.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1601_36x340_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... . 322 patterns found. (out of a total of 340 sites) . 79 sites without polymorphism (23.24%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 28Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7117.5136] [ 1173] [depth= 2] . ( 2 sec) [ -7104.8003] [ 1171] [depth= 2] . ( 3 sec) [ -7102.6634] [ 1163] [depth= 4] . ( 3 sec) [ -7098.6557] [ 1162] [depth= 1] . ( 6 sec) [ -7097.7360] [ 1162] [depth= 1] . ( 7 sec) [ -7083.0388] [ 1161] [depth= 4] . ( 7 sec) [ -7081.2492] [ 1165] [depth= 1] . ( 9 sec) [ -7078.6615] [ 1167] [depth= 1] . ( 11 sec) [ -7072.1113] [ 1162] [depth= 2] . ( 20 sec) [ -7062.2238] [ 1161] [depth= 1] . ( 20 sec) [ -7061.4939] [ 1162] [depth= 1] . ( 21 sec) [ -7060.7871] [ 1161] [depth= 1] . ( 22 sec) [ -7060.6584] [ 1163] [depth= 1] . ( 22 sec) [ -7057.8967] [ 1162] [depth= 1] . ( 23 sec) [ -7056.5354] [ 1163] [depth= 1] . ( 23 sec) [ -7056.1726] [ 1162] [depth= 1] . ( 32 sec) [ -7054.8793] [ 1162] [depth= 1] . ( 34 sec) [ -7054.8656] [ 1162] [depth= 1] . ( 35 sec) [ -7051.8914] [ 1161] [depth= 1] . ( 35 sec) [ -7049.2666] [ 1161] [depth= 4] . ( 41 sec) [ -7049.1419] [ 1164] [depth= 1] . ( 41 sec) [ -7042.0243] [ 1159] [depth= 2] . ( 44 sec) [ -7041.6419] [ 1160] [depth= 1] . ( 49 sec) [ -7041.2720] [ 1159] [depth= 1] . ( 50 sec) [ -7040.0826] [ 1158] [depth= 1] . ( 56 sec) [ -7038.6105] [ 1159] [depth= 1] . ( 56 sec) [ -7036.1355] [ 1158] [depth= 1] . ( 62 sec) [ -7032.7690] [ 1157] [depth= 1] . ( 63 sec) [ -7032.3250] [ 1157] [depth= 1] . ( 75 sec) [ -7006.5351] [Branch lengths ] . ( 78 sec) [ -7006.4552] [ 1159] [depth= 4] . ( 120 sec) [ -7006.2451] [ 1154] [depth= 3] . ( 152 sec) [ -7001.9341] [Branch lengths ] . ( 156 sec) [ -6999.7530] [ 1155] [depth= 4] . ( 166 sec) [ -6999.4522] [ 1155] [depth= 1] . ( 236 sec) [ -6998.2573] [Branch lengths ] . ( 322 sec) [ -6997.8301] [Branch lengths ] . ( 322 sec) [ -6997.8301] [Topology ] . ( 325 sec) [ -6997.7183] [Topology ] . ( 328 sec) [ -6997.6549] [Topology ] . ( 331 sec) [ -6997.6089] [Topology ] . ( 334 sec) [ -6997.5748] [Topology ] . ( 338 sec) [ -6997.5495] [Topology ] . ( 341 sec) [ -6997.5306] [Topology ] . ( 341 sec) [ -6997.5306] [Topology ] . ( 344 sec) [ -6997.5165] [Topology ] . ( 347 sec) [ -6997.5060] [Topology ] . ( 350 sec) [ -6997.4982] [Topology ] . ( 354 sec) [ -6997.4924] [Topology ] . ( 357 sec) [ -6997.4880] [Topology ] . ( 360 sec) [ -6997.4848] [Topology ] . ( 360 sec) [ -6997.4848] [Topology ] . ( 363 sec) [ -6997.4823] [Topology ] . ( 367 sec) [ -6997.4805] [Topology ] . ( 370 sec) [ -6997.4791] [Topology ] . ( 373 sec) [ -6997.4781] [Topology ] . ( 376 sec) [ -6997.4773] [Topology ] . ( 376 sec) [ -6997.4773] [Topology ] . ( 379 sec) [ -6997.4767] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6997.476734. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 83 3.232517 0.789000 0.200826 56 1.825172 0.203000 0.272517 99 66.095510 0.997000 1.000861 83 4.967167 0.827000 0.035049 33 4.028713 0.750000 0.014135 30 22.110137 0.898000 0.035268 56 18.131085 0.921000 0.086217 38 0.364231 0.108000 0.012900 35 5.463648 0.742000 0.013065 73 18.106011 0.945000 0.056072 90 29.134203 0.970000 0.099427 100 48.479807 0.987000 0.138502 56 6.902635 0.828000 0.018365 20 1.083315 0.752000 0.005749 93 158.367679 1.000000 0.134850 76 12.209436 0.858000 0.010539 68 10.159162 0.741000 0.004826 44 1.974403 0.397000 0.010139 72 9.804585 0.730000 0.019836 26 0.021959 0.000000 0.002414 100 40.140363 0.981000 0.076134 28 11.620046 0.831000 0.013872 41 8.700918 0.858000 0.053353 100 42.087834 0.992000 0.212037 53 11.256599 0.875000 0.020455 75 13.005789 0.919000 0.025360 18 -1.000000 0.000000 0.000000 47 8.108565 0.831000 0.009138 61 2.539322 0.734000 0.006296 59 12.636026 0.877000 0.023646 96 54.411067 0.997000 0.093366 49 -1.000000 0.000000 0.000011 74 10.117915 0.840000 0.009589 . Printing the most likely tree in file 'proteic_M1601_36x340_2003.phy_phyml_tree.txt'... . Time used 10h19m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo