.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2363_38x251_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... . 244 patterns found. (out of a total of 251 sites) . 24 sites without polymorphism (9.56%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12349.1907] [ 2705] [depth= 1] . ( 2 sec) [ -12348.9510] [ 2701] [depth= 1] . ( 2 sec) [ -12329.4746] [ 2699] [depth= 1] . ( 2 sec) [ -12329.1105] [ 2704] [depth= 1] . ( 3 sec) [ -12318.6708] [ 2708] [depth= 1] . ( 3 sec) [ -12315.0262] [ 2704] [depth= 1] . ( 4 sec) [ -12307.0370] [ 2703] [depth= 1] . ( 4 sec) [ -12301.2724] [ 2703] [depth= 1] . ( 5 sec) [ -12296.8550] [ 2706] [depth= 1] . ( 5 sec) [ -12288.5867] [ 2703] [depth= 1] . ( 6 sec) [ -12286.4953] [ 2704] [depth= 1] . ( 8 sec) [ -12274.1281] [ 2705] [depth= 2] . ( 9 sec) [ -12198.7165] [ 2702] [depth= 2] . ( 9 sec) [ -12180.9742] [ 2704] [depth= 1] . ( 10 sec) [ -12156.8191] [ 2699] [depth= 2] . ( 11 sec) [ -12151.2786] [ 2701] [depth= 1] . ( 13 sec) [ -12136.8885] [ 2699] [depth= 1] . ( 13 sec) [ -12128.8923] [ 2699] [depth= 1] . ( 14 sec) [ -12127.2029] [ 2700] [depth= 1] . ( 14 sec) [ -12126.0242] [ 2699] [depth= 1] . ( 15 sec) [ -12125.6240] [ 2699] [depth= 1] . ( 15 sec) [ -12082.4591] [ 2701] [depth= 2] . ( 16 sec) [ -12066.9619] [ 2707] [depth= 1] . ( 16 sec) [ -12066.8621] [ 2705] [depth= 2] . ( 17 sec) [ -12059.9594] [ 2702] [depth= 1] . ( 17 sec) [ -12053.1414] [ 2704] [depth= 1] . ( 18 sec) [ -12048.6874] [ 2689] [depth= 8] . ( 18 sec) [ -12046.9296] [ 2694] [depth= 2] . ( 19 sec) [ -12043.0601] [ 2690] [depth= 4] . ( 19 sec) [ -12040.5150] [ 2689] [depth= 5] . ( 20 sec) [ -12033.8234] [ 2685] [depth= 8] . ( 20 sec) [ -12019.4293] [ 2687] [depth= 3] . ( 21 sec) [ -12019.0569] [ 2679] [depth= 3] . ( 21 sec) [ -12017.4001] [ 2680] [depth= 4] . ( 22 sec) [ -12016.8613] [ 2678] [depth= 4] . ( 22 sec) [ -12016.2879] [ 2677] [depth= 1] . ( 23 sec) [ -12012.4580] [ 2675] [depth= 3] . ( 23 sec) [ -12010.5149] [ 2678] [depth= 1] . ( 23 sec) [ -12010.4692] [ 2677] [depth= 4] . ( 24 sec) [ -11976.6379] [ 2678] [depth= 1] . ( 25 sec) [ -11973.7729] [ 2677] [depth= 1] . ( 25 sec) [ -11973.6378] [ 2679] [depth= 1] . ( 26 sec) [ -11970.7600] [ 2678] [depth= 1] . ( 26 sec) [ -11969.6506] [ 2679] [depth= 1] . ( 27 sec) [ -11964.3471] [ 2680] [depth= 1] . ( 27 sec) [ -11964.0186] [ 2679] [depth= 1] . ( 28 sec) [ -11963.6704] [ 2682] [depth= 3] . ( 29 sec) [ -11961.6175] [ 2685] [depth= 2] . ( 30 sec) [ -11944.3209] [ 2690] [depth= 4] . ( 31 sec) [ -11943.0896] [ 2691] [depth= 3] . ( 32 sec) [ -11870.1333] [Branch lengths ] . ( 33 sec) [ -11869.4654] [ 2691] [depth= 1] . ( 34 sec) [ -11868.7562] [ 2691] [depth= 1] . ( 36 sec) [ -11868.4016] [ 2690] [depth= 1] . ( 41 sec) [ -11867.9479] [ 2695] [depth= 1] . ( 45 sec) [ -11864.8719] [ 2691] [depth= 3] . ( 46 sec) [ -11862.7258] [ 2691] [depth= 1] . ( 47 sec) [ -11861.5218] [ 2691] [depth= 1] . ( 49 sec) [ -11861.0869] [ 2683] [depth= 1] . ( 49 sec) [ -11853.3500] [ 2677] [depth= 10] . ( 51 sec) [ -11852.8200] [ 2682] [depth= 1] . ( 52 sec) [ -11851.5138] [ 2682] [depth= 1] . ( 52 sec) [ -11848.7885] [ 2681] [depth= 1] . ( 54 sec) [ -11848.7608] [ 2682] [depth= 6] . ( 58 sec) [ -11848.6447] [ 2682] [depth= 1] . ( 59 sec) [ -11847.3489] [ 2683] [depth= 1] . ( 59 sec) [ -11844.8871] [ 2677] [depth= 6] . ( 60 sec) [ -11844.6109] [ 2676] [depth= 2] . ( 61 sec) [ -11844.0261] [ 2679] [depth= 1] . ( 62 sec) [ -11843.0349] [ 2682] [depth= 1] . ( 66 sec) [ -11842.6230] [ 2680] [depth= 1] . ( 68 sec) [ -11842.3696] [ 2685] [depth= 2] . ( 69 sec) [ -11842.2547] [ 2684] [depth= 1] . ( 71 sec) [ -11841.7552] [ 2686] [depth= 4] . ( 74 sec) [ -11821.3524] [Branch lengths ] . ( 100 sec) [ -11820.1410] [ 2678] [depth= 2] . ( 112 sec) [ -11820.0793] [ 2680] [depth= 1] . ( 113 sec) [ -11819.8976] [ 2678] [depth= 1] . ( 114 sec) [ -11819.6882] [ 2680] [depth= 1] . ( 126 sec) [ -11813.1877] [Branch lengths ] . ( 179 sec) [ -11811.5030] [Branch lengths ] . ( 179 sec) [ -11811.5030] [Topology ] . ( 181 sec) [ -11809.8646] [Topology ] . ( 184 sec) [ -11808.8485] [Topology ] . ( 186 sec) [ -11808.4375] [Topology ] . ( 188 sec) [ -11808.1849] [Topology ] . ( 190 sec) [ -11808.0366] [Topology ] . ( 193 sec) [ -11807.9423] [Topology ] . ( 195 sec) [ -11807.8818] [Topology ] . ( 195 sec) [ -11807.8818] [Topology ] . ( 197 sec) [ -11807.8412] [Topology ] . ( 200 sec) [ -11807.8133] [Topology ] . ( 202 sec) [ -11807.7934] [Topology ] . ( 204 sec) [ -11807.7788] [Topology ] . ( 207 sec) [ -11807.7678] [Topology ] . ( 209 sec) [ -11807.7592] [Topology ] . ( 209 sec) [ -11807.7592] [Topology ] . ( 211 sec) [ -11807.7524] [Topology ] . ( 214 sec) [ -11807.7469] [Topology ] . ( 216 sec) [ -11807.7423] [Topology ] . ( 218 sec) [ -11807.7386] [Topology ] . ( 220 sec) [ -11807.7354] [Topology ] . ( 223 sec) [ -11807.7328] [Topology ] . ( 223 sec) [ -11807.7328] [Topology ] . ( 225 sec) [ -11807.7305] [Topology ] . ( 227 sec) [ -11807.7285] [Topology ] . ( 230 sec) [ -11807.7268] [Topology ] . ( 232 sec) [ -11807.7254] [Topology ] . ( 234 sec) [ -11807.7241] [Topology ] . ( 237 sec) [ -11807.7231] [Topology ] . ( 237 sec) [ -11807.7231] [Topology ] . ( 239 sec) [ -11807.7221] [Topology ] . Checking for NNIs, optimizing five branches... . ( 266 sec) [ -11807.5975] [Topology ] . Checking for NNIs, optimizing five branches... . ( 294 sec) [ -11807.5075] [Topology ] . Checking for NNIs, optimizing five branches... . ( 323 sec) [ -11807.4509] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11807.450881. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 48.078595 0.999000 1.641412 27 3.900069 0.808000 0.407964 88 39.039341 0.993000 1.233087 10 0.980493 0.697000 0.142889 6 0.537651 0.432000 0.153102 3 -1.000000 0.000000 0.000029 23 5.063073 0.809000 0.375672 28 4.140408 0.782000 1.136418 79 10.195789 0.890000 1.837742 78 7.487124 0.859000 1.523038 51 5.947357 0.862000 1.933144 31 15.442776 0.953000 1.330223 75 7.933790 0.848000 0.387059 16 3.680667 0.621000 0.506413 75 5.304946 0.856000 2.809399 100 35.953337 0.994000 6.381520 28 0.561331 0.409000 0.157570 37 50.591387 0.984000 0.280479 17 0.400416 0.627000 0.491626 67 27.315989 0.942000 2.619077 30 0.146484 0.000000 0.139938 42 5.518197 0.815000 0.601186 57 1.452201 0.425000 0.331828 83 13.973575 0.928000 0.509636 97 19.808147 0.941000 0.414949 97 15.675212 0.945000 0.226629 97 30.076512 0.984000 0.666726 49 0.053838 0.000000 0.058417 43 0.113260 0.000000 0.033292 76 3.378221 0.664000 0.081077 87 19.463800 0.965000 0.118863 42 1.162639 0.339000 0.285754 100 31.260973 0.994000 1.064362 100 72.680603 0.999000 1.612306 49 1.072930 0.231000 0.091234 . Printing the most likely tree in file 'proteic_M2363_38x251_2004.phy_phyml_tree.txt'... . Time used 10h54m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo