.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2933_99x1634_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 : 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... . 578 patterns found. (out of a total of 1634 sites) . 1151 sites without polymorphism (70.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -7976.1365] [GTR parameters ] . ( 6 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 13 sec) [ -7919.7111] [ 1130] [depth= 1] . ( 13 sec) [ -7892.1045] [ 1125] [depth= 1] . ( 13 sec) [ -7886.8255] [ 1122] [depth= 3] . ( 14 sec) [ -7877.2862] [ 1120] [depth= 2] . ( 14 sec) [ -7877.1208] [ 1120] [depth= 1] . ( 34 sec) [ -7877.0627] [ 1125] [depth= 1] . ( 38 sec) [ -7876.7699] [ 1125] [depth= 1] . ( 38 sec) [ -7876.5142] [ 1125] [depth= 1] . ( 38 sec) [ -7876.4680] [ 1125] [depth= 1] . ( 38 sec) [ -7876.4563] [ 1125] [depth= 2] . ( 60 sec) [ -7868.1623] [ 1124] [depth= 1] . ( 68 sec) [ -7864.8399] [ 1124] [depth= 1] . ( 70 sec) [ -7862.7022] [ 1124] [depth= 1] . ( 75 sec) [ -7843.2854] [ 1125] [depth= 2] . ( 75 sec) [ -7842.2243] [ 1124] [depth= 2] . ( 75 sec) [ -7841.6203] [ 1124] [depth= 1] . ( 75 sec) [ -7839.4831] [ 1126] [depth= 1] . ( 79 sec) [ -7839.1417] [ 1126] [depth= 2] . ( 79 sec) [ -7831.6930] [ 1124] [depth= 1] . ( 90 sec) [ -7831.6502] [ 1124] [depth= 1] . ( 91 sec) [ -7831.3547] [ 1124] [depth= 1] . ( 106 sec) [ -7801.4069] [ 1118] [depth= 9] . ( 107 sec) [ -7799.2532] [ 1118] [depth= 1] . ( 117 sec) [ -7798.0461] [ 1116] [depth= 1] . ( 121 sec) [ -7797.4228] [ 1116] [depth= 2] . ( 124 sec) [ -7796.2635] [ 1111] [depth= 1] . ( 124 sec) [ -7796.1892] [ 1111] [depth= 1] . ( 124 sec) [ -7795.6908] [ 1111] [depth= 2] . ( 125 sec) [ -7790.8073] [ 1117] [depth= 3] . ( 128 sec) [ -7787.4798] [ 1116] [depth= 1] . ( 129 sec) [ -7787.4149] [ 1115] [depth= 1] . ( 136 sec) [ -7786.2047] [ 1116] [depth= 1] . ( 136 sec) [ -7783.0405] [ 1115] [depth= 1] . ( 142 sec) [ -7782.8881] [ 1115] [depth= 1] . ( 142 sec) [ -7782.7501] [ 1115] [depth= 1] . ( 142 sec) [ -7780.4356] [ 1114] [depth= 4] . ( 142 sec) [ -7771.1903] [ 1112] [depth= 4] . ( 143 sec) [ -7770.7882] [ 1112] [depth= 3] . ( 143 sec) [ -7770.7249] [ 1112] [depth= 2] . ( 143 sec) [ -7770.6306] [ 1112] [depth= 1] . ( 143 sec) [ -7770.0619] [ 1112] [depth= 3] . ( 151 sec) [ -7765.4010] [ 1111] [depth= 2] . ( 154 sec) [ -7765.2654] [ 1111] [depth= 1] . ( 154 sec) [ -7765.0889] [ 1111] [depth= 1] . ( 154 sec) [ -7764.1434] [ 1111] [depth= 1] . ( 154 sec) [ -7763.2515] [ 1111] [depth= 2] . ( 155 sec) [ -7759.9209] [ 1110] [depth= 2] . ( 155 sec) [ -7746.3412] [ 1108] [depth= 6] . ( 155 sec) [ -7745.7006] [ 1108] [depth= 1] . ( 155 sec) [ -7744.9003] [ 1108] [depth= 1] . ( 155 sec) [ -7744.2216] [ 1108] [depth= 4] . ( 155 sec) [ -7744.1157] [ 1108] [depth= 2] . ( 156 sec) [ -7743.9350] [ 1108] [depth= 5] . ( 156 sec) [ -7743.7424] [ 1108] [depth= 2] . ( 156 sec) [ -7743.2760] [ 1108] [depth= 1] . ( 156 sec) [ -7743.1701] [ 1108] [depth= 1] . ( 157 sec) [ -7742.4983] [ 1109] [depth= 2] . ( 157 sec) [ -7741.5463] [ 1109] [depth= 1] . ( 157 sec) [ -7741.3276] [ 1109] [depth= 1] . ( 157 sec) [ -7740.0695] [ 1108] [depth= 3] . ( 165 sec) [ -7739.9119] [ 1108] [depth= 1] . ( 165 sec) [ -7739.2058] [ 1108] [depth= 1] . ( 167 sec) [ -7737.6184] [ 1108] [depth= 1] . ( 167 sec) [ -7731.9762] [ 1108] [depth= 1] . ( 167 sec) [ -7726.3227] [ 1107] [depth= 1] . ( 167 sec) [ -7724.2945] [ 1106] [depth= 1] . ( 170 sec) [ -7724.2588] [ 1106] [depth= 1] . ( 175 sec) [ -7722.5682] [ 1107] [depth= 1] . ( 178 sec) [ -7721.1633] [ 1106] [depth= 1] . ( 180 sec) [ -7720.9370] [ 1106] [depth= 1] . ( 186 sec) [ -7720.1417] [ 1108] [depth= 2] . ( 186 sec) [ -7719.5808] [ 1110] [depth= 1] . ( 187 sec) [ -7719.4213] [ 1109] [depth= 1] . ( 192 sec) [ -7719.0485] [ 1110] [depth= 1] . ( 192 sec) [ -7715.0833] [ 1107] [depth= 5] . ( 192 sec) [ -7715.0697] [ 1107] [depth= 1] . ( 192 sec) [ -7714.9894] [ 1107] [depth= 1] . ( 195 sec) [ -7711.1012] [ 1107] [depth= 6] . ( 196 sec) [ -7704.5976] [ 1106] [depth= 4] . ( 196 sec) [ -7704.3947] [ 1106] [depth= 2] . ( 196 sec) [ -7701.0246] [ 1106] [depth= 4] . ( 198 sec) [ -7698.6120] [ 1106] [depth= 4] . ( 198 sec) [ -7698.5515] [ 1106] [depth= 1] . ( 198 sec) [ -7698.5197] [ 1106] [depth= 2] . ( 201 sec) [ -7697.6860] [ 1106] [depth= 1] . ( 202 sec) [ -7697.3610] [ 1106] [depth= 2] . ( 202 sec) [ -7697.2918] [ 1106] [depth= 1] . ( 204 sec) [ -7696.2709] [ 1108] [depth= 9] . ( 204 sec) [ -7695.6693] [ 1108] [depth= 2] . ( 204 sec) [ -7695.4750] [ 1108] [depth= 1] . ( 205 sec) [ -7694.7486] [ 1108] [depth= 1] . ( 205 sec) [ -7692.2043] [ 1107] [depth= 1] . ( 208 sec) [ -7691.9391] [ 1107] [depth= 1] . ( 210 sec) [ -7689.4517] [ 1106] [depth= 5] . ( 219 sec) [ -7689.0203] [ 1106] [depth= 1] . ( 219 sec) [ -7688.1665] [ 1105] [depth= 1] . ( 222 sec) [ -7688.0721] [ 1106] [depth= 5] . ( 222 sec) [ -7685.1713] [ 1106] [depth= 3] . ( 222 sec) [ -7684.9594] [ 1106] [depth= 1] . ( 222 sec) [ -7684.8730] [ 1106] [depth= 1] . ( 222 sec) [ -7684.7338] [ 1106] [depth= 5] . ( 223 sec) [ -7684.7062] [ 1106] [depth= 2] . ( 223 sec) [ -7684.6863] [ 1106] [depth= 4] . ( 223 sec) [ -7684.6580] [ 1106] [depth= 1] . ( 224 sec) [ -7684.6275] [ 1106] [depth= 3] . ( 230 sec) [ -7684.6093] [ 1106] [depth= 1] . ( 238 sec) [ -7684.5960] [ 1106] [depth= 1] . ( 263 sec) [ -7652.1703] [Branch lengths ] . ( 268 sec) [ -7649.5014] [GTR parameters ] . ( 268 sec) [ -7646.2923] [Alpha ][ 0.414131] . ( 281 sec) [ -7645.3863] [ 1096] [depth= 3] . ( 375 sec) [ -7645.3102] [ 1096] [depth= 2] . ( 456 sec) [ -7644.6827] [ 1098] [depth= 2] . ( 461 sec) [ -7644.5409] [ 1099] [depth= 1] . ( 476 sec) [ -7644.4781] [ 1099] [depth= 1] . ( 523 sec) [ -7644.4605] [ 1099] [depth= 3] . ( 541 sec) [ -7644.1069] [ 1098] [depth= 1] . ( 565 sec) [ -7641.1253] [ 1097] [depth= 2] . ( 599 sec) [ -7640.6810] [ 1096] [depth= 2] . ( 603 sec) [ -7640.5387] [ 1096] [depth= 2] . ( 622 sec) [ -7640.5251] [ 1096] [depth= 2] . ( 633 sec) [ -7639.7240] [ 1096] [depth= 4] . ( 637 sec) [ -7639.7064] [ 1096] [depth= 2] . ( 643 sec) [ -7638.5687] [ 1094] [depth= 5] . ( 643 sec) [ -7638.5368] [ 1094] [depth= 3] . ( 655 sec) [ -7634.4059] [ 1094] [depth= 1] . ( 663 sec) [ -7634.3321] [ 1094] [depth= 1] . ( 667 sec) [ -7634.1106] [ 1094] [depth= 1] . ( 677 sec) [ -7633.9359] [ 1094] [depth= 2] . ( 678 sec) [ -7633.9120] [ 1094] [depth= 1] . ( 680 sec) [ -7633.8492] [ 1094] [depth= 1] . ( 699 sec) [ -7633.4598] [ 1094] [depth= 7] . ( 703 sec) [ -7633.4353] [ 1094] [depth= 2] . ( 710 sec) [ -7633.3381] [ 1094] [depth= 1] . ( 753 sec) [ -7626.9722] [Branch lengths ] . ( 757 sec) [ -7626.7898] [GTR parameters ] . ( 757 sec) [ -7626.6623] [Alpha ][ 0.399270] . ( 775 sec) [ -7626.5176] [ 1098] [depth= 8] . ( 966 sec) [ -7626.0460] [ 1095] [depth= 2] . ( 1047 sec) [ -7625.8954] [ 1094] [depth= 4] . ( 1369 sec) [ -7623.7520] [Branch lengths ] . ( 1374 sec) [ -7623.7145] [GTR parameters ] . ( 1375 sec) [ -7623.7082] [Alpha ][ 0.402576] . ( 2072 sec) [ -7623.5333] [Branch lengths ] . ( 2263 sec) [ -7623.4988] [Branch lengths ] . ( 2263 sec) [ -7623.4988] [Topology ] . ( 2266 sec) [ -7623.4928] [Topology ] . ( 2269 sec) [ -7623.4899] [Topology ] . ( 2273 sec) [ -7623.4880] [Topology ] . ( 2276 sec) [ -7623.4869] [Topology ] . ( 2279 sec) [ -7623.4861] [Topology ] . ( 2280 sec) [ -7623.4852] [GTR parameters ] . ( 2281 sec) [ -7623.4846] [Alpha ][ 0.403613] . ( 2281 sec) [ -7623.4846] [Topology ] . ( 2284 sec) [ -7623.4838] [Topology ] . ( 2284 sec) [ -7623.4838] [GTR parameters ] . ( 2285 sec) [ -7623.4838] [Alpha ][ 0.404016] . Checking for NNIs, optimizing five branches... . ( 2309 sec) [ -7623.4260] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2334 sec) [ -7623.4259] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2359 sec) [ -7623.4208] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7623.420772. . Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'... . Time used 0h39m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1820.00user 0.00system 39:46.64elapsed 76%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps