.......................... 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 : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . 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 SPR moves)... . ( 1 sec) [ -16473.3756] [ 2558] [depth= 1] . ( 2 sec) [ -16472.1250] [ 2557] [depth= 1] . ( 5 sec) [ -16471.4641] [ 2558] [depth= 1] . ( 7 sec) [ -16470.8155] [ 2558] [depth= 1] . ( 8 sec) [ -16469.8455] [ 2556] [depth= 1] . ( 22 sec) [ -16460.2069] [ 2557] [depth= 1] . ( 24 sec) [ -16450.0234] [ 2556] [depth= 1] . ( 28 sec) [ -16445.1036] [ 2557] [depth= 1] . ( 35 sec) [ -16440.7086] [ 2556] [depth= 1] . ( 44 sec) [ -16438.2211] [ 2559] [depth= 1] . ( 54 sec) [ -16435.5582] [ 2556] [depth= 1] . ( 55 sec) [ -16434.3856] [ 2556] [depth= 1] . ( 56 sec) [ -16421.2713] [ 2554] [depth= 1] . ( 58 sec) [ -16420.3089] [ 2556] [depth= 1] . ( 67 sec) [ -16420.1763] [ 2554] [depth= 2] . ( 70 sec) [ -16408.0027] [ 2552] [depth= 1] . ( 71 sec) [ -16392.8874] [ 2553] [depth= 1] . ( 72 sec) [ -16389.8137] [ 2552] [depth= 1] . ( 73 sec) [ -16384.3770] [ 2551] [depth= 1] . ( 74 sec) [ -16376.4617] [ 2551] [depth= 1] . ( 76 sec) [ -16375.8006] [ 2554] [depth= 2] . ( 77 sec) [ -16367.1341] [ 2552] [depth= 2] . ( 80 sec) [ -16365.8988] [ 2554] [depth= 1] . ( 83 sec) [ -16360.6084] [ 2558] [depth= 1] . ( 84 sec) [ -16351.3103] [ 2559] [depth= 1] . ( 86 sec) [ -16349.1406] [ 2561] [depth= 1] . ( 90 sec) [ -16344.9402] [ 2559] [depth= 1] . ( 91 sec) [ -16343.4468] [ 2548] [depth= 4] . ( 93 sec) [ -16339.8329] [ 2547] [depth= 1] . ( 94 sec) [ -16331.6871] [ 2547] [depth= 1] . ( 95 sec) [ -16315.1241] [ 2545] [depth= 3] . ( 97 sec) [ -16310.9016] [ 2544] [depth= 3] . ( 100 sec) [ -16309.0729] [ 2548] [depth= 1] . ( 101 sec) [ -16305.1175] [ 2544] [depth= 1] . ( 104 sec) [ -16302.4098] [ 2545] [depth= 1] . ( 108 sec) [ -16288.7939] [ 2544] [depth= 1] . ( 112 sec) [ -16288.4631] [ 2547] [depth= 1] . ( 113 sec) [ -16286.3763] [ 2544] [depth= 1] . ( 114 sec) [ -16280.6872] [ 2542] [depth= 1] . ( 115 sec) [ -16278.1127] [ 2544] [depth= 1] . ( 119 sec) [ -16277.8972] [ 2542] [depth= 1] . ( 125 sec) [ -16273.5097] [ 2540] [depth= 1] . ( 127 sec) [ -16272.7779] [ 2542] [depth= 1] . ( 128 sec) [ -16271.4561] [ 2540] [depth= 1] . ( 134 sec) [ -16270.6234] [ 2542] [depth= 1] . ( 142 sec) [ -16270.3640] [ 2541] [depth= 1] . ( 145 sec) [ -16179.9671] [Branch lengths ] . ( 188 sec) [ -16177.4969] [ 2540] [depth= 1] . ( 191 sec) [ -16175.2456] [ 2540] [depth= 1] . ( 216 sec) [ -16175.2143] [ 2542] [depth= 1] . ( 224 sec) [ -16174.5446] [ 2540] [depth= 1] . ( 266 sec) [ -16174.2021] [ 2540] [depth= 1] . ( 269 sec) [ -16174.0981] [ 2540] [depth= 1] . ( 301 sec) [ -16161.5282] [Branch lengths ] . ( 466 sec) [ -16159.5084] [Branch lengths ] . ( 467 sec) [ -16159.5084] [Topology ] . ( 475 sec) [ -16159.2019] [Topology ] . ( 483 sec) [ -16159.0757] [Topology ] . ( 490 sec) [ -16158.9997] [Topology ] . ( 498 sec) [ -16158.9401] [Topology ] . ( 506 sec) [ -16158.8073] [Topology ] . ( 514 sec) [ -16158.1102] [Topology ] . ( 515 sec) [ -16158.1102] [Topology ] . ( 523 sec) [ -16155.7227] [Topology ] . ( 531 sec) [ -16154.6714] [Topology ] . ( 539 sec) [ -16154.4501] [Topology ] . ( 547 sec) [ -16154.3820] [Topology ] . ( 555 sec) [ -16154.3595] [Topology ] . ( 563 sec) [ -16154.3514] [Topology ] . ( 564 sec) [ -16154.3514] [Topology ] . ( 572 sec) [ -16154.3484] [Topology ] . ( 580 sec) [ -16154.3472] [Topology ] . ( 588 sec) [ -16154.3467] [Topology ] . ( 588 sec) [ -16154.3467] [Topology ] . ( 596 sec) [ -16154.3465] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16154.346509. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 38 1.016400 0.150000 0.002484 57 5.935999 0.773000 0.002767 50 8.047205 0.773000 0.003018 100 55.086682 0.989000 0.022240 75 14.468092 0.846000 0.015952 100 51.770340 0.987000 0.029882 91 23.674327 0.905000 0.023925 94 57.675076 0.988000 0.043200 85 28.822079 0.914000 0.024789 99 11.543874 0.891000 0.013065 53 3.164480 0.311000 0.028243 100 240.649384 1.000000 0.168449 58 1.622829 0.721000 0.019434 96 29.849669 0.973000 0.069897 77 32.622799 0.949000 0.043438 83 58.403650 0.991000 0.054278 16 2.520875 0.612000 0.012699 8 0.718031 0.167000 0.003814 99 63.647936 0.993000 0.078588 97 18.728819 0.927000 0.041973 40 21.092575 0.953000 0.027099 100 59.967257 0.994000 0.085032 71 7.859728 0.835000 0.021151 84 9.931761 0.882000 0.023247 100 90.242943 0.997000 0.096794 77 0.907241 0.143000 0.013435 96 28.800671 0.967000 0.038961 89 12.456130 0.889000 0.021379 67 14.551488 0.897000 0.022357 51 6.716669 0.642000 0.011286 63 6.721484 0.803000 0.015194 48 15.189291 0.896000 0.033408 100 80.130740 0.997000 0.116760 61 20.722111 0.944000 0.050220 94 68.668399 0.992000 0.078831 36 7.771195 0.813000 0.016829 12 0.035201 0.000000 0.001277 29 12.931663 0.848000 0.021735 23 3.270875 0.540000 0.015243 85 42.961508 0.981000 0.057132 44 15.211102 0.895000 0.024897 100 99.323242 1.000000 0.135768 66 10.584557 0.773000 0.024621 45 14.285596 0.920000 0.037534 81 34.409461 0.967000 0.048047 62 8.925736 0.838000 0.025998 83 12.659341 0.904000 0.038530 41 2.701846 0.510000 0.031142 72 13.586663 0.926000 0.044028 . Printing the most likely tree in file 'proteic_M1487_52x981_2003.phy_phyml_tree.txt'... . Time used 20h56m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo