.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2928_81x1651_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 . Compressing sequences... . 507 patterns found. (out of a total of 1651 sites) . 1189 sites without polymorphism (72.02%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -7271.1166] [GTR parameters ] . ( 1 sec) [ -7211.7409] [Alpha ][ 0.500960] . ( 1 sec) [ -7211.7409] [Topology ] . ( 3 sec) [ -7160.8695] [Topology ] . ( 5 sec) [ -7154.3487] [Topology ] . ( 7 sec) [ -7153.3527] [Topology ] . ( 8 sec) [ -7153.1361] [Topology ] . ( 10 sec) [ -7153.0829] [Topology ] . ( 11 sec) [ -7153.0680] [Topology ] . ( 13 sec) [ -7153.0627] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -7153.0624] [Topology ] . ( 23 sec) [ -6779.6365] [GTR parameters ] . ( 24 sec) [ -6743.8588] [Alpha ][ 0.250961] . ( 24 sec) [ -6743.8588] [Topology ] . ( 25 sec) [ -6741.1234] [Topology ] . ( 26 sec) [ -6739.6027] [Topology ] . ( 28 sec) [ -6739.2739] [Topology ] . ( 29 sec) [ -6738.9728] [Topology ] . ( 31 sec) [ -6738.7325] [Topology ] . ( 32 sec) [ -6738.6617] [Topology ] . ( 33 sec) [ -6738.6343] [Topology ] . ( 35 sec) [ -6738.6228] [Topology ] . ( 36 sec) [ -6738.6179] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -6738.6022] [Topology ] . ( 52 sec) [ -6693.1323] [GTR parameters ] . ( 52 sec) [ -6690.7125] [Alpha ][ 0.206643] . ( 52 sec) [ -6690.7125] [Topology ] . ( 53 sec) [ -6690.0654] [Topology ] . ( 55 sec) [ -6689.9338] [Topology ] . ( 56 sec) [ -6689.8854] [Topology ] . ( 58 sec) [ -6689.8660] [Topology ] . ( 59 sec) [ -6689.8580] [Topology ] . ( 60 sec) [ -6689.8546] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -6689.8543] [Topology ] . ( 74 sec) [ -6689.7198] [GTR parameters ] . ( 74 sec) [ -6689.7187] [Alpha ][ 0.205782] . ( 74 sec) [ -6689.7187] [Topology ] . ( 75 sec) [ -6689.7127] [Topology ] . ( 77 sec) [ -6689.7105] [Topology ] . ( 78 sec) [ -6689.7096] [Topology ] . Checking for NNIs, optimizing five branches... . ( 88 sec) [ -6689.7095] [Topology ] . ( 89 sec) [ -6689.7092] [GTR parameters ] . ( 89 sec) [ -6689.7091] [Alpha ][ 0.206039] . ( 89 sec) [ -6689.7091] [Topology ] . ( 90 sec) [ -6689.7086] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 110 sec) [ -7271.1166] [GTR parameters ] . ( 110 sec) [ -7211.7409] [Alpha ][ 0.500960] . ( 111 sec) [ -7211.1362] [ 888] [depth= 1] . ( 111 sec) [ -7210.8001] [ 888] [depth= 1] . ( 111 sec) [ -7210.5133] [ 888] [depth= 3] . ( 111 sec) [ -7210.3174] [ 888] [depth= 2] . ( 111 sec) [ -7209.9139] [ 888] [depth= 2] . ( 112 sec) [ -7209.8287] [ 888] [depth= 3] . ( 112 sec) [ -7209.7725] [ 888] [depth= 1] . ( 112 sec) [ -7209.7412] [ 888] [depth= 3] . ( 113 sec) [ -7209.7265] [ 888] [depth= 1] . ( 113 sec) [ -7209.7034] [ 888] [depth= 2] . ( 114 sec) [ -7208.7158] [ 888] [depth= 1] . ( 114 sec) [ -7208.6945] [ 888] [depth= 1] . ( 115 sec) [ -7208.5133] [ 888] [depth= 1] . ( 115 sec) [ -7208.4151] [ 888] [depth= 1] . ( 115 sec) [ -7208.3997] [ 888] [depth= 1] . ( 115 sec) [ -7208.2465] [ 888] [depth= 2] . ( 116 sec) [ -7207.4561] [ 889] [depth= 1] . ( 116 sec) [ -7206.4516] [ 887] [depth= 1] . ( 116 sec) [ -7205.6860] [ 889] [depth= 1] . ( 116 sec) [ -7203.5849] [ 887] [depth= 1] . ( 117 sec) [ -7190.0457] [ 884] [depth= 1] . ( 117 sec) [ -7190.0119] [ 884] [depth= 1] . ( 117 sec) [ -7189.9991] [ 884] [depth= 1] . ( 118 sec) [ -7189.8583] [ 884] [depth= 1] . ( 118 sec) [ -7188.2574] [ 884] [depth= 2] . ( 118 sec) [ -7188.0455] [ 885] [depth= 3] . ( 118 sec) [ -7185.7992] [ 885] [depth= 3] . ( 118 sec) [ -7183.8886] [ 885] [depth= 3] . ( 118 sec) [ -7181.8647] [ 884] [depth= 3] . ( 118 sec) [ -7177.9590] [ 884] [depth= 1] . ( 119 sec) [ -7176.6290] [ 885] [depth= 2] . ( 119 sec) [ -7176.5645] [ 885] [depth= 3] . ( 119 sec) [ -7176.5506] [ 885] [depth= 2] . ( 119 sec) [ -7176.4118] [ 885] [depth= 1] . ( 119 sec) [ -7176.1060] [ 885] [depth= 1] . ( 119 sec) [ -7176.0425] [ 885] [depth= 7] . ( 119 sec) [ -7175.8736] [ 885] [depth= 6] . ( 119 sec) [ -7175.6326] [ 885] [depth= 2] . ( 120 sec) [ -7175.3919] [ 885] [depth= 6] . ( 120 sec) [ -7175.2108] [ 885] [depth= 5] . ( 120 sec) [ -7175.1302] [ 885] [depth= 4] . ( 120 sec) [ -7175.0121] [ 885] [depth= 4] . ( 121 sec) [ -7174.9287] [ 885] [depth= 1] . ( 123 sec) [ -7174.6081] [ 885] [depth= 1] . ( 123 sec) [ -7174.3594] [ 885] [depth= 1] . ( 125 sec) [ -7174.1200] [ 885] [depth= 2] . ( 125 sec) [ -7174.1077] [ 885] [depth= 4] . ( 126 sec) [ -7173.9541] [ 885] [depth= 2] . ( 130 sec) [ -7172.2775] [ 884] [depth= 4] . ( 132 sec) [ -7172.2667] [ 884] [depth= 2] . ( 134 sec) [ -7171.5736] [ 884] [depth= 1] . ( 134 sec) [ -7170.9054] [ 883] [depth= 3] . ( 135 sec) [ -7170.8902] [ 883] [depth= 1] . ( 135 sec) [ -7170.8767] [ 883] [depth= 1] . ( 135 sec) [ -7170.8318] [ 883] [depth= 2] . ( 136 sec) [ -7170.8179] [ 883] [depth= 1] . ( 136 sec) [ -7170.7352] [ 884] [depth= 1] . ( 136 sec) [ -7170.6708] [ 884] [depth= 1] . ( 137 sec) [ -7170.6602] [ 884] [depth= 1] . ( 146 sec) [ -7155.7635] [Branch lengths ] . ( 147 sec) [ -6772.7925] [GTR parameters ] . ( 147 sec) [ -6736.3579] [Alpha ][ 0.250961] . ( 151 sec) [ -6736.2701] [ 884] [depth= 2] . ( 152 sec) [ -6736.2579] [ 883] [depth= 1] . ( 152 sec) [ -6736.2305] [ 884] [depth= 1] . ( 152 sec) [ -6736.1014] [ 886] [depth= 1] . ( 153 sec) [ -6736.0379] [ 886] [depth= 1] . ( 153 sec) [ -6733.4532] [ 890] [depth= 1] . ( 191 sec) [ -6729.9131] [Branch lengths ] . ( 196 sec) [ -6694.7153] [GTR parameters ] . ( 196 sec) [ -6692.2429] [Alpha ][ 0.206118] . ( 201 sec) [ -6691.2192] [ 889] [depth= 1] . ( 240 sec) [ -6690.0092] [Branch lengths ] . ( 243 sec) [ -6689.8642] [GTR parameters ] . ( 243 sec) [ -6689.8635] [Alpha ][ 0.205413] . ( 273 sec) [ -6689.8496] [ 888] [depth= 1] . ( 275 sec) [ -6689.8367] [ 889] [depth= 2] . ( 285 sec) [ -6689.6848] [Branch lengths ] . ( 289 sec) [ -6689.6763] [GTR parameters ] . ( 289 sec) [ -6689.6762] [Alpha ][ 0.205699] . ( 355 sec) [ -6689.6603] [Branch lengths ] . ( 355 sec) [ -6689.6603] [Topology ] . ( 357 sec) [ -6689.6592] [Topology ] . ( 358 sec) [ -6689.6589] [Topology ] . ( 360 sec) [ -6689.6587] [GTR parameters ] . ( 360 sec) [ -6689.6586] [Alpha ][ 0.205936] . ( 360 sec) [ -6689.6586] [Topology ] . ( 362 sec) [ -6689.6584] [Topology ] . ( 362 sec) [ -6689.6584] [GTR parameters ] . ( 362 sec) [ -6689.6584] [Alpha ][ 0.205936] . Checking for NNIs, optimizing five branches... . ( 372 sec) [ -6689.6583] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6689.708590 . Log likelihood obtained after SPR moves : -6689.658291 . Log likelihood of the current tree: -6689.658291. . Printing the most likely tree in file 'nucleic_M2928_81x1651_2006.phy_phyml_tree.txt'... . Time used 0h6m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 382.27user 0.00system 6:24.11elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps