.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2944_80x1495_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 494 patterns found. (out of a total of 1495 sites) . 1077 sites without polymorphism (72.04%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -9336.8033] [GTR parameters ] . ( 4 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 4 sec) [ -9236.3667] [Topology ] . ( 6 sec) [ -9106.7265] [Topology ] . ( 8 sec) [ -9073.5495] [Topology ] . ( 10 sec) [ -9062.8635] [Topology ] . ( 11 sec) [ -9058.7107] [Topology ] . ( 13 sec) [ -9056.6216] [Topology ] . ( 15 sec) [ -9055.9627] [Topology ] . ( 17 sec) [ -9055.6109] [Topology ] . ( 19 sec) [ -9055.0866] [Topology ] . ( 21 sec) [ -9053.7351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -9052.4667] [GTR parameters ] . ( 37 sec) [ -9024.8575] [Alpha ][ 0.313875] . ( 37 sec) [ -9024.8575] [Topology ] . ( 39 sec) [ -9024.3363] [Topology ] . ( 41 sec) [ -9024.0852] [Topology ] . ( 43 sec) [ -9023.9339] [Topology ] . ( 45 sec) [ -9023.8381] [Topology ] . ( 46 sec) [ -9023.7762] [Topology ] . ( 48 sec) [ -9023.7359] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -9023.4456] [GTR parameters ] . ( 62 sec) [ -9023.4363] [Alpha ][ 0.311241] . ( 62 sec) [ -9023.4363] [Topology ] . ( 64 sec) [ -9023.4001] [Topology ] . ( 66 sec) [ -9023.3767] [Topology ] . ( 68 sec) [ -9023.3613] [Topology ] . ( 70 sec) [ -9023.3512] [Topology ] . ( 71 sec) [ -9023.3445] [Topology ] . ( 73 sec) [ -9023.3401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -9023.3391] [GTR parameters ] . ( 86 sec) [ -9023.3390] [Alpha ][ 0.310868] . ( 86 sec) [ -9023.3390] [Topology ] . ( 88 sec) [ -9023.3357] [Topology ] . ( 90 sec) [ -9023.3336] [Topology ] . ( 92 sec) [ -9023.3322] [Topology ] . ( 94 sec) [ -9023.3312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 106 sec) [ -9023.3306] [GTR parameters ] . ( 107 sec) [ -9023.3306] [Alpha ][ 0.310868] . ( 107 sec) [ -9023.3306] [Topology ] . ( 108 sec) [ -9023.3300] [Topology ] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -9023.3299] [GTR parameters ] . ( 121 sec) [ -9023.3299] [Alpha ][ 0.310868] . ( 121 sec) [ -9023.3299] [Topology ] . ( 123 sec) [ -9023.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 153 sec) [ -9336.8033] [GTR parameters ] . ( 153 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 154 sec) [ -9234.6589] [ 1259] [depth= 1] . ( 154 sec) [ -9230.9702] [ 1259] [depth= 1] . ( 154 sec) [ -9228.1890] [ 1256] [depth= 1] . ( 154 sec) [ -9227.9857] [ 1257] [depth= 1] . ( 154 sec) [ -9225.8774] [ 1257] [depth= 1] . ( 154 sec) [ -9225.2595] [ 1257] [depth= 1] . ( 155 sec) [ -9222.6440] [ 1256] [depth= 1] . ( 155 sec) [ -9219.7109] [ 1257] [depth= 1] . ( 156 sec) [ -9218.8532] [ 1256] [depth= 1] . ( 156 sec) [ -9218.4006] [ 1255] [depth= 1] . ( 157 sec) [ -9212.6493] [ 1254] [depth= 1] . ( 157 sec) [ -9212.2838] [ 1255] [depth= 1] . ( 158 sec) [ -9208.1121] [ 1254] [depth= 1] . ( 158 sec) [ -9207.8081] [ 1255] [depth= 1] . ( 158 sec) [ -9206.2989] [ 1254] [depth= 1] . ( 159 sec) [ -9205.5922] [ 1254] [depth= 1] . ( 159 sec) [ -9203.7407] [ 1253] [depth= 2] . ( 159 sec) [ -9198.4128] [ 1251] [depth= 1] . ( 159 sec) [ -9197.9473] [ 1251] [depth= 1] . ( 159 sec) [ -9194.8922] [ 1253] [depth= 4] . ( 160 sec) [ -9194.1529] [ 1253] [depth= 1] . ( 160 sec) [ -9194.0345] [ 1254] [depth= 1] . ( 161 sec) [ -9193.9770] [ 1255] [depth= 1] . ( 161 sec) [ -9190.8641] [ 1255] [depth= 1] . ( 161 sec) [ -9190.1195] [ 1255] [depth= 1] . ( 161 sec) [ -9186.4363] [ 1254] [depth= 1] . ( 161 sec) [ -9186.4252] [ 1254] [depth= 1] . ( 161 sec) [ -9184.3388] [ 1254] [depth= 1] . ( 162 sec) [ -9184.1906] [ 1254] [depth= 1] . ( 162 sec) [ -9179.8249] [ 1255] [depth= 3] . ( 163 sec) [ -9173.4594] [ 1253] [depth= 1] . ( 164 sec) [ -9173.2643] [ 1253] [depth= 1] . ( 164 sec) [ -9172.8667] [ 1252] [depth= 1] . ( 164 sec) [ -9171.3737] [ 1252] [depth= 4] . ( 164 sec) [ -9166.4254] [ 1250] [depth= 3] . ( 165 sec) [ -9164.5478] [ 1250] [depth= 2] . ( 165 sec) [ -9157.2810] [ 1248] [depth= 2] . ( 165 sec) [ -9156.6451] [ 1248] [depth= 1] . ( 166 sec) [ -9155.3311] [ 1250] [depth= 2] . ( 166 sec) [ -9154.9412] [ 1250] [depth= 1] . ( 167 sec) [ -9154.9160] [ 1250] [depth= 1] . ( 167 sec) [ -9154.5267] [ 1251] [depth= 1] . ( 168 sec) [ -9153.4468] [ 1250] [depth= 1] . ( 169 sec) [ -9136.8895] [ 1253] [depth= 1] . ( 169 sec) [ -9111.0896] [ 1247] [depth= 2] . ( 170 sec) [ -9103.5037] [ 1246] [depth= 2] . ( 171 sec) [ -9102.0583] [ 1246] [depth= 1] . ( 172 sec) [ -9098.5560] [ 1245] [depth= 2] . ( 172 sec) [ -9096.5242] [ 1245] [depth= 1] . ( 174 sec) [ -9094.9666] [ 1245] [depth= 1] . ( 174 sec) [ -9094.7728] [ 1245] [depth= 1] . ( 174 sec) [ -9094.4759] [ 1245] [depth= 1] . ( 175 sec) [ -9091.9699] [ 1244] [depth= 4] . ( 175 sec) [ -9091.8945] [ 1245] [depth= 6] . ( 177 sec) [ -9091.6959] [ 1245] [depth= 1] . ( 178 sec) [ -9090.6316] [ 1245] [depth= 1] . ( 178 sec) [ -9089.6504] [ 1244] [depth= 5] . ( 178 sec) [ -9089.1977] [ 1244] [depth= 1] . ( 180 sec) [ -9037.4453] [Branch lengths ] . ( 183 sec) [ -9036.9712] [GTR parameters ] . ( 183 sec) [ -9010.3820] [Alpha ][ 0.310787] . ( 185 sec) [ -9009.8194] [ 1243] [depth= 1] . ( 187 sec) [ -9008.7390] [ 1241] [depth= 1] . ( 190 sec) [ -9008.5657] [ 1241] [depth= 3] . ( 190 sec) [ -9007.6255] [ 1241] [depth= 1] . ( 194 sec) [ -9006.0591] [ 1241] [depth= 4] . ( 196 sec) [ -9006.0276] [ 1241] [depth= 1] . ( 197 sec) [ -9005.9448] [ 1241] [depth= 1] . ( 198 sec) [ -9005.8222] [ 1241] [depth= 1] . ( 200 sec) [ -9005.7829] [ 1242] [depth= 1] . ( 204 sec) [ -9005.7502] [ 1243] [depth= 2] . ( 209 sec) [ -9005.4718] [ 1243] [depth= 3] . ( 210 sec) [ -9005.1910] [ 1243] [depth= 2] . ( 210 sec) [ -9004.7966] [ 1244] [depth= 1] . ( 211 sec) [ -9002.4169] [ 1243] [depth= 1] . ( 211 sec) [ -9002.3837] [ 1243] [depth= 1] . ( 211 sec) [ -9002.3174] [ 1243] [depth= 1] . ( 212 sec) [ -9002.2916] [ 1243] [depth= 1] . ( 213 sec) [ -9002.1439] [ 1243] [depth= 1] . ( 217 sec) [ -8993.9006] [Branch lengths ] . ( 219 sec) [ -8993.4244] [GTR parameters ] . ( 219 sec) [ -8993.4054] [Alpha ][ 0.314504] . ( 241 sec) [ -8993.3373] [ 1243] [depth= 1] . ( 257 sec) [ -8991.8159] [Branch lengths ] . ( 257 sec) [ -8991.8158] [GTR parameters ] . ( 257 sec) [ -8991.8157] [Alpha ][ 0.314190] . ( 296 sec) [ -8991.4819] [Branch lengths ] . ( 343 sec) [ -8991.4406] [ 1240] [depth= 2] . ( 343 sec) [ -8991.1315] [ 1240] [depth= 1] . ( 344 sec) [ -8991.0860] [ 1239] [depth= 1] . ( 345 sec) [ -8991.0359] [ 1240] [depth= 1] . ( 374 sec) [ -8989.7562] [Branch lengths ] . ( 376 sec) [ -8989.7255] [GTR parameters ] . ( 376 sec) [ -8989.7255] [Alpha ][ 0.314190] . ( 458 sec) [ -8989.6755] [Branch lengths ] . ( 459 sec) [ -8989.6755] [Topology ] . ( 460 sec) [ -8989.6664] [Topology ] . ( 462 sec) [ -8989.6619] [Topology ] . ( 464 sec) [ -8989.6590] [Topology ] . ( 466 sec) [ -8989.6571] [Topology ] . ( 468 sec) [ -8989.6559] [Topology ] . ( 470 sec) [ -8989.6550] [Topology ] . ( 471 sec) [ -8989.6541] [GTR parameters ] . ( 471 sec) [ -8989.6536] [Alpha ][ 0.313531] . ( 471 sec) [ -8989.6536] [Topology ] . ( 473 sec) [ -8989.6529] [Topology ] . ( 474 sec) [ -8989.6528] [GTR parameters ] . ( 474 sec) [ -8989.6528] [Alpha ][ 0.313531] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9023.329451 . Log likelihood obtained after SPR moves : -8989.652837 . Log likelihood of the current tree: -8989.652837. . Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'... . Time used 0h8m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 481.62user 0.00system 8:06.93elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps