.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12664.0248] [Ts/ts ratio ][ 3.196983] . ( 0 sec) [ -12662.4511] [ 2714] [depth= 1] . ( 0 sec) [ -12662.1390] [ 2714] [depth= 1] . ( 1 sec) [ -12658.9490] [ 2714] [depth= 1] . ( 1 sec) [ -12655.4311] [ 2714] [depth= 1] . ( 1 sec) [ -12653.5546] [ 2714] [depth= 1] . ( 1 sec) [ -12642.7628] [ 2712] [depth= 2] . ( 1 sec) [ -12641.8106] [ 2712] [depth= 1] . ( 2 sec) [ -12641.7479] [ 2712] [depth= 1] . ( 2 sec) [ -12630.2874] [ 2712] [depth= 1] . ( 2 sec) [ -12625.1379] [ 2712] [depth= 1] . ( 2 sec) [ -12624.9721] [ 2712] [depth= 1] . ( 3 sec) [ -12606.6550] [ 2704] [depth= 1] . ( 3 sec) [ -12606.6076] [ 2704] [depth= 1] . ( 3 sec) [ -12593.5448] [ 2702] [depth= 1] . ( 3 sec) [ -12583.7139] [ 2704] [depth= 1] . ( 4 sec) [ -12582.9489] [ 2704] [depth= 1] . ( 4 sec) [ -12582.6605] [ 2704] [depth= 1] . ( 4 sec) [ -12561.0149] [ 2704] [depth= 1] . ( 5 sec) [ -12558.5571] [ 2706] [depth= 1] . ( 5 sec) [ -12558.3191] [ 2704] [depth= 1] . ( 5 sec) [ -12526.7957] [ 2704] [depth= 4] . ( 5 sec) [ -12508.2129] [ 2693] [depth= 4] . ( 5 sec) [ -12503.2931] [ 2694] [depth= 1] . ( 5 sec) [ -12497.9647] [ 2692] [depth= 2] . ( 6 sec) [ -12466.2854] [ 2697] [depth= 1] . ( 6 sec) [ -12464.7452] [ 2699] [depth= 1] . ( 6 sec) [ -12463.0787] [ 2697] [depth= 1] . ( 6 sec) [ -12460.8879] [ 2693] [depth= 1] . ( 6 sec) [ -12458.7266] [ 2691] [depth= 2] . ( 6 sec) [ -12458.2960] [ 2693] [depth= 1] . ( 7 sec) [ -12445.0952] [ 2693] [depth= 2] . ( 7 sec) [ -12434.2439] [ 2690] [depth= 1] . ( 7 sec) [ -12432.9539] [ 2684] [depth= 4] . ( 8 sec) [ -12430.9538] [ 2683] [depth= 2] . ( 8 sec) [ -12427.9821] [ 2681] [depth= 1] . ( 8 sec) [ -12425.7899] [ 2680] [depth= 1] . ( 8 sec) [ -12418.5022] [ 2682] [depth= 1] . ( 9 sec) [ -12382.7128] [ 2677] [depth= 1] . ( 9 sec) [ -12382.4334] [ 2677] [depth= 1] . ( 9 sec) [ -12382.4192] [ 2677] [depth= 1] . ( 9 sec) [ -12382.3586] [ 2677] [depth= 1] . ( 10 sec) [ -12382.2962] [ 2677] [depth= 1] . ( 10 sec) [ -12374.6829] [ 2677] [depth= 1] . ( 10 sec) [ -12373.0492] [ 2677] [depth= 1] . ( 11 sec) [ -12373.0263] [ 2677] [depth= 2] . ( 11 sec) [ -12372.5478] [ 2677] [depth= 1] . ( 11 sec) [ -12372.4364] [ 2677] [depth= 1] . ( 11 sec) [ -12372.2683] [ 2677] [depth= 1] . ( 16 sec) [ -12371.4374] [ 2677] [depth= 1] . ( 16 sec) [ -12368.7437] [ 2677] [depth= 1] . ( 16 sec) [ -12368.3574] [ 2677] [depth= 4] . ( 16 sec) [ -12368.3430] [ 2677] [depth= 7] . ( 18 sec) [ -12364.0298] [ 2678] [depth= 9] . ( 18 sec) [ -12360.6417] [ 2677] [depth= 9] . ( 18 sec) [ -12359.4856] [ 2676] [depth= 3] . ( 18 sec) [ -12358.2492] [ 2676] [depth= 3] . ( 19 sec) [ -12357.8219] [ 2676] [depth= 1] . ( 19 sec) [ -12357.6332] [ 2676] [depth= 1] . ( 19 sec) [ -12357.2744] [ 2676] [depth= 2] . ( 19 sec) [ -12357.2534] [ 2676] [depth= 6] . ( 20 sec) [ -12357.2162] [ 2676] [depth= 6] . ( 20 sec) [ -12357.1954] [ 2676] [depth= 3] . ( 30 sec) [ -12278.1616] [Branch lengths ] . ( 30 sec) [ -12270.1663] [Ts/ts ratio ][ 3.817208] . ( 31 sec) [ -12270.1330] [ 2676] [depth= 1] . ( 32 sec) [ -12270.0881] [ 2676] [depth= 1] . ( 33 sec) [ -12270.0076] [ 2676] [depth= 1] . ( 34 sec) [ -12269.7356] [ 2679] [depth= 1] . ( 35 sec) [ -12269.7087] [ 2683] [depth= 2] . ( 35 sec) [ -12269.5200] [ 2684] [depth= 1] . ( 36 sec) [ -12269.4109] [ 2678] [depth= 1] . ( 37 sec) [ -12268.8827] [ 2683] [depth= 1] . ( 37 sec) [ -12268.4266] [ 2681] [depth= 1] . ( 37 sec) [ -12268.2468] [ 2682] [depth= 1] . ( 39 sec) [ -12267.5116] [ 2682] [depth= 1] . ( 48 sec) [ -12267.4920] [ 2682] [depth= 1] . ( 49 sec) [ -12267.4735] [ 2682] [depth= 2] . ( 49 sec) [ -12267.4479] [ 2682] [depth= 2] . ( 62 sec) [ -12258.5928] [Branch lengths ] . ( 62 sec) [ -12258.0629] [Ts/ts ratio ][ 3.997514] . ( 63 sec) [ -12258.0519] [ 2682] [depth= 1] . ( 68 sec) [ -12257.1775] [ 2686] [depth= 2] . ( 68 sec) [ -12257.1639] [ 2686] [depth= 1] . ( 70 sec) [ -12257.1330] [ 2686] [depth= 1] . ( 95 sec) [ -12253.2156] [Branch lengths ] . ( 95 sec) [ -12253.1873] [Ts/ts ratio ][ 4.040192] . ( 128 sec) [ -12252.8789] [Branch lengths ] . ( 150 sec) [ -12252.3667] [ 2681] [depth= 1] . ( 153 sec) [ -12251.8015] [ 2686] [depth= 2] . ( 206 sec) [ -12251.1588] [Branch lengths ] . ( 206 sec) [ -12251.1560] [Ts/ts ratio ][ 4.053641] . ( 285 sec) [ -12251.0120] [Branch lengths ] . ( 285 sec) [ -12251.0120] [Topology ] . ( 287 sec) [ -12250.7259] [Topology ] . ( 288 sec) [ -12249.5600] [Topology ] . ( 290 sec) [ -12247.8097] [Topology ] . ( 292 sec) [ -12247.2018] [Topology ] . ( 293 sec) [ -12246.9906] [Topology ] . ( 295 sec) [ -12246.9091] [Topology ] . ( 295 sec) [ -12246.8992] [Ts/ts ratio ][ 4.079248] . ( 296 sec) [ -12246.8992] [Topology ] . ( 297 sec) [ -12246.8630] [Topology ] . ( 299 sec) [ -12246.8464] [Topology ] . ( 301 sec) [ -12246.8386] [Topology ] . ( 302 sec) [ -12246.8346] [Topology ] . ( 304 sec) [ -12246.8323] [Topology ] . ( 306 sec) [ -12246.8310] [Topology ] . ( 306 sec) [ -12246.8310] [Ts/ts ratio ][ 4.079248] . ( 306 sec) [ -12246.8310] [Topology ] . ( 308 sec) [ -12246.8304] [Topology ] . ( 308 sec) [ -12246.8304] [Ts/ts ratio ][ 4.079248] . Checking for NNIs, optimizing five branches... . ( 323 sec) [ -12246.8303] [Topology ] . Checking for NNIs, optimizing five branches... . ( 338 sec) [ -12246.8300] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12246.829995. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 84 -1.000000 0.000000 0.000000 100 60.281512 0.999000 0.109743 100 99.234795 1.000000 0.123534 99 93.971004 1.000000 0.161681 34 8.728192 0.833000 0.033407 75 20.351382 0.955000 0.034298 42 7.868326 0.899000 0.038394 95 75.230060 1.000000 0.147986 28 -1.000000 0.000000 0.000000 31 8.471513 0.854000 0.026342 95 125.117928 1.000000 0.107578 21 1.478616 0.211000 0.019063 100 124.756422 1.000000 0.107243 100 141.103402 1.000000 0.107630 94 12.723649 0.897000 0.002050 34 -1.000000 0.000000 0.000000 94 24.236259 0.981000 0.050262 31 2.439839 0.747000 0.017986 59 19.599719 0.922000 0.086952 40 15.878847 0.931000 0.120605 36 6.981912 0.797000 0.109171 49 6.239693 0.775000 0.137455 15 4.250977 0.476000 0.052221 100 50.861794 0.991000 0.173601 12 0.185310 0.000000 0.031905 63 8.281017 0.825000 0.032536 99 99.910881 1.000000 0.102798 70 12.886779 0.892000 0.028206 100 107.147459 1.000000 0.094276 30 -1.000000 0.000000 0.000000 72 17.532607 0.938000 0.040324 93 139.887558 1.000000 0.126761 8 15.603812 0.922000 0.038905 100 106.412343 1.000000 0.096822 93 57.365494 0.994000 0.057679 98 40.594095 0.997000 0.039054 70 0.087381 0.000000 0.000959 91 17.483514 0.942000 0.024080 98 44.232108 0.996000 0.036092 99 67.973902 0.999000 0.031618 69 2.190344 0.756000 0.000954 56 4.234505 0.748000 0.001117 5 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 1 0.000218 0.000000 0.000000 1 0.000287 0.000000 0.000816 2 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 80 8.803411 0.757000 0.013256 99 44.846786 0.996000 0.017836 100 62.055934 0.997000 0.020701 3 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 14 8.304378 0.800000 0.000992 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000095 3 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 7h19m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo