e+00;
233 q[6][17]=7.3114099162219e-02; q[6][18]=7.6470588235294e-01;
234 q[6][19]=1.3058823529412e+00;
236 q[7][8]=3.7906768788150e-01; q[7][9]=2.3128004846840e-02;
237 q[7][10]=2.5776602775942e-01; q[7][11]=9.6662260409782e-01;
238 q[7][12]=6.0145406477198e-01; q[7][13]=5.4775280898876e-01;
239 q[7][14]=1.2382877804129e+00; q[7][15]=8.2853366065527e+00;
240 q[7][16]=1.1110604644803e+00; q[7][17]=1.2888301387971e-01;
241 q[7][18]=1.7114723586662e-02; q[7][19]=1.9233311302049e+00;
243 q[8][9]=2.7354343963341e-01; q[8][10]=1.5876246692449e+00;
244 q[8][11]=9.6993944636678e-01; q[8][12]=1.2544085640577e-01;
245 q[8][13]=1.6868512110727e+00; q[8][14]=3.3075513942601e+00;
246 q[8][15]=1.2530894710826e+00; q[8][16]=8.1434196396611e-01;
247 q[8][17]=1.0121107266436e+00; q[8][18]=4.4982698961938e+00;
248 q[8][19]=1.5570934256055e+00;
250 q[9][10]=9.2275320303002e+00; q[9][11]=1.6663354531002e+00;
251 q[9][12]=1.1780604133545e+01; q[9][13]=6.9753577106518e+00;
252 q[9][14]=4.2551201720752e-01; q[9][15]=8.8575970928912e-01;
253 q[9][16]=6.8951811852420e+00; q[9][17]=9.8802836705702e-02;
254 q[9][18]=1.3434022257552e+00; q[9][19]=3.1526232114467e+01;
256 q[10][11]=6.5787197231834e-01; q[10][12]=1.8622837370242e+01;
257 q[10][13]=5.6340830449827e+00; q[10][14]=1.1377976796255e+00;
258 q[10][15]=6.1690558576372e-01; q[10][16]=1.2098794893211e+00;
259 q[10][17]=1.7543252595156e+00; q[10][18]=1.0346020761246e+00;
260 q[10][19]=6.2906574394464e+00;
262 q[11][12]=8.6029411764706e+00; q[11][13]=6.6640454965565e-03;
263 q[11][14]=1.2089100346021e+00; q[11][15]=3.4411764705882e+00;
264 q[11][16]=4.9442190669371e+00; q[11][17]=3.4272233982290e-02;
265 q[11][18]=4.7794117647059e-01; q[11][19]=3.7500000000000e-01;
267 q[12][13]=3.2500000000000e+00; q[12][14]=5.9976931949250e-01;
268 q[12][15]=2.1848739495798e+00; q[12][16]=3.6916835699797e+00;
269 q[12][17]=1.6247577591604e-01; q[12][18]=1.1508700794053e-01;
270 q[12][19]=9.0588235294118e+00;
272 q[13][14]=3.9359861591695e-01; q[13][15]=1.6386554621849e+00;
273 q[13][16]=4.9442190669371e-01; q[13][17]=2.8676470588235e+00;
274 q[13][18]=2.4852941176471e+01; q[13][19]=4.4117647058824e-01;
276 q[14][15]=8.6431043005437e+00; q[14][16]=2.8308077795013e+00;
277 q[14][17]=3.5840244687362e-02; q[14][18]=4.3804743506776e-02;
278 q[14][19]=1.7301038062284e+00;
280 q[15][16]=1.9663865546218e+01; q[15][17]=2.7857142857143e+00;
281 q[15][18]=1.2016806722689e+00; q[15][19]=1.0840336134454e+00;
283 q[16][17]=4.2019597219666e-02; q[16][18]=1.5162271805274e+00;
284 q[16][19]=5.6592292089249e+00;
286 q[17][18]=2.2941176470588e+00; q[17][19]=1.2654363316538e-01;
288 q[18][19]=1.0000000000000e+00;
291 f[0] = 0.087; f[1] = 0.041; f[2] = 0.040; f[3] = 0.047;
292 f[4] = 0.033; f[5] = 0.038; f[6] = 0.05; f[7] = 0.089;
293 f[8] = 0.034; f[9] = 0.037; f[10] = 0.085; f[11] = 0.08;
294 f[12] = 0.015; f[13] = 0.04; f[14] = 0.051; f[15] = 0.07;
295 f[16] = 0.058; f[17] = 0.01; f[18] = 0.03; f[19] = 0.065;
298 void mtrevdata(dmatrix q, double *f)
301 * mtREV24 model of amino acid evolution
302 * (complete sequence data of mtDNA from 24 vertebrate species)
303 * Adachi, J. and Hasegawa, M. (1996)
306 q[0][1]=1.2199217606346e+01; q[0][2]=1.4182139942122e+01;
307 q[0][3]=9.2985091873208e+00; q[0][4]=3.1542792981957e+01;
308 q[0][5]=1.0025852846688e+00; q[0][6]=5.1418866803338e+00;
309 q[0][7]=6.3531246495131e+01; q[0][8]=7.3137132861715e+00;
310 q[0][9]=5.0782382656186e+01; q[0][10]=1.3399741808481e+01;
311 q[0][11]=4.4021672780560e+00; q[0][12]=7.4673480520104e+01;
312 q[0][13]=3.3513021631978e+00; q[0][14]=2.8582502221773e+01;
313 q[0][15]=2.0413623195312e+02; q[0][16]=2.5301305153906e+02;
314 q[0][17]=1.0000000000000e+00; q[0][18]=3.4084158197615e+00;
315 q[0][19]=1.0266468401249e+02;
317 q[1][2]=6.9661274444534e+00; q[1][3]=1.0000000000000e+00;
318 q[1][4]=5.4384584796568e+01; q[1][5]=1.1631134513343e+02;
319 q[1][6]=1.0000000000000e+00; q[1][7]=1.2122831341194e+01;
320 q[1][8]=8.6961067087353e+01; q[1][9]=1.0000000000000e+00;
321 q[1][10]=8.1976829394538e+00; q[1][11]=7.4423215395318e+01;
322 q[1][12]=1.0000000000000e+00; q[1][13]=2.4659158338099e+00;
323 q[1][14]=1.2439947713615e+01; q[1][15]=3.1791814866372e+00;
324 q[1][16]=1.0935327216119e+00; q[1][17]=1.1550775790126e+01;
325 q[1][18]=1.0000000000000e+00; q[1][19]=4.0211417480338e+00;
327 q[2][3]=4.1809325468160e+02; q[2][4]=3.1020979842967e+01;
328 q[2][5]=9.1349622725361e+01; q[2][6]=3.3185663516310e+01;
329 q[2][7]=2.8052324651124e+01; q[2][8]=2.6112087577885e+02;
330 q[2][9]=1.4261453863336e+01; q[2][10]=7.9775653461977e+00;
331 q[2][11]=3.2036829276162e+02; q[2][12]=3.4424354918739e+01;
332 q[2][13]=7.9996445145608e+00; q[2][14]=3.8586541461044e+01;
333 q[2][15]=2.6020426225852e+02; q[2][16]=1.2550758780474e+02;
334 q[2][17]=5.6207759736659e+00; q[2][18]=1.0071406219571e+02;
335 q[2][19]=1.0000000000000e+00;
337 q[3][4]=1.0000000000000e+00; q[3][5]=2.9097352675564e+01;
338 q[3][6]=3.0713149855302e+02; q[3][7]=2.9877072751897e+01;
339 q[3][8]=5.9995408885817e+01; q[3][9]=2.2827096245105e+00;
340 q[3][10]=1.0000000000000e+00; q[3][11]=1.2183938185384e+00;
341 q[3][12]=1.0000000000000e+00; q[3][13]=2.6221929413096e+00;
342 q[3][14]=7.0708004204733e+00; q[3][15]=3.6327934317139e+01;
343 q[3][16]=1.4743408713748e+01; q[3][17]=1.0453246057102e+01;
344 q[3][18]=1.1165627147496e+01; q[3][19]=1.0000000000000e+00;
346 q[4][5]=3.9599394038972e+01; q[4][6]=1.0000000000000e+00;
347 q[4][7]=1.6163581056674e+01; q[4][8]=7.4467985406234e+01;
348 q[4][9]=3.3018175376623e+01; q[4][10]=1.3500725995091e+01;
349 q[4][11]=1.0000000000000e+00; q[4][12]=3.2504095376923e+00;
350 q[4][13]=3.7264767083096e+01; q[4][14]=1.6454136037822e+01;
351 q[4][15]=1.4581783243113e+02; q[4][16]=9.4720031458442e+01;
352 q[4][17]=1.7684087896962e+01; q[4][18]=1.3409157685926e+02;
353 q[4][19]=1.0000000000000e+00;
355 q[5][6]=1.6503249008836e+02; q[5][7]=3.5530760735494e+00;
356 q[5][8]=3.0652523140859e+02; q[5][9]=4.3905393139325e+00;
357 q[5][10]=2.0895470525345e+01; q[5][11]=2.4504076430724e+02;
358 q[5][12]=2.4931300477797e+01; q[5][13]=1.0059428264289e+01;
359 q[5][14]=7.2256314165467e+01; q[5][15]=2.8480937892158e+01;
360 q[5][16]=4.9962974409828e+01; q[5][17]=1.0000000000000e+00;
361 q[5][18]=2.0430790980529e+01; q[5][19]=9.9986289000676e+00;
363 q[6][7]=1.4884496769963e+01; q[6][8]=2.5853576435567e+01;
364 q[6][9]=1.7418201388328e+00; q[6][10]=1.0000000000000e+00;
365 q[6][11]=1.6519126809071e+02; q[6][12]=1.0000000000000e+00;
366 q[6][13]=1.4067850525292e+00; q[6][14]=6.7547121641947e+00;
367 q[6][15]=2.8794794140840e+01; q[6][16]=7.8001372062558e+00;
368 q[6][17]=1.0000000000000e+00; q[6][18]=6.9067239183061e+00;
369 q[6][19]=1.1127702362585e+01;
371 q[7][8]=1.0000000000000e+00; q[7][9]=3.1466649021550e+00;
372 q[7][10]=1.2699794194865e+00; q[7][11]=1.1962111069278e+01;
373 q[7][12]=1.0000000000000e+00; q[7][13]=1.0000000000000e+00;
374 q[7][14]=1.0000000000000e+00; q[7][15]=6.6277950574411e+01;
375 q[7][16]=5.8800079133028e+00; q[7][17]=5.7494182626674e+00;
376 q[7][18]=1.6887657206208e+00; q[7][19]=1.3320553471351e+00;
378 q[8][9]=6.4536986087271e+00; q[8][10]=6.0472584534958e+00;
379 q[8][11]=6.7197196398961e+01; q[8][12]=6.2977633277779e+00;
380 q[8][13]=2.5347805183364e+01; q[8][14]=3.2089868698728e+01;
381 q[8][15]=4.0766987134407e+01; q[8][16]=2.3570850628539e+01;
382 q[8][17]=3.7286635325194e+00; q[8][18]=3.5270764890474e+02;
383 q[8][19]=1.0000000000000e+00;
385 q[9][10]=1.7320653206333e+02; q[9][11]=1.0298655619743e+01;
386 q[9][12]=2.7262244199514e+02; q[9][13]=4.4561065036310e+01;
387 q[9][14]=1.0856482766156e+01; q[9][15]=2.5107659603898e+01;
388 q[9][16]=1.9391167162525e+02; q[9][17]=1.0000000000000e+00;
389 q[9][18]=1.3161329199391e+01; q[9][19]=6.4365086389428e+02;
391 q[10][11]=7.8314019154706e+00; q[10][12]=2.8290920517725e+02;
392 q[10][13]=1.1371735519833e+02; q[10][14]=2.1105885757279e+01;
393 q[10][15]=3.8741359395934e+01; q[10][16]=6.6524559321657e+01;
394 q[10][17]=1.7071378554833e+01; q[10][18]=2.3234516108847e+01;
395 q[10][19]=4.8247261078055e+01;
397 q[11][12]=4.8092094826036e+01; q[11][13]=3.3887559483420e+00;
398 q[11][14]=2.6368577564199e+01; q[11][15]=5.5679895711418e+01;
399 q[11][16]=7.1750284708933e+01; q[11][17]=1.2631893872825e+01;
400 q[11][18]=2.6932728996777e+01; q[11][19]=1.0000000000000e+00;
402 q[12][13]=4.7798798034572e+01; q[12][14]=9.9165053447429e+00;
403 q[12][15]=5.8505442466161e+01; q[12][16]=2.7798190504760e+02;
404 q[12][17]=1.1427000119701e+01; q[12][18]=2.1029990530586e+01;
405 q[12][19]=2.0397078683768e+02;
407 q[13][14]=9.1089574817139e+00; q[13][15]=3.3835737720574e+01;
408 q[13][16]=1.7815549567056e+01; q[13][17]=4.1272404968214e+00;
409 q[13][18]=2.4504156395152e+02; q[13][19]=3.3435675442163e+00;
411 q[14][15]=8.9421193040709e+01; q[14][16]=6.7485067008375e+01;
412 q[14][17]=2.2161693733113e+00; q[14][18]=8.5338209390745e+00;
413 q[14][19]=4.3342126659660e+00;
415 q[15][16]=3.1432036618746e+02; q[15][17]=2.0305343047059e+01;
416 q[15][18]=3.4167877957799e+01; q[15][19]=1.0000000000000e+00;
418 q[16][17]=5.2559565123081e+00; q[16][18]=2.0382362288681e+01;
419 q[16][19]=1.0765527137500e+02;
421 q[17][18]=1.3814733274637e+01; q[17][19]=2.8259139240676e+00;
423 q[18][19]=1.0000000000000e+00;
426 /* amino acid frequencies */
427 f[0]=0.072; f[1]=0.019; f[2]=0.039; f[3]=0.019; f[4]=0.006;
428 f[5]=0.025; f[6]=0.024; f[7]=0.056; f[8]=0.028; f[9]=0.088;
429 f[10]=0.168; f[11]=0.023; f[12]=0.054; f[13]=0.061; f[14]=0.054;
430 f[15]=0.072; f[16]=0.086; f[17]=0.029; f[18]=0.033; f[19]=0.043;
433 void blosum62data(dmatrix q, double *f)
436 * BLOSUM62 model of amino acid evolution
438 * S. Henikoff and J. G. Henikoff. 1992. PNAS USA 89:10915-10919.
442 q[0][1]=7.3579038969751e-01; q[0][2]=4.8539105546575e-01;
443 q[0][3]=5.4316182089867e-01; q[0][4]=1.4599953104700e+00;
444 q[0][5]=1.1997057046020e+00; q[0][6]=1.1709490427999e+00;
445 q[0][7]=1.9558835749595e+00; q[0][8]=7.1624144499779e-01;
446 q[0][9]=6.0589900368677e-01; q[0][10]=8.0001653051838e-01;
447 q[0][11]=1.2952012667833e+00; q[0][12]=1.2537582666635e+00;
448 q[0][13]=4.9296467974759e-01; q[0][14]=1.1732759009239e+00;
449 q[0][15]=4.3250926870566e+00; q[0][16]=1.7291780194850e+00;
450 q[0][17]=4.6583936772479e-01; q[0][18]=7.1820669758623e-01;
451 q[0][19]=2.1877745220045e+00;
453 q[1][2]=1.2974467051337e+00; q[1][3]=5.0096440855513e-01;
454 q[1][4]=2.2782657420895e-01; q[1][5]=3.0208336100636e+00;
455 q[1][6]=1.3605741904203e+00; q[1][7]=4.1876330851753e-01;
456 q[1][8]=1.4561411663360e+00; q[1][9]=2.3203644514174e-01;
457 q[1][10]=6.2271166969249e-01; q[1][11]=5.4111151414889e+00;
458 q[1][12]=9.8369298745695e-01; q[1][13]=3.7164469320875e-01;
459 q[1][14]=4.4813366171831e-01; q[1][15]=1.1227831042096e+00;
460 q[1][16]=9.1466595456337e-01; q[1][17]=4.2638231012175e-01;
461 q[1][18]=7.2051744121611e-01; q[1][19]=4.3838834377202e-01;
463 q[2][3]=3.1801000482161e+00; q[2][4]=3.9735894989702e-01;
464 q[2][5]=1.8392161469920e+00; q[2][6]=1.2404885086396e+00;
465 q[2][7]=1.3558723444845e+00; q[2][8]=2.4145014342081e+00;
466 q[2][9]=2.8301732627800e-01; q[2][10]=2.1188815961519e-01;
467 q[2][11]=1.5931370434574e+00; q[2][12]=6.4844127878707e-01;
468 q[2][13]=3.5486124922252e-01; q[2][14]=4.9488704370192e-01;
469 q[2][15]=2.9041016564560e+00; q[2][16]=1.8981736345332e+00;
470 q[2][17]=1.9148204624678e-01; q[2][18]=5.3822251903674e-01;
471 q[2][19]=3.1285879799342e-01;
473 q[3][4]=2.4083661480204e-01; q[3][5]=1.1909457033960e+00;
474 q[3][6]=3.7616252083685e+00; q[3][7]=7.9847324896839e-01;
475 q[3][8]=7.7814266402188e-01; q[3][9]=4.1855573246161e-01;
476 q[3][10]=2.1813157759360e-01; q[3][11]=1.0324479249521e+00;
477 q[3][12]=2.2262189795786e-01; q[3][13]=2.8173069420651e-01;
478 q[3][14]=7.3062827299842e-01; q[3][15]=1.5827541420653e+00;
479 q[3][16]=9.3418750943056e-01; q[3][17]=1.4534504627853e-01;
480 q[3][18]=2.6142220896504e-01; q[3][19]=2.5812928941763e-01;
482 q[4][5]=3.2980150463028e-01; q[4][6]=1.4074889181440e-01;
483 q[4][7]=4.1820319228376e-01; q[4][8]=3.5405810983129e-01;
484 q[4][9]=7.7489402279418e-01; q[4][10]=8.3184264014158e-01;
485 q[4][11]=2.8507880090648e-01; q[4][12]=7.6768882347954e-01;
486 q[4][13]=4.4133747118660e-01; q[4][14]=3.5600849876863e-01;
487 q[4][15]=1.1971884150942e+00; q[4][16]=1.1198313585160e+00;
488 q[4][17]=5.2766441887169e-01; q[4][18]=4.7023773369610e-01;
489 q[4][19]=1.1163524786062e+00;
491 q[5][6]=5.5289191779282e+00; q[5][7]=6.0984630538281e-01;
492 q[5][8]=2.4353411311401e+00; q[5][9]=2.3620245120365e-01;
493 q[5][10]=5.8073709318144e-01; q[5][11]=3.9452776745146e+00;
494 q[5][12]=2.4948960771127e+00; q[5][13]=1.4435695975031e-01;
495 q[5][14]=8.5857057567418e-01; q[5][15]=1.9348709245965e+00;
496 q[5][16]=1.2774802945956e+00; q[5][17]=7.5865380864172e-01;
497 q[5][18]=9.5898974285014e-01; q[5][19]=5.3078579012486e-01;
499 q[6][7]=4.2357999217628e-01; q[6][8]=1.6268910569817e+00;
500 q[6][9]=1.8684804693170e-01; q[6][10]=3.7262517508685e-01;
501 q[6][11]=2.8024271516787e+00; q[6][12]=5.5541539747043e-01;
502 q[6][13]=2.9140908416530e-01; q[6][14]=9.2656393484598e-01;
503 q[6][15]=1.7698932389373e+00; q[6][16]=1.0710972360073e+00;
504 q[6][17]=4.0763564893830e-01; q[6][18]=5.9671930034577e-01;
505 q[6][19]=5.2425384633796e-01;
507 q[7][8]=5.3985912495418e-01; q[7][9]=1.8929629237636e-01;
508 q[7][10]=2.1772115923623e-01; q[7][11]=7.5204244030271e-01;
509 q[7][12]=4.5943617357855e-01; q[7][13]=3.6816646445253e-01;
510 q[7][14]=5.0408659952683e-01; q[7][15]=1.5093262532236e+00;
511 q[7][16]=6.4143601140497e-01; q[7][17]=5.0835892463812e-01;
512 q[7][18]=3.0805573703500e-01; q[7][19]=2.5334079019018e-01;
514 q[8][9]=2.5271844788492e-01; q[8][10]=3.4807220979697e-01;
515 q[8][11]=1.0225070358890e+00; q[8][12]=9.8431152535870e-01;
516 q[8][13]=7.1453370392764e-01; q[8][14]=5.2700733915060e-01;
517 q[8][15]=1.1170297629105e+00; q[8][16]=5.8540709022472e-01;
518 q[8][17]=3.0124860078016e-01; q[8][18]=4.2189539693890e+00;
519 q[8][19]=2.0155597175031e-01;
521 q[9][10]=3.8909637733035e+00; q[9][11]=4.0619358664202e-01;
522 q[9][12]=3.3647977631042e+00; q[9][13]=1.5173593259539e+00;
523 q[9][14]=3.8835540920564e-01; q[9][15]=3.5754441245967e-01;
524 q[9][16]=1.1790911972601e+00; q[9][17]=3.4198578754023e-01;
525 q[9][18]=6.7461709322842e-01; q[9][19]=8.3118394054582e+00;
527 q[10][11]=4.4557027426059e-01; q[10][12]=6.0305593795716e+00;
528 q[10][13]=2.0648397032375e+00; q[10][14]=3.7455568747097e-01;
529 q[10][15]=3.5296918452729e-01; q[10][16]=9.1525985769421e-01;
530 q[10][17]=6.9147463459998e-01; q[10][18]=8.1124585632307e-01;
531 q[10][19]=2.2314056889131e+00;
533 q[11][12]=1.0730611843319e+00; q[11][13]=2.6692475051102e-01;
534 q[11][14]=1.0473834507215e+00; q[11][15]=1.7521659178195e+00;
535 q[11][16]=1.3038752007987e+00; q[11][17]=3.3224304063396e-01;
536 q[11][18]=7.1799348690032e-01; q[11][19]=4.9813847530407e-01;
538 q[12][13]=1.7738551688305e+00; q[12][14]=4.5412362510273e-01;
539 q[12][15]=9.1872341574605e-01; q[12][16]=1.4885480537218e+00;
540 q[12][17]=8.8810109815193e-01; q[12][18]=9.5168216224591e-01;
541 q[12][19]=2.5758507553153e+00;
543 q[13][14]=2.3359790962888e-01; q[13][15]=5.4002764482413e-01;
544 q[13][16]=4.8820611879305e-01; q[13][17]=2.0743248934965e+00;
545 q[13][18]=6.7472604308008e+00; q[13][19]=8.3811961017754e-01;
547 q[14][15]=1.1691295777157e+00; q[14][16]=1.0054516831488e+00;
548 q[14][17]=2.5221483002727e-01; q[14][18]=3.6940531935451e-01;
549 q[14][19]=4.9690841067567e-01;
551 q[15][16]=5.1515562922704e+00; q[15][17]=3.8792562209837e-01;
552 q[15][18]=7.9675152076106e-01; q[15][19]=5.6192545744165e-01;
554 q[16][17]=5.1312812689059e-01; q[16][18]=8.0101024319939e-01;
555 q[16][19]=2.2530740511763e+00;
557 q[17][18]=4.0544190065580e+00; q[17][19]=2.6650873142646e-01;
559 q[18][19]=1.0000000000000e+00;
562 f[0]=0.074; f[1]=0.052; f[2]=0.045; f[3]=0.054;
563 f[4]=0.025; f[5]=0.034; f[6]=0.054; f[7]=0.074;
564 f[8]=0.026; f[9]=0.068; f[10]=0.099; f[11]=0.058;
565 f[12]=0.025; f[13]=0.047; f[14]=0.039; f[15]=0.057;
566 f[16]=0.051; f[17]=0.013; f[18]=0.032; f[19]=0.073;
571 void vtmvdata(dmatrix q, double *f)
574 * variable time (VT) model for amino acid evolution
575 * Mueller, T. and Vingron, M. (1999)
576 * "Modeling Amino Acid Replacement"
577 * Journal of Comp. Biology
580 /* amino acid frequencies */
613 q[0][10] = 0.424630 ;
614 q[0][11] = 0.393245 ;
615 q[0][12] = 0.211550 ;
616 q[0][13] = 0.116646 ;
617 q[0][14] = 0.399143 ;
618 q[0][15] = 1.817198 ;
619 q[0][16] = 0.877877 ;
620 q[0][17] = 0.030309 ;
621 q[0][18] = 0.087061 ;
622 q[0][19] = 1.230985 ;
632 q[1][10] = 0.192364 ;
633 q[1][11] = 1.755838 ;
634 q[1][12] = 0.087930 ;
635 q[1][13] = 0.042569 ;
636 q[1][14] = 0.128480 ;
637 q[1][15] = 0.292327 ;
638 q[1][16] = 0.204109 ;
639 q[1][17] = 0.046417 ;
640 q[1][18] = 0.097010 ;
641 q[1][19] = 0.113146 ;
650 q[2][10] = 0.069245 ;
651 q[2][11] = 0.503060 ;
652 q[2][12] = 0.057420 ;
653 q[2][13] = 0.039769 ;
654 q[2][14] = 0.083956 ;
655 q[2][15] = 0.847049 ;
656 q[2][16] = 0.471268 ;
657 q[2][17] = 0.010459 ;
658 q[2][18] = 0.093268 ;
659 q[2][19] = 0.049824 ;
667 q[3][10] = 0.060863 ;
668 q[3][11] = 0.261101 ;
669 q[3][12] = 0.012182 ;
670 q[3][13] = 0.016577 ;
671 q[3][14] = 0.160063 ;
672 q[3][15] = 0.461519 ;
673 q[3][16] = 0.178197 ;
674 q[3][17] = 0.011393 ;
675 q[3][18] = 0.051664 ;
676 q[3][19] = 0.048769 ;
683 q[4][10] = 0.091709 ;
684 q[4][11] = 0.004067 ;
685 q[4][12] = 0.023690 ;
686 q[4][13] = 0.051127 ;
687 q[4][14] = 0.011137 ;
688 q[4][15] = 0.175270 ;
689 q[4][16] = 0.079511 ;
690 q[4][17] = 0.007732 ;
691 q[4][18] = 0.042823 ;
692 q[4][19] = 0.163831 ;
698 q[5][10] = 0.243530 ;
699 q[5][11] = 0.738208 ;
700 q[5][12] = 0.120801 ;
701 q[5][13] = 0.026235 ;
702 q[5][14] = 0.156570 ;
703 q[5][15] = 0.358017 ;
704 q[5][16] = 0.248992 ;
705 q[5][17] = 0.021248 ;
706 q[5][18] = 0.062544 ;
707 q[5][19] = 0.112027 ;
712 q[6][10] = 0.151924 ;
713 q[6][11] = 0.888630 ;
714 q[6][12] = 0.058643 ;
715 q[6][13] = 0.028168 ;
716 q[6][14] = 0.205134 ;
717 q[6][15] = 0.406035 ;
718 q[6][16] = 0.321028 ;
719 q[6][17] = 0.018844 ;
720 q[6][18] = 0.055200 ;
721 q[6][19] = 0.205868 ;
725 q[7][10] = 0.087056 ;
726 q[7][11] = 0.193243 ;
727 q[7][12] = 0.046560 ;
728 q[7][13] = 0.050143 ;
729 q[7][14] = 0.124492 ;
730 q[7][15] = 0.612843 ;
731 q[7][16] = 0.136266 ;
732 q[7][17] = 0.023990 ;
733 q[7][18] = 0.037568 ;
734 q[7][19] = 0.082579 ;
737 q[8][10] = 0.103552 ;
738 q[8][11] = 0.153323 ;
739 q[8][12] = 0.021157 ;
740 q[8][13] = 0.079807 ;
741 q[8][14] = 0.078892 ;
742 q[8][15] = 0.167406 ;
743 q[8][16] = 0.101117 ;
744 q[8][17] = 0.020009 ;
745 q[8][18] = 0.286027 ;
746 q[8][19] = 0.068575 ;
748 q[9][10] = 2.089890 ;
749 q[9][11] = 0.093181 ;
750 q[9][12] = 0.493845 ;
751 q[9][13] = 0.321020 ;
752 q[9][14] = 0.054797 ;
753 q[9][15] = 0.081567 ;
754 q[9][16] = 0.376588 ;
755 q[9][17] = 0.034954 ;
756 q[9][18] = 0.086237 ;
757 q[9][19] = 3.654430 ;
759 q[10][11] = 0.201204 ;
760 q[10][12] = 1.105667 ;
761 q[10][13] = 0.946499 ;
762 q[10][14] = 0.169784 ;
763 q[10][15] = 0.214977 ;
764 q[10][16] = 0.243227 ;
765 q[10][17] = 0.083439 ;
766 q[10][18] = 0.189842 ;
767 q[10][19] = 1.337571 ;
769 q[11][12] = 0.096474 ;
770 q[11][13] = 0.038261 ;
771 q[11][14] = 0.212302 ;
772 q[11][15] = 0.400072 ;
773 q[11][16] = 0.446646 ;
774 q[11][17] = 0.023321 ;
775 q[11][18] = 0.068689 ;
776 q[11][19] = 0.144587 ;
778 q[12][13] = 0.173052 ;
779 q[12][14] = 0.010363 ;
780 q[12][15] = 0.090515 ;
781 q[12][16] = 0.184609 ;
782 q[12][17] = 0.022019 ;
783 q[12][18] = 0.073223 ;
784 q[12][19] = 0.307309 ;
786 q[13][14] = 0.042564 ;
787 q[13][15] = 0.138119 ;
788 q[13][16] = 0.085870 ;
789 q[13][17] = 0.128050 ;
790 q[13][18] = 0.898663 ;
791 q[13][19] = 0.247329 ;
793 q[14][15] = 0.430431 ;
794 q[14][16] = 0.207143 ;
795 q[14][17] = 0.014584 ;
796 q[14][18] = 0.032043 ;
797 q[14][19] = 0.129315 ;
799 q[15][16] = 1.767766 ;
800 q[15][17] = 0.035933 ;
801 q[15][18] = 0.121979 ;
802 q[15][19] = 0.127700 ;
804 q[16][17] = 0.020437 ;
805 q[16][18] = 0.094617 ;
806 q[16][19] = 0.740372 ;
808 q[17][18] = 0.124746 ;
809 q[17][19] = 0.022134 ;
811 q[18][19] = 0.125733 ;
817 * WAG matrix: Simon Whelan and Nick Goldman
821 void wagdata(dmatrix q, double *f)
824 * WAG model of amino acid evolution
826 * S. Whelan and N. Goldman. 2000. In prep.
828 * presented at the MASAMB-X workshop in Cambridge
830 * Whelan, S., and N. Goldman. 2000.
831 * The WAG amino acid rate matrix.
832 * Manuscript in prep.
836 q[0][1] = 0.610810; q[0][2] = 0.569079;
837 q[0][3] = 0.821500; q[0][4] = 1.141050;
838 q[0][5] = 1.011980; q[0][6] = 1.756410;
839 q[0][7] = 1.572160; q[0][8] = 0.354813;
840 q[0][9] = 0.219023; q[0][10] = 0.443935;
841 q[0][11] = 1.005440; q[0][12] = 0.989475;
842 q[0][13] = 0.233492; q[0][14] = 1.594890;
843 q[0][15] = 3.733380; q[0][16] = 2.349220;
844 q[0][17] = 0.125227; q[0][18] = 0.268987;
847 q[1][2] = 0.711690; q[1][3] = 0.165074;
848 q[1][4] = 0.585809; q[1][5] = 3.360330;
849 q[1][6] = 0.488649; q[1][7] = 0.650469;
850 q[1][8] = 2.362040; q[1][9] = 0.206722;
851 q[1][10] = 0.551450; q[1][11] = 5.925170;
852 q[1][12] = 0.758446; q[1][13] = 0.116821;
853 q[1][14] = 0.753467; q[1][15] = 1.357640;
854 q[1][16] = 0.613776; q[1][17] = 1.294610;
855 q[1][18] = 0.423612; q[1][19] = 0.280336;
857 q[2][3] = 6.013660; q[2][4] = 0.296524;
858 q[2][5] = 1.716740; q[2][6] = 1.056790;
859 q[2][7] = 1.253910; q[2][8] = 4.378930;
860 q[2][9] = 0.615636; q[2][10] = 0.147156;
861 q[2][11] = 3.334390; q[2][12] = 0.224747;
862 q[2][13] = 0.110793; q[2][14] = 0.217538;
863 q[2][15] = 4.394450; q[2][16] = 2.257930;
864 q[2][17] = 0.078463; q[2][18] = 1.208560;
867 q[3][4] = 0.033379; q[3][5] = 0.691268;
868 q[3][6] = 6.833400; q[3][7] = 0.961142;
869 q[3][8] = 1.032910; q[3][9] = 0.043523;
870 q[3][10] = 0.093930; q[3][11] = 0.533362;
871 q[3][12] = 0.116813; q[3][13] = 0.052004;
872 q[3][14] = 0.472601; q[3][15] = 1.192810;
873 q[3][16] = 0.417372; q[3][17] = 0.146348;
874 q[3][18] = 0.363243; q[3][19] = 0.169417;
876 q[4][5] = 0.109261; q[4][6] = 0.023920;
877 q[4][7] = 0.341086; q[4][8] = 0.275403;
878 q[4][9] = 0.189890; q[4][10] = 0.428414;
879 q[4][11] = 0.083649; q[4][12] = 0.437393;
880 q[4][13] = 0.441300; q[4][14] = 0.122303;
881 q[4][15] = 1.560590; q[4][16] = 0.570186;
882 q[4][17] = 0.795736; q[4][18] = 0.604634;
885 q[5][6] = 6.048790; q[5][7] = 0.366510;
886 q[5][8] = 4.749460; q[5][9] = 0.131046;
887 q[5][10] = 0.964886; q[5][11] = 4.308310;
888 q[5][12] = 1.705070; q[5][13] = 0.110744;
889 q[5][14] = 1.036370; q[5][15] = 1.141210;
890 q[5][16] = 0.954144; q[5][17] = 0.243615;
891 q[5][18] = 0.252457; q[5][19] = 0.333890;
893 q[6][7] = 0.630832; q[6][8] = 0.635025;
894 q[6][9] = 0.141320; q[6][10] = 0.172579;
895 q[6][11] = 2.867580; q[6][12] = 0.353912;
896 q[6][13] = 0.092310; q[6][14] = 0.755791;
897 q[6][15] = 0.782467; q[6][16] = 0.914814;
898 q[6][17] = 0.172682; q[6][18] = 0.217549;
901 q[7][8] = 0.276379; q[7][9] = 0.034151;
902 q[7][10] = 0.068651; q[7][11] = 0.415992;
903 q[7][12] = 0.194220; q[7][13] = 0.055288;
904 q[7][14] = 0.273149; q[7][15] = 1.486700;
905 q[7][16] = 0.251477; q[7][17] = 0.374321;
906 q[7][18] = 0.114187; q[7][19] = 0.209108;
908 q[8][9] = 0.152215; q[8][10] = 0.555096;
909 q[8][11] = 0.992083; q[8][12] = 0.450867;
910 q[8][13] = 0.756080; q[8][14] = 0.771387;
911 q[8][15] = 0.822459; q[8][16] = 0.525511;
912 q[8][17] = 0.289998; q[8][18] = 4.290350;
915 q[9][10] = 3.517820; q[9][11] = 0.360574;
916 q[9][12] = 4.714220; q[9][13] = 1.177640;
917 q[9][14] = 0.111502; q[9][15] = 0.353443;
918 q[9][16] = 1.615050; q[9][17] = 0.234326;
919 q[9][18] = 0.468951; q[9][19] = 8.659740;
921 q[10][11] = 0.287583; q[10][12] = 5.375250;
922 q[10][13] = 2.348200; q[10][14] = 0.462018;
923 q[10][15] = 0.382421; q[10][16] = 0.364222;
924 q[10][17] = 0.740259; q[10][18] = 0.443205;
925 q[10][19] = 1.997370;
927 q[11][12] = 1.032220; q[11][13] = 0.098843;
928 q[11][14] = 0.619503; q[11][15] = 1.073780;
929 q[11][16] = 1.537920; q[11][17] = 0.152232;
930 q[11][18] = 0.147411; q[11][19] = 0.342012;
932 q[12][13] = 1.320870; q[12][14] = 0.194864;
933 q[12][15] = 0.556353; q[12][16] = 1.681970;
934 q[12][17] = 0.570369; q[12][18] = 0.473810;
935 q[12][19] = 2.282020;
937 q[13][14] = 0.179896; q[13][15] = 0.606814;
938 q[13][16] = 0.191467; q[13][17] = 1.699780;
939 q[13][18] = 7.154480; q[13][19] = 0.725096;
941 q[14][15] = 1.786490; q[14][16] = 0.885349;
942 q[14][17] = 0.156619; q[14][18] = 0.239607;
943 q[14][19] = 0.351250;
945 q[15][16] = 4.847130; q[15][17] = 0.578784;
946 q[15][18] = 0.872519; q[15][19] = 0.258861;
948 q[16][17] = 0.126678; q[16][18] = 0.325490;
949 q[16][19] = 1.547670;
951 q[17][18] = 2.763540; q[17][19] = 0.409817;
953 q[18][19] = 0.347826;
955 /* original frequencies */
978 void cprev45data(dmatrix q, double *f)
980 /* cpREV45 model of amino acid evolution
981 * Adachi, J., P.J. Waddell, W. Martin, and M. Hasegawa. 2000.
982 * J. Mol. Evol. 50:348-358
983 * (reconstructed from 45 chloroplast genomes)
985 q[0][1] = 105; q[0][2] = 227;
986 q[0][3] = 175; q[0][4] = 669;
987 q[0][5] = 157; q[0][6] = 499;
988 q[0][7] = 665; q[0][8] = 66;
989 q[0][9] = 145; q[0][10] = 197;
990 q[0][11] = 236; q[0][12] = 185;
991 q[0][13] = 68; q[0][14] = 490;
992 q[0][15] = 2440; q[0][16] = 1340;
993 q[0][17] = 14; q[0][18] = 56;
996 q[1][2] = 357; q[1][3] = 43;
997 q[1][4] = 823; q[1][5] = 1745;
998 q[1][6] = 152; q[1][7] = 243;
999 q[1][8] = 715; q[1][9] = 136;
1000 q[1][10] = 203; q[1][11] = 4482;
1001 q[1][12] = 125; q[1][13] = 53;
1002 q[1][14] = 87; q[1][15] = 385;
1003 q[1][16] = 314; q[1][17] = 230;
1004 q[1][18] = 323; q[1][19] = 92;
1006 q[2][3] = 4435; q[2][4] = 538;
1007 q[2][5] = 768; q[2][6] = 1055;
1008 q[2][7] = 653; q[2][8] = 1405;
1009 q[2][9] = 168; q[2][10] = 113;
1010 q[2][11] = 2430; q[2][12] = 61;
1011 q[2][13] = 97; q[2][14] = 173;
1012 q[2][15] = 2085; q[2][16] = 1393;
1013 q[2][17] = 40; q[2][18] = 754;
1016 q[3][4] = 10; q[3][5] = 400;
1017 q[3][6] = 3691; q[3][7] = 431;
1018 q[3][8] = 331; q[3][9] = 10;
1019 q[3][10] = 10; q[3][11] = 412;
1020 q[3][12] = 47; q[3][13] = 22;
1021 q[3][14] = 170; q[3][15] = 590;
1022 q[3][16] = 266; q[3][17] = 18;
1023 q[3][18] = 281; q[3][19] = 75;
1025 q[4][5] = 10; q[4][6] = 10;
1026 q[4][7] = 303; q[4][8] = 441;
1027 q[4][9] = 280; q[4][10] = 396;
1028 q[4][11] = 48; q[4][12] = 159;
1029 q[4][13] = 726; q[4][14] = 285;
1030 q[4][15] = 2331; q[4][16] = 576;
1031 q[4][17] = 435; q[4][18] = 1466;
1034 q[5][6] = 3122; q[5][7] = 133;
1035 q[5][8] = 1269; q[5][9] = 92;
1036 q[5][10] = 286; q[5][11] = 3313;
1037 q[5][12] = 202; q[5][13] = 10;
1038 q[5][14] = 323; q[5][15] = 396;
1039 q[5][16] = 241; q[5][17] = 53;
1040 q[5][18] = 391; q[5][19] = 54;
1042 q[6][7] = 379; q[6][8] = 162;
1043 q[6][9] = 148; q[6][10] = 82;
1044 q[6][11] = 2629; q[6][12] = 113;
1045 q[6][13] = 145; q[6][14] = 185;
1046 q[6][15] = 568; q[6][16] = 369;
1047 q[6][17] = 63; q[6][18] = 142;
1050 q[7][8] = 19; q[7][9] = 40;
1051 q[7][10] = 20; q[7][11] = 263;
1052 q[7][12] = 21; q[7][13] = 25;
1053 q[7][14] = 28; q[7][15] = 691;
1054 q[7][16] = 92; q[7][17] = 82;
1055 q[7][18] = 10; q[7][19] = 91;
1057 q[8][9] = 29; q[8][10] = 66;
1058 q[8][11] = 305; q[8][12] = 10;
1059 q[8][13] = 127; q[8][14] = 152;
1060 q[8][15] = 303; q[8][16] = 32;
1061 q[8][17] = 69; q[8][18] = 1971;
1064 q[9][10] = 1745; q[9][11] = 345;
1065 q[9][12] = 1772; q[9][13] = 454;
1066 q[9][14] = 117; q[9][15] = 216;
1067 q[9][16] = 1040; q[9][17] = 42;
1068 q[9][18] = 89; q[9][19] = 4797;
1070 q[10][11] = 218; q[10][12] = 1351;
1071 q[10][13] = 1268; q[10][14] = 219;
1072 q[10][15] = 516; q[10][16] = 156;
1073 q[10][17] = 159; q[10][18] = 189;
1076 q[11][12] = 193; q[11][13] = 72;
1077 q[11][14] = 302; q[11][15] = 868;
1078 q[11][16] = 918; q[11][17] = 10;
1079 q[11][18] = 247; q[11][19] = 249;
1081 q[12][13] = 327; q[12][14] = 100;
1082 q[12][15] = 93; q[12][16] = 645;
1083 q[12][17] = 86; q[12][18] = 215;
1086 q[13][14] = 43; q[13][15] = 487;
1087 q[13][16] = 148; q[13][17] = 468;
1088 q[13][18] = 2370; q[13][19] = 317;
1090 q[14][15] = 1202; q[14][16] = 260;
1091 q[14][17] = 49; q[14][18] = 97;
1094 q[15][16] = 2151; q[15][17] = 73;
1095 q[15][18] = 522; q[15][19] = 167;
1097 q[16][17] = 29; q[16][18] = 71;
1100 q[17][18] = 346; q[17][19] = 10;