.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2478_30x276_2005.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... . 249 patterns found. (out of a total of 276 sites) . 41 sites without polymorphism (14.86%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8776.5704] [ 1681] [depth= 1] . ( 4 sec) [ -8773.1128] [ 1678] [depth= 1] . ( 6 sec) [ -8772.2492] [ 1678] [depth= 1] . ( 7 sec) [ -8771.7973] [ 1678] [depth= 1] . ( 7 sec) [ -8768.6259] [ 1678] [depth= 1] . ( 9 sec) [ -8767.7471] [ 1678] [depth= 1] . ( 10 sec) [ -8764.7338] [ 1674] [depth= 2] . ( 10 sec) [ -8764.0184] [ 1675] [depth= 1] . ( 11 sec) [ -8762.7610] [ 1676] [depth= 1] . ( 11 sec) [ -8754.6056] [ 1672] [depth= 1] . ( 11 sec) [ -8749.4000] [ 1669] [depth= 2] . ( 11 sec) [ -8748.1958] [ 1671] [depth= 1] . ( 17 sec) [ -8747.8937] [ 1672] [depth= 1] . ( 17 sec) [ -8746.3551] [ 1674] [depth= 1] . ( 18 sec) [ -8746.2835] [ 1672] [depth= 1] . ( 18 sec) [ -8746.0436] [ 1672] [depth= 1] . ( 18 sec) [ -8744.8910] [ 1673] [depth= 1] . ( 19 sec) [ -8741.0770] [ 1673] [depth= 1] . ( 21 sec) [ -8740.8230] [ 1673] [depth= 1] . ( 22 sec) [ -8712.7190] [Branch lengths ] . ( 32 sec) [ -8711.5991] [ 1673] [depth= 1] . ( 52 sec) [ -8707.7899] [Branch lengths ] . ( 82 sec) [ -8707.4217] [Branch lengths ] . ( 82 sec) [ -8707.4217] [Topology ] . ( 84 sec) [ -8707.3266] [Topology ] . ( 85 sec) [ -8707.2782] [Topology ] . ( 87 sec) [ -8707.2458] [Topology ] . ( 89 sec) [ -8707.2239] [Topology ] . ( 91 sec) [ -8707.2092] [Topology ] . ( 92 sec) [ -8707.1992] [Topology ] . ( 92 sec) [ -8707.1992] [Topology ] . ( 94 sec) [ -8707.1925] [Topology ] . ( 96 sec) [ -8707.1880] [Topology ] . ( 98 sec) [ -8707.1850] [Topology ] . ( 99 sec) [ -8707.1830] [Topology ] . ( 101 sec) [ -8707.1816] [Topology ] . ( 103 sec) [ -8707.1807] [Topology ] . ( 103 sec) [ -8707.1807] [Topology ] . ( 104 sec) [ -8707.1801] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8707.180068. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 264.073695 1.000000 0.472093 20 0.021842 0.000000 0.003785 34 0.677959 0.081000 0.039028 99 125.706272 1.000000 0.231023 27 1.151478 0.159000 0.030689 100 76.203812 0.995000 0.238622 71 2.452178 0.407000 0.028772 100 96.256139 1.000000 0.142725 85 19.301832 0.932000 0.056051 99 64.507524 0.993000 0.128353 100 79.171977 1.000000 0.119956 98 22.375376 0.953000 0.066833 75 9.099601 0.861000 0.033200 100 122.145853 0.999000 0.185679 72 8.671006 0.869000 0.033597 95 36.841170 0.982000 0.113939 47 4.826933 0.673000 0.022801 97 40.755320 0.981000 0.147374 77 18.591405 0.948000 0.107888 60 8.495316 0.783000 0.050960 92 35.330759 0.966000 0.079993 100 48.956694 0.994000 0.097718 100 43.419695 0.994000 0.105047 100 21.430553 0.951000 0.092666 78 25.753886 0.935000 0.062242 99 44.379276 0.988000 0.109057 73 8.131744 0.762000 0.142646 . Printing the most likely tree in file 'proteic_M2478_30x276_2005.phy_phyml_tree.txt'... . Time used 2h56m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo