.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1992_46x68_2004.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... . 68 patterns found. (out of a total of 68 sites) . 1 sites without polymorphism (1.47%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3068.1619] [ 599] [depth= 1] . ( 2 sec) [ -3066.8174] [ 599] [depth= 1] . ( 2 sec) [ -3066.2690] [ 599] [depth= 1] . ( 3 sec) [ -3066.0983] [ 599] [depth= 1] . ( 4 sec) [ -3012.9975] [ 600] [depth= 4] . ( 4 sec) [ -3005.7083] [ 600] [depth= 3] . ( 5 sec) [ -3002.4912] [ 598] [depth= 3] . ( 5 sec) [ -2999.6958] [ 597] [depth= 3] . ( 5 sec) [ -2999.2649] [ 595] [depth= 2] . ( 5 sec) [ -2997.2148] [ 596] [depth= 3] . ( 5 sec) [ -2996.8087] [ 600] [depth= 2] . ( 7 sec) [ -2991.9587] [ 594] [depth= 2] . ( 7 sec) [ -2990.4658] [ 596] [depth= 1] . ( 7 sec) [ -2990.3461] [ 594] [depth= 1] . ( 7 sec) [ -2989.4193] [ 596] [depth= 1] . ( 9 sec) [ -2989.3923] [ 596] [depth= 1] . ( 9 sec) [ -2989.0391] [ 596] [depth= 1] . ( 9 sec) [ -2988.9566] [ 596] [depth= 1] . ( 9 sec) [ -2988.9196] [ 596] [depth= 1] . ( 10 sec) [ -2987.1966] [ 594] [depth= 1] . ( 12 sec) [ -2983.8569] [ 594] [depth= 1] . ( 12 sec) [ -2983.2008] [ 594] [depth= 1] . ( 13 sec) [ -2983.1555] [ 596] [depth= 1] . ( 13 sec) [ -2982.3419] [ 597] [depth= 1] . ( 14 sec) [ -2982.2988] [ 598] [depth= 2] . ( 15 sec) [ -2982.2681] [ 599] [depth= 1] . ( 16 sec) [ -2982.0454] [ 598] [depth= 1] . ( 17 sec) [ -2981.5923] [ 597] [depth= 1] . ( 17 sec) [ -2979.9943] [ 597] [depth= 1] . ( 18 sec) [ -2979.9714] [ 599] [depth= 1] . ( 18 sec) [ -2979.7603] [ 600] [depth= 1] . ( 19 sec) [ -2979.2895] [ 599] [depth= 2] . ( 19 sec) [ -2977.9803] [ 597] [depth= 1] . ( 19 sec) [ -2977.8283] [ 597] [depth= 1] . ( 21 sec) [ -2976.2475] [ 598] [depth= 1] . ( 21 sec) [ -2975.7768] [ 598] [depth= 1] . ( 24 sec) [ -2975.3472] [ 598] [depth= 1] . ( 24 sec) [ -2975.2084] [ 598] [depth= 1] . ( 25 sec) [ -2975.1660] [ 598] [depth= 1] . ( 27 sec) [ -2974.8650] [ 598] [depth= 1] . ( 27 sec) [ -2972.7725] [ 597] [depth= 1] . ( 27 sec) [ -2972.5418] [ 598] [depth= 1] . ( 28 sec) [ -2969.5822] [ 597] [depth= 1] . ( 30 sec) [ -2969.1717] [ 599] [depth= 2] . ( 30 sec) [ -2968.8621] [ 599] [depth= 1] . ( 32 sec) [ -2955.9467] [Branch lengths ] . ( 34 sec) [ -2955.9325] [ 599] [depth= 1] . ( 39 sec) [ -2955.9180] [ 602] [depth= 2] . ( 39 sec) [ -2955.9016] [ 601] [depth= 4] . ( 40 sec) [ -2955.8740] [ 601] [depth= 1] . ( 46 sec) [ -2955.8616] [ 599] [depth= 3] . ( 46 sec) [ -2955.8376] [ 597] [depth= 4] . ( 46 sec) [ -2955.4382] [ 596] [depth= 1] . ( 50 sec) [ -2955.2879] [ 594] [depth= 1] . ( 64 sec) [ -2955.2044] [ 596] [depth= 1] . ( 71 sec) [ -2955.1311] [ 597] [depth= 1] . ( 72 sec) [ -2954.4686] [ 597] [depth= 5] . ( 73 sec) [ -2954.4316] [ 599] [depth= 2] . ( 79 sec) [ -2951.8021] [Branch lengths ] . ( 95 sec) [ -2951.7538] [ 604] [depth= 3] . ( 95 sec) [ -2951.7297] [ 603] [depth= 1] . ( 101 sec) [ -2951.6770] [ 604] [depth= 1] . ( 105 sec) [ -2951.6385] [ 604] [depth= 1] . ( 118 sec) [ -2951.6000] [ 604] [depth= 1] . ( 132 sec) [ -2951.0597] [Branch lengths ] . ( 132 sec) [ -2951.0597] [Topology ] . ( 133 sec) [ -2950.9145] [Topology ] . ( 134 sec) [ -2950.8032] [Topology ] . ( 135 sec) [ -2950.6889] [Topology ] . ( 136 sec) [ -2950.5625] [Topology ] . ( 137 sec) [ -2950.4157] [Topology ] . ( 138 sec) [ -2950.2396] [Topology ] . ( 138 sec) [ -2950.2396] [Topology ] . ( 139 sec) [ -2950.0253] [Topology ] . ( 140 sec) [ -2949.7676] [Topology ] . ( 141 sec) [ -2949.4716] [Topology ] . ( 142 sec) [ -2949.1206] [Topology ] . ( 143 sec) [ -2948.4227] [Topology ] . ( 144 sec) [ -2948.1032] [Topology ] . ( 145 sec) [ -2947.8880] [Topology ] . ( 146 sec) [ -2947.7442] [Topology ] . ( 147 sec) [ -2947.6497] [Topology ] . ( 148 sec) [ -2947.5877] [Topology ] . ( 149 sec) [ -2947.5472] [Topology ] . ( 150 sec) [ -2947.5204] [Topology ] . ( 151 sec) [ -2947.5022] [Topology ] . ( 152 sec) [ -2947.4895] [Topology ] . ( 153 sec) [ -2947.4802] [Topology ] . ( 154 sec) [ -2947.4731] [Topology ] . ( 154 sec) [ -2947.4731] [Topology ] . ( 155 sec) [ -2947.4672] [Topology ] . ( 156 sec) [ -2947.4623] [Topology ] . ( 157 sec) [ -2947.4578] [Topology ] . ( 158 sec) [ -2947.4538] [Topology ] . ( 159 sec) [ -2947.4499] [Topology ] . ( 161 sec) [ -2947.4462] [Topology ] . ( 161 sec) [ -2947.4462] [Topology ] . ( 162 sec) [ -2947.4426] [Topology ] . ( 163 sec) [ -2947.4390] [Topology ] . ( 164 sec) [ -2947.4355] [Topology ] . ( 165 sec) [ -2947.4320] [Topology ] . ( 166 sec) [ -2947.4286] [Topology ] . ( 167 sec) [ -2947.4252] [Topology ] . ( 167 sec) [ -2947.4252] [Topology ] . ( 168 sec) [ -2947.4218] [Topology ] . ( 169 sec) [ -2947.4184] [Topology ] . ( 170 sec) [ -2947.4150] [Topology ] . ( 171 sec) [ -2947.4124] [Topology ] . ( 172 sec) [ -2947.4112] [Topology ] . ( 173 sec) [ -2947.4109] [Topology ] . ( 173 sec) [ -2947.4109] [Topology ] . ( 174 sec) [ -2947.4107] [Topology ] . Checking for NNIs, optimizing five branches... . ( 181 sec) [ -2947.3671] [Topology ] . Checking for NNIs, optimizing five branches... . ( 188 sec) [ -2947.3667] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2947.366697. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 98 48.973917 0.968000 0.102780 67 9.334252 0.762000 0.024975 1 -1.000000 0.000000 0.000001 11 0.498835 0.759000 0.151330 100 437.623008 1.000000 100.000000 12 0.000298 0.000000 0.005314 17 30.505237 0.985000 0.919215 34 1.989599 0.725000 0.178056 85 10.675303 0.839000 0.277291 55 2.242759 0.759000 0.044579 10 1.325857 0.306000 0.224390 57 10.771707 0.915000 0.685233 65 3.074113 0.658000 0.446307 61 3.288475 0.630000 0.291566 86 21.155081 0.968000 0.381389 70 3.603992 0.744000 0.024034 39 -1.000000 0.000000 0.000001 14 0.929340 0.257000 0.213803 4 0.422065 0.643000 0.026550 13 11.697594 0.861000 0.124616 17 2.099059 0.762000 0.101770 88 15.342470 0.937000 0.309473 76 0.933319 0.665000 0.066605 29 0.087858 0.000000 0.045837 52 11.977725 0.908000 0.142348 43 15.263943 0.929000 0.256624 49 46.604588 0.994000 0.519882 2 -1.000000 0.000000 0.000002 7 -1.000000 0.000000 0.000001 12 10.486624 0.759000 0.024166 23 10.759012 0.912000 0.047089 37 10.717076 0.885000 0.095956 46 7.769865 0.768000 0.057441 15 -1.000000 0.000000 0.000002 10 7.084307 0.819000 0.063511 85 3.743174 0.781000 0.063566 15 28.862376 0.990000 0.579964 49 3.741274 0.376000 0.266589 26 1.339346 0.677000 0.095806 25 3.549315 0.635000 0.103310 59 25.676290 0.958000 0.949302 54 4.890265 0.848000 0.435340 42 5.679869 0.822000 0.170931 . Printing the most likely tree in file 'proteic_M1992_46x68_2004.phy_phyml_tree.txt'... . Time used 5h2m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo