.......................... 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 : 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 SPR moves)... . ( 4 sec) [ -9336.8033] [GTR parameters ] . ( 4 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 5 sec) [ -9234.6589] [ 1259] [depth= 1] . ( 5 sec) [ -9230.9702] [ 1259] [depth= 1] . ( 5 sec) [ -9228.1890] [ 1256] [depth= 1] . ( 5 sec) [ -9227.9857] [ 1257] [depth= 1] . ( 5 sec) [ -9225.8774] [ 1257] [depth= 1] . ( 5 sec) [ -9225.2595] [ 1257] [depth= 1] . ( 6 sec) [ -9222.6440] [ 1256] [depth= 1] . ( 6 sec) [ -9219.7109] [ 1257] [depth= 1] . ( 6 sec) [ -9218.8532] [ 1256] [depth= 1] . ( 6 sec) [ -9218.4006] [ 1255] [depth= 1] . ( 7 sec) [ -9212.6493] [ 1254] [depth= 1] . ( 7 sec) [ -9212.2838] [ 1255] [depth= 1] . ( 7 sec) [ -9208.1121] [ 1254] [depth= 1] . ( 7 sec) [ -9207.8081] [ 1255] [depth= 1] . ( 7 sec) [ -9206.2989] [ 1254] [depth= 1] . ( 8 sec) [ -9205.5922] [ 1254] [depth= 1] . ( 8 sec) [ -9203.7407] [ 1253] [depth= 2] . ( 8 sec) [ -9198.4128] [ 1251] [depth= 1] . ( 8 sec) [ -9197.9473] [ 1251] [depth= 1] . ( 8 sec) [ -9194.8922] [ 1253] [depth= 4] . ( 8 sec) [ -9194.1529] [ 1253] [depth= 1] . ( 9 sec) [ -9194.0345] [ 1254] [depth= 1] . ( 9 sec) [ -9193.9770] [ 1255] [depth= 1] . ( 9 sec) [ -9190.8641] [ 1255] [depth= 1] . ( 9 sec) [ -9190.1195] [ 1255] [depth= 1] . ( 9 sec) [ -9186.4363] [ 1254] [depth= 1] . ( 9 sec) [ -9186.4252] [ 1254] [depth= 1] . ( 9 sec) [ -9184.3388] [ 1254] [depth= 1] . ( 10 sec) [ -9184.1906] [ 1254] [depth= 1] . ( 10 sec) [ -9179.8249] [ 1255] [depth= 3] . ( 10 sec) [ -9173.4594] [ 1253] [depth= 1] . ( 10 sec) [ -9173.2643] [ 1253] [depth= 1] . ( 10 sec) [ -9172.8667] [ 1252] [depth= 1] . ( 11 sec) [ -9171.3737] [ 1252] [depth= 4] . ( 11 sec) [ -9166.4254] [ 1250] [depth= 3] . ( 11 sec) [ -9164.5478] [ 1250] [depth= 2] . ( 11 sec) [ -9157.2810] [ 1248] [depth= 2] . ( 11 sec) [ -9156.6451] [ 1248] [depth= 1] . ( 11 sec) [ -9156.1559] [ 1247] [depth= 1] . ( 12 sec) [ -9153.5001] [ 1246] [depth= 1] . ( 12 sec) [ -9137.0777] [ 1249] [depth= 1] . ( 12 sec) [ -9111.6503] [ 1243] [depth= 2] . ( 13 sec) [ -9104.1931] [ 1242] [depth= 2] . ( 13 sec) [ -9102.7641] [ 1242] [depth= 1] . ( 13 sec) [ -9099.2700] [ 1241] [depth= 2] . ( 13 sec) [ -9097.2641] [ 1241] [depth= 1] . ( 13 sec) [ -9095.6827] [ 1241] [depth= 1] . ( 14 sec) [ -9095.5789] [ 1241] [depth= 1] . ( 14 sec) [ -9095.2832] [ 1241] [depth= 1] . ( 14 sec) [ -9092.7641] [ 1240] [depth= 4] . ( 14 sec) [ -9092.0947] [ 1240] [depth= 4] . ( 15 sec) [ -9091.9905] [ 1240] [depth= 1] . ( 15 sec) [ -9090.8224] [ 1241] [depth= 1] . ( 15 sec) [ -9034.1156] [Branch lengths ] . ( 18 sec) [ -9033.5602] [GTR parameters ] . ( 18 sec) [ -9007.3457] [Alpha ][ 0.311672] . ( 19 sec) [ -9006.7832] [ 1240] [depth= 1] . ( 21 sec) [ -9005.7059] [ 1238] [depth= 1] . ( 22 sec) [ -9005.5125] [ 1238] [depth= 3] . ( 22 sec) [ -9004.4699] [ 1238] [depth= 1] . ( 24 sec) [ -9004.4285] [ 1238] [depth= 1] . ( 26 sec) [ -9004.2694] [ 1238] [depth= 1] . ( 26 sec) [ -9003.9619] [ 1237] [depth= 1] . ( 27 sec) [ -9002.7609] [ 1237] [depth= 6] . ( 27 sec) [ -9002.1758] [ 1237] [depth= 1] . ( 27 sec) [ -9001.9873] [ 1238] [depth= 1] . ( 28 sec) [ -9001.7663] [ 1238] [depth= 1] . ( 28 sec) [ -9001.7268] [ 1237] [depth= 1] . ( 29 sec) [ -8992.8601] [Branch lengths ] . ( 30 sec) [ -8992.5110] [GTR parameters ] . ( 30 sec) [ -8992.4940] [Alpha ][ 0.315200] . ( 37 sec) [ -8991.9895] [ 1237] [depth= 2] . ( 38 sec) [ -8991.8028] [ 1237] [depth= 1] . ( 40 sec) [ -8990.0626] [Branch lengths ] . ( 42 sec) [ -8990.0454] [GTR parameters ] . ( 42 sec) [ -8990.0454] [Alpha ][ 0.314884] . ( 52 sec) [ -8989.6684] [Branch lengths ] . ( 105 sec) [ -8989.6474] [ 1238] [depth= 1] . ( 133 sec) [ -8989.5203] [Branch lengths ] . ( 135 sec) [ -8989.5184] [GTR parameters ] . ( 135 sec) [ -8989.5178] [Alpha ][ 0.314200] . ( 135 sec) [ -8989.5178] [Topology ] . ( 137 sec) [ -8989.4925] [Topology ] . ( 139 sec) [ -8989.4799] [Topology ] . ( 141 sec) [ -8989.4719] [Topology ] . ( 143 sec) [ -8989.4666] [Topology ] . ( 145 sec) [ -8989.4632] [Topology ] . ( 146 sec) [ -8989.4610] [Topology ] . ( 147 sec) [ -8989.4604] [GTR parameters ] . ( 148 sec) [ -8989.4603] [Alpha ][ 0.313828] . ( 148 sec) [ -8989.4603] [Topology ] . ( 149 sec) [ -8989.4587] [Topology ] . ( 151 sec) [ -8989.4576] [Topology ] . ( 153 sec) [ -8989.4569] [Topology ] . ( 154 sec) [ -8989.4568] [GTR parameters ] . ( 154 sec) [ -8989.4568] [Alpha ][ 0.313828] . ( 154 sec) [ -8989.4568] [Topology ] . ( 156 sec) [ -8989.4564] [Topology ] . ( 156 sec) [ -8989.4564] [GTR parameters ] . ( 156 sec) [ -8989.4564] [Alpha ][ 0.313828] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8989.456351. . Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'... . Time used 0h2m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 167.27user 0.00system 2:48.65elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps