.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2899_25x444_2006.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... . 365 patterns found. (out of a total of 444 sites) . 112 sites without polymorphism (25.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -9965.1878] [ 1783] [depth= 1] . ( 3 sec) [ -9963.5499] [ 1782] [depth= 1] . ( 6 sec) [ -9958.5821] [ 1781] [depth= 1] . ( 6 sec) [ -9958.3454] [ 1785] [depth= 1] . ( 6 sec) [ -9955.7740] [ 1781] [depth= 1] . ( 7 sec) [ -9954.1438] [ 1783] [depth= 1] . ( 8 sec) [ -9948.8479] [ 1779] [depth= 1] . ( 10 sec) [ -9936.5672] [ 1781] [depth= 1] . ( 10 sec) [ -9933.7198] [ 1779] [depth= 1] . ( 11 sec) [ -9930.6953] [ 1783] [depth= 1] . ( 11 sec) [ -9927.3347] [ 1779] [depth= 1] . ( 11 sec) [ -9918.6694] [ 1781] [depth= 1] . ( 13 sec) [ -9917.5807] [ 1780] [depth= 1] . ( 13 sec) [ -9916.4727] [ 1778] [depth= 1] . ( 15 sec) [ -9912.5669] [ 1776] [depth= 1] . ( 16 sec) [ -9911.9720] [ 1775] [depth= 1] . ( 16 sec) [ -9907.6625] [ 1775] [depth= 1] . ( 17 sec) [ -9907.6124] [ 1775] [depth= 1] . ( 17 sec) [ -9897.8805] [ 1775] [depth= 2] . ( 21 sec) [ -9879.2295] [Branch lengths ] . ( 44 sec) [ -9874.9161] [Branch lengths ] . ( 44 sec) [ -9874.9161] [Topology ] . ( 46 sec) [ -9873.6208] [Topology ] . ( 48 sec) [ -9872.9590] [Topology ] . ( 50 sec) [ -9872.5151] [Topology ] . ( 52 sec) [ -9872.2083] [Topology ] . ( 53 sec) [ -9871.9944] [Topology ] . ( 55 sec) [ -9871.8448] [Topology ] . ( 56 sec) [ -9871.8448] [Topology ] . ( 57 sec) [ -9871.7400] [Topology ] . ( 59 sec) [ -9871.6666] [Topology ] . ( 61 sec) [ -9871.6151] [Topology ] . ( 63 sec) [ -9871.5790] [Topology ] . ( 65 sec) [ -9871.5536] [Topology ] . ( 67 sec) [ -9871.5358] [Topology ] . ( 67 sec) [ -9871.5358] [Topology ] . ( 69 sec) [ -9871.5233] [Topology ] . ( 71 sec) [ -9871.5146] [Topology ] . ( 73 sec) [ -9871.5084] [Topology ] . ( 75 sec) [ -9871.5041] [Topology ] . ( 77 sec) [ -9871.5011] [Topology ] . ( 78 sec) [ -9871.4989] [Topology ] . ( 79 sec) [ -9871.4989] [Topology ] . ( 80 sec) [ -9871.4974] [Topology ] . ( 82 sec) [ -9871.4964] [Topology ] . ( 84 sec) [ -9871.4956] [Topology ] . ( 84 sec) [ -9871.4956] [Topology ] . ( 86 sec) [ -9871.4951] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -9870.4994] [Topology ] . Checking for NNIs, optimizing five branches... . ( 118 sec) [ -9869.5615] [Topology ] . Checking for NNIs, optimizing five branches... . ( 133 sec) [ -9869.3713] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9869.371348. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 77 6.388266 0.839000 0.013677 100 24.518258 0.940000 0.017745 100 45.091648 0.996000 0.057925 99 52.197047 0.985000 0.055534 85 6.247389 0.852000 0.023890 100 123.617744 1.000000 0.097602 26 3.403646 0.422000 0.019284 97 119.745874 1.000000 0.148892 77 22.932353 0.948000 0.051305 42 15.426535 0.925000 0.034407 46 8.306440 0.863000 0.033070 86 41.724837 0.987000 0.091962 96 50.962004 0.983000 0.114410 60 3.842395 0.619000 0.035863 46 2.680258 0.226000 0.059068 19 4.718789 0.457000 0.039196 35 7.826183 0.884000 0.063688 9 0.380203 0.030000 0.020124 91 67.886955 0.993000 0.107558 69 8.206650 0.824000 0.030904 20 1.176122 0.626000 0.026403 81 3.457687 0.440000 0.073270 . Printing the most likely tree in file 'proteic_M2899_25x444_2006.phy_phyml_tree.txt'... . Time used 3h34m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo