.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2480_40x430_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... . 399 patterns found. (out of a total of 430 sites) . 44 sites without polymorphism (10.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 11 sec) [ -23958.5106] [ 5034] [depth= 4] . ( 11 sec) [ -23953.5991] [ 5013] [depth= 5] . ( 13 sec) [ -23952.9512] [ 5017] [depth= 1] . ( 14 sec) [ -23946.4962] [ 5011] [depth= 1] . ( 15 sec) [ -23945.7473] [ 5011] [depth= 1] . ( 17 sec) [ -23934.8223] [ 5013] [depth= 2] . ( 18 sec) [ -23934.1421] [ 5012] [depth= 1] . ( 19 sec) [ -23933.9845] [ 5016] [depth= 2] . ( 22 sec) [ -23933.8089] [ 5020] [depth= 1] . ( 23 sec) [ -23933.2544] [ 5017] [depth= 1] . ( 23 sec) [ -23924.2779] [ 5013] [depth= 1] . ( 24 sec) [ -23919.3084] [ 5012] [depth= 1] . ( 25 sec) [ -23917.3998] [ 5006] [depth= 1] . ( 25 sec) [ -23914.4918] [ 5009] [depth= 1] . ( 27 sec) [ -23907.0783] [ 5009] [depth= 2] . ( 30 sec) [ -23905.9136] [ 5009] [depth= 1] . ( 31 sec) [ -23903.0425] [ 5008] [depth= 6] . ( 32 sec) [ -23892.1189] [ 5011] [depth= 2] . ( 32 sec) [ -23891.1455] [ 5009] [depth= 2] . ( 33 sec) [ -23890.8890] [ 5008] [depth= 1] . ( 33 sec) [ -23887.3810] [ 5009] [depth= 1] . ( 34 sec) [ -23887.1836] [ 5011] [depth= 3] . ( 37 sec) [ -23883.5015] [ 5012] [depth= 1] . ( 43 sec) [ -23882.6659] [ 5017] [depth= 1] . ( 44 sec) [ -23878.4805] [ 5020] [depth= 1] . ( 44 sec) [ -23877.1850] [ 5015] [depth= 1] . ( 50 sec) [ -23876.8599] [ 5016] [depth= 2] . ( 52 sec) [ -23876.6888] [ 5021] [depth= 1] . ( 52 sec) [ -23874.3808] [ 5015] [depth= 1] . ( 53 sec) [ -23870.9772] [ 5016] [depth= 1] . ( 53 sec) [ -23869.5374] [ 5016] [depth= 1] . ( 57 sec) [ -23820.0767] [Branch lengths ] . ( 68 sec) [ -23793.8834] [ 5016] [depth= 13] . ( 82 sec) [ -23793.6877] [ 5014] [depth= 1] . ( 110 sec) [ -23793.5345] [ 5014] [depth= 2] . ( 138 sec) [ -23787.7787] [Branch lengths ] . ( 160 sec) [ -23787.1698] [ 5014] [depth= 1] . ( 180 sec) [ -23785.7696] [ 5018] [depth= 2] . ( 210 sec) [ -23785.3296] [ 5017] [depth= 2] . ( 213 sec) [ -23784.7823] [ 5020] [depth= 1] . ( 223 sec) [ -23778.8647] [Branch lengths ] . ( 278 sec) [ -23778.6769] [ 5021] [depth= 4] . ( 330 sec) [ -23777.1485] [Branch lengths ] . ( 366 sec) [ -23777.0958] [ 5019] [depth= 1] . ( 425 sec) [ -23776.5810] [Branch lengths ] . ( 425 sec) [ -23776.5810] [Topology ] . ( 429 sec) [ -23776.1156] [Topology ] . ( 432 sec) [ -23776.4911] [Topology ] . Moving backward . ( 432 sec) [ -23775.4660] [Topology ] . ( 436 sec) [ -23775.0389] [Topology ] . ( 439 sec) [ -23774.9752] [Topology ] . ( 442 sec) [ -23774.9594] [Topology ] . ( 445 sec) [ -23774.9543] [Topology ] . ( 449 sec) [ -23774.9524] [Topology ] . ( 452 sec) [ -23774.9515] [Topology ] . ( 452 sec) [ -23774.9515] [Topology ] . ( 455 sec) [ -23774.9511] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23774.951107. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 90 31.295192 0.963000 0.132203 100 186.054547 1.000000 0.266552 57 16.014685 0.870000 0.047647 33 48.377067 0.991000 0.100421 76 19.292512 0.926000 0.066046 21 15.301530 0.881000 0.041715 90 14.708900 0.886000 0.068326 71 33.870512 0.985000 0.121823 100 110.737748 1.000000 0.298451 3 14.261316 0.909000 0.040773 3 7.762380 0.686000 0.032349 100 84.825142 0.997000 0.146372 85 10.736181 0.757000 0.061657 24 26.969447 0.947000 0.056632 18 5.222845 0.555000 0.027369 72 29.313132 0.978000 0.126838 39 5.221931 0.550000 0.073561 100 71.251783 0.999000 0.223568 17 3.631449 0.340000 0.079383 97 54.288532 0.998000 0.267220 0 3.651976 0.446000 0.017891 19 40.283470 0.969000 0.063174 31 22.674291 0.968000 0.065073 18 1.092218 0.143000 0.025536 100 140.043021 1.000000 0.203465 95 24.000803 0.940000 0.063713 23 2.852225 0.419000 0.029881 85 27.839033 0.974000 0.056105 34 20.462749 0.968000 0.063065 65 47.432736 0.997000 0.160403 37 8.109997 0.746000 0.055656 69 20.735688 0.933000 0.082584 6 2.236236 0.260000 0.039337 14 18.905120 0.928000 0.062564 37 21.475367 0.935000 0.069283 24 1.248807 0.238000 0.037012 45 2.059926 0.156000 0.060139 . Printing the most likely tree in file 'proteic_M2480_40x430_2005.phy_phyml_tree.txt'... . Time used 7h27m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo