.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1487_52x981_2003.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... . 623 patterns found. (out of a total of 981 sites) . 470 sites without polymorphism (47.91%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 78Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -16605.2876] [Alpha ][ 0.500960] . ( 5 sec) [ -16605.2876] [Topology ] . ( 12 sec) [ -16414.2448] [Topology ] . ( 20 sec) [ -16352.8333] [Topology ] . ( 27 sec) [ -16338.9484] [Topology ] . ( 35 sec) [ -16328.2423] [Topology ] . ( 43 sec) [ -16325.0301] [Topology ] . ( 50 sec) [ -16323.8529] [Topology ] . ( 58 sec) [ -16322.4261] [Topology ] . ( 66 sec) [ -16319.2864] [Topology ] . ( 74 sec) [ -16312.8466] [Topology ] . ( 83 sec) [ -16294.9689] [Alpha ][ 0.387752] . ( 84 sec) [ -16294.9689] [Topology ] . ( 92 sec) [ -16292.1804] [Topology ] . ( 99 sec) [ -16291.4873] [Topology ] . ( 107 sec) [ -16291.2953] [Topology ] . ( 115 sec) [ -16291.2163] [Topology ] . ( 123 sec) [ -16291.1787] [Topology ] . ( 131 sec) [ -16291.1592] [Topology ] . ( 138 sec) [ -16291.1484] [Topology ] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -16291.0909] [Alpha ][ 0.381762] . ( 202 sec) [ -16291.0909] [Topology ] . ( 209 sec) [ -16291.0737] [Topology ] . ( 217 sec) [ -16291.0635] [Topology ] . ( 225 sec) [ -16291.0572] [Topology ] . ( 233 sec) [ -16291.0534] [Topology ] . ( 240 sec) [ -16291.0510] [Topology ] . ( 248 sec) [ -16291.0495] [Topology ] . Checking for NNIs, optimizing five branches... . ( 316 sec) [ -16291.0454] [Alpha ][ 0.380025] . ( 317 sec) [ -16291.0454] [Topology ] . ( 326 sec) [ -16291.0433] [Topology ] . ( 336 sec) [ -16291.0420] [Topology ] . ( 346 sec) [ -16291.0412] [Topology ] . Checking for NNIs, optimizing five branches... . ( 416 sec) [ -16291.0411] [Alpha ][ 0.379644] . ( 416 sec) [ -16291.0411] [Topology ] . ( 425 sec) [ -16291.0404] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 569 sec) [ -16605.2876] [Alpha ][ 0.500960] . ( 570 sec) [ -16595.4016] [ 2560] [depth= 1] . ( 571 sec) [ -16593.3251] [ 2559] [depth= 1] . ( 574 sec) [ -16591.2562] [ 2558] [depth= 1] . ( 591 sec) [ -16581.8807] [ 2559] [depth= 1] . ( 592 sec) [ -16572.7899] [ 2558] [depth= 1] . ( 596 sec) [ -16569.0639] [ 2559] [depth= 1] . ( 604 sec) [ -16562.4481] [ 2557] [depth= 1] . ( 608 sec) [ -16561.5336] [ 2558] [depth= 1] . ( 617 sec) [ -16554.3289] [ 2558] [depth= 1] . ( 617 sec) [ -16550.8681] [ 2558] [depth= 1] . ( 619 sec) [ -16542.7190] [ 2558] [depth= 3] . ( 620 sec) [ -16541.9999] [ 2558] [depth= 1] . ( 630 sec) [ -16525.8312] [ 2553] [depth= 3] . ( 632 sec) [ -16522.8339] [ 2552] [depth= 1] . ( 633 sec) [ -16520.3052] [ 2551] [depth= 1] . ( 634 sec) [ -16517.7199] [ 2551] [depth= 1] . ( 636 sec) [ -16516.4984] [ 2556] [depth= 2] . ( 640 sec) [ -16507.2109] [ 2559] [depth= 3] . ( 641 sec) [ -16499.0775] [ 2555] [depth= 3] . ( 642 sec) [ -16486.0382] [ 2550] [depth= 1] . ( 644 sec) [ -16470.9384] [ 2551] [depth= 1] . ( 645 sec) [ -16469.5869] [ 2550] [depth= 2] . ( 646 sec) [ -16469.4201] [ 2549] [depth= 1] . ( 647 sec) [ -16463.8042] [ 2551] [depth= 1] . ( 651 sec) [ -16460.9952] [ 2552] [depth= 1] . ( 652 sec) [ -16458.6746] [ 2547] [depth= 1] . ( 655 sec) [ -16456.2940] [ 2549] [depth= 1] . ( 656 sec) [ -16455.7503] [ 2546] [depth= 1] . ( 657 sec) [ -16445.6869] [ 2546] [depth= 1] . ( 657 sec) [ -16444.6771] [ 2545] [depth= 1] . ( 658 sec) [ -16439.3687] [ 2548] [depth= 1] . ( 663 sec) [ -16438.0344] [ 2551] [depth= 1] . ( 664 sec) [ -16434.4046] [ 2548] [depth= 1] . ( 667 sec) [ -16430.2810] [ 2549] [depth= 1] . ( 674 sec) [ -16416.3164] [ 2548] [depth= 1] . ( 684 sec) [ -16415.7550] [ 2548] [depth= 1] . ( 685 sec) [ -16414.6868] [ 2548] [depth= 1] . ( 687 sec) [ -16413.3543] [ 2549] [depth= 2] . ( 688 sec) [ -16413.0612] [ 2546] [depth= 3] . ( 689 sec) [ -16407.3849] [ 2545] [depth= 3] . ( 690 sec) [ -16405.8978] [ 2546] [depth= 1] . ( 699 sec) [ -16405.3278] [ 2545] [depth= 1] . ( 705 sec) [ -16404.8001] [ 2546] [depth= 1] . ( 707 sec) [ -16402.0362] [ 2545] [depth= 3] . ( 712 sec) [ -16401.4646] [ 2546] [depth= 1] . ( 715 sec) [ -16321.5849] [Branch lengths ] . ( 717 sec) [ -16300.1920] [Alpha ][ 0.362572] . ( 753 sec) [ -16294.2916] [ 2545] [depth= 1] . ( 805 sec) [ -16294.2145] [ 2546] [depth= 1] . ( 807 sec) [ -16293.2434] [ 2546] [depth= 1] . ( 850 sec) [ -16286.6503] [ 2546] [depth= 3] . ( 853 sec) [ -16285.1681] [ 2545] [depth= 1] . ( 856 sec) [ -16284.9352] [ 2545] [depth= 1] . ( 857 sec) [ -16284.8298] [ 2543] [depth= 2] . ( 888 sec) [ -16277.9422] [Branch lengths ] . ( 889 sec) [ -16277.8551] [Alpha ][ 0.369611] . ( 989 sec) [ -16277.5752] [ 2541] [depth= 1] . ( 1060 sec) [ -16277.0647] [Branch lengths ] . ( 1062 sec) [ -16277.0386] [Alpha ][ 0.373691] . ( 1062 sec) [ -16277.0386] [Topology ] . ( 1070 sec) [ -16276.9571] [Topology ] . ( 1078 sec) [ -16276.9103] [Topology ] . ( 1086 sec) [ -16276.8919] [Topology ] . ( 1094 sec) [ -16276.8822] [Topology ] . ( 1102 sec) [ -16276.8767] [Topology ] . ( 1110 sec) [ -16276.8734] [Topology ] . ( 1118 sec) [ -16276.8715] [Topology ] . ( 1125 sec) [ -16276.8703] [Topology ] . ( 1127 sec) [ -16276.8569] [Alpha ][ 0.376619] . ( 1127 sec) [ -16276.8569] [Topology ] . ( 1135 sec) [ -16276.8537] [Topology ] . ( 1143 sec) [ -16276.8519] [Topology ] . ( 1151 sec) [ -16276.8508] [Topology ] . ( 1159 sec) [ -16276.8502] [Topology ] . ( 1160 sec) [ -16276.8497] [Alpha ][ 0.377100] . ( 1161 sec) [ -16276.8497] [Topology ] . ( 1169 sec) [ -16276.8491] [Topology ] . ( 1170 sec) [ -16276.8491] [Alpha ][ 0.377100] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -16291.040410 . Log likelihood obtained after SPR moves : -16276.849102 . Log likelihood of the current tree: -16276.849102. . Printing the most likely tree in file 'proteic_M1487_52x981_2003.phy_phyml_tree.txt'... . Time used 0h20m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1193.58user 0.00system 20:32.84elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps