.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2382_28x162_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 129 patterns found. (out of a total of 162 sites) . 75 sites without polymorphism (46.30%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2775.6744] [Alpha ][ 0.500960] . ( 0 sec) [ -2775.6744] [Topology ] . ( 1 sec) [ -2730.2341] [Topology ] . ( 2 sec) [ -2719.9969] [Topology ] . ( 2 sec) [ -2718.4262] [Topology ] . ( 3 sec) [ -2717.6659] [Topology ] . ( 4 sec) [ -2717.6758] [Topology ] . Moving backward . ( 4 sec) [ -2717.0282] [Topology ] . ( 5 sec) [ -2716.6701] [Topology ] . ( 6 sec) [ -2716.5370] [Topology ] . ( 7 sec) [ -2716.4326] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -2712.7833] [Alpha ][ 0.369792] . ( 14 sec) [ -2712.7833] [Topology ] . ( 15 sec) [ -2712.6795] [Topology ] . ( 16 sec) [ -2712.6614] [Topology ] . ( 17 sec) [ -2712.6561] [Topology ] . ( 18 sec) [ -2712.6542] [Topology ] . ( 18 sec) [ -2712.6534] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -2712.4946] [Topology ] . ( 25 sec) [ -2712.4788] [Alpha ][ 0.362808] . ( 25 sec) [ -2712.4788] [Topology ] . ( 26 sec) [ -2712.4666] [Topology ] . ( 26 sec) [ -2712.4622] [Topology ] . ( 27 sec) [ -2712.4600] [Topology ] . ( 28 sec) [ -2712.4589] [Topology ] . ( 29 sec) [ -2712.4584] [Topology ] . Checking for NNIs, optimizing five branches... . ( 35 sec) [ -2712.4580] [Alpha ][ 0.363809] . ( 35 sec) [ -2712.4580] [Topology ] . ( 36 sec) [ -2712.4577] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -2775.6744] [Alpha ][ 0.500960] . ( 49 sec) [ -2775.5328] [ 461] [depth= 1] . ( 49 sec) [ -2773.6500] [ 461] [depth= 1] . ( 51 sec) [ -2772.3263] [ 462] [depth= 1] . ( 52 sec) [ -2771.9961] [ 461] [depth= 1] . ( 52 sec) [ -2767.8684] [ 459] [depth= 1] . ( 52 sec) [ -2766.9550] [ 461] [depth= 1] . ( 52 sec) [ -2766.3284] [ 461] [depth= 5] . ( 55 sec) [ -2762.6262] [ 461] [depth= 2] . ( 56 sec) [ -2762.2303] [ 464] [depth= 3] . ( 56 sec) [ -2759.9008] [ 465] [depth= 1] . ( 59 sec) [ -2759.1950] [ 462] [depth= 1] . ( 60 sec) [ -2756.3415] [ 461] [depth= 3] . ( 63 sec) [ -2756.2298] [ 460] [depth= 1] . ( 66 sec) [ -2754.7662] [ 460] [depth= 1] . ( 66 sec) [ -2753.0177] [ 460] [depth= 1] . ( 66 sec) [ -2750.3352] [ 460] [depth= 1] . ( 67 sec) [ -2749.6121] [ 459] [depth= 1] . ( 67 sec) [ -2747.3322] [ 458] [depth= 3] . ( 67 sec) [ -2746.4446] [ 457] [depth= 2] . ( 67 sec) [ -2745.2296] [ 456] [depth= 1] . ( 68 sec) [ -2745.0250] [ 461] [depth= 4] . ( 70 sec) [ -2737.8765] [ 460] [depth= 10] . ( 72 sec) [ -2735.8249] [ 457] [depth= 5] . ( 74 sec) [ -2735.7022] [ 459] [depth= 1] . ( 78 sec) [ -2734.9231] [ 460] [depth= 3] . ( 79 sec) [ -2730.5330] [ 457] [depth= 2] . ( 90 sec) [ -2730.1559] [ 457] [depth= 1] . ( 91 sec) [ -2730.0889] [ 458] [depth= 1] . ( 96 sec) [ -2728.6132] [ 458] [depth= 2] . ( 101 sec) [ -2727.6571] [ 458] [depth= 1] . ( 102 sec) [ -2715.7082] [Branch lengths ] . ( 102 sec) [ -2711.2884] [Alpha ][ 0.350558] . ( 102 sec) [ -2710.3906] [ 459] [depth= 1] . ( 112 sec) [ -2709.5078] [ 459] [depth= 9] . ( 113 sec) [ -2709.0064] [ 460] [depth= 1] . ( 114 sec) [ -2704.5035] [ 455] [depth= 3] . ( 136 sec) [ -2703.9234] [ 455] [depth= 1] . ( 138 sec) [ -2703.7549] [ 456] [depth= 1] . ( 139 sec) [ -2703.6862] [ 455] [depth= 1] . ( 145 sec) [ -2702.5294] [ 454] [depth= 1] . ( 151 sec) [ -2701.9852] [ 454] [depth= 6] . ( 182 sec) [ -2698.6579] [Branch lengths ] . ( 182 sec) [ -2698.6432] [Alpha ][ 0.343831] . ( 212 sec) [ -2698.2040] [ 454] [depth= 5] . ( 214 sec) [ -2698.1853] [ 455] [depth= 1] . ( 267 sec) [ -2697.3130] [Branch lengths ] . ( 267 sec) [ -2697.3105] [Alpha ][ 0.346531] . ( 357 sec) [ -2697.2351] [Branch lengths ] . ( 357 sec) [ -2697.2351] [Topology ] . ( 358 sec) [ -2697.2303] [Topology ] . ( 359 sec) [ -2697.2290] [Topology ] . ( 360 sec) [ -2697.2285] [Topology ] . ( 360 sec) [ -2697.2270] [Alpha ][ 0.348618] . ( 360 sec) [ -2697.2270] [Topology ] . ( 361 sec) [ -2697.2265] [Topology ] . ( 361 sec) [ -2697.2265] [Alpha ][ 0.348618] . Checking for NNIs, optimizing five branches... . ( 368 sec) [ -2697.1624] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2712.457654 . Log likelihood obtained after SPR moves : -2697.162387 . Log likelihood of the current tree: -2697.162387. . Printing the most likely tree in file 'proteic_M2382_28x162_2005.phy_phyml_tree.txt'... . Time used 0h6m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 373.40user 0.00system 6:15.47elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps