.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2564_142x1130_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 . Compressing sequences... . 780 patterns found. (out of a total of 1130 sites) . 486 sites without polymorphism (43.01%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21258.1993] [Ts/ts ratio ][ 2.236742] . ( 3 sec) [ -21255.9861] [ 4073] [depth= 1] . ( 3 sec) [ -21240.5795] [ 4068] [depth= 1] . ( 3 sec) [ -21234.5485] [ 4054] [depth= 1] . ( 4 sec) [ -21234.2573] [ 4061] [depth= 1] . ( 5 sec) [ -21222.1271] [ 4072] [depth= 1] . ( 5 sec) [ -21208.9386] [ 4061] [depth= 1] . ( 6 sec) [ -21208.5613] [ 4066] [depth= 1] . ( 6 sec) [ -21199.4297] [ 4061] [depth= 1] . ( 7 sec) [ -21196.5319] [ 4065] [depth= 1] . ( 7 sec) [ -21183.2536] [ 4061] [depth= 1] . ( 8 sec) [ -21183.0741] [ 4063] [depth= 1] . ( 8 sec) [ -21173.3563] [ 4061] [depth= 1] . ( 9 sec) [ -21172.0168] [ 4065] [depth= 1] . ( 10 sec) [ -21165.0617] [ 4061] [depth= 1] . ( 11 sec) [ -21164.9031] [ 4066] [depth= 1] . ( 11 sec) [ -21140.2954] [ 4074] [depth= 4] . ( 11 sec) [ -21137.5692] [ 4078] [depth= 2] . ( 11 sec) [ -21135.7628] [ 4075] [depth= 1] . ( 12 sec) [ -21134.2996] [ 4076] [depth= 2] . ( 13 sec) [ -21133.8844] [ 4070] [depth= 1] . ( 13 sec) [ -21132.9917] [ 4065] [depth= 1] . ( 13 sec) [ -21125.7297] [ 4072] [depth= 1] . ( 14 sec) [ -21118.4344] [ 4065] [depth= 1] . ( 14 sec) [ -21117.8252] [ 4067] [depth= 1] . ( 14 sec) [ -21117.7511] [ 4069] [depth= 1] . ( 16 sec) [ -21117.3662] [ 4071] [depth= 1] . ( 16 sec) [ -21110.4709] [ 4068] [depth= 1] . ( 17 sec) [ -21109.8000] [ 4071] [depth= 1] . ( 17 sec) [ -21102.9558] [ 4070] [depth= 1] . ( 18 sec) [ -21102.3865] [ 4073] [depth= 1] . ( 19 sec) [ -21096.4558] [ 4072] [depth= 1] . ( 19 sec) [ -21091.7631] [ 4073] [depth= 1] . ( 19 sec) [ -21088.1786] [ 4070] [depth= 1] . ( 22 sec) [ -21058.5287] [ 4061] [depth= 5] . ( 22 sec) [ -21058.3238] [ 4061] [depth= 2] . ( 22 sec) [ -21058.2739] [ 4059] [depth= 1] . ( 24 sec) [ -21056.7649] [ 4061] [depth= 1] . ( 24 sec) [ -21054.3635] [ 4059] [depth= 1] . ( 25 sec) [ -21053.0800] [ 4058] [depth= 1] . ( 25 sec) [ -21052.5637] [ 4059] [depth= 1] . ( 25 sec) [ -21045.2699] [ 4057] [depth= 11] . ( 26 sec) [ -21041.1989] [ 4058] [depth= 1] . ( 26 sec) [ -21038.6722] [ 4056] [depth= 1] . ( 28 sec) [ -21035.6431] [ 4054] [depth= 1] . ( 28 sec) [ -21026.6079] [ 4054] [depth= 7] . ( 28 sec) [ -21011.8267] [ 4050] [depth= 4] . ( 28 sec) [ -21010.6007] [ 4050] [depth= 6] . ( 29 sec) [ -21002.4809] [ 4049] [depth= 6] . ( 29 sec) [ -20993.8569] [ 4048] [depth= 2] . ( 30 sec) [ -20989.4600] [ 4048] [depth= 1] . ( 30 sec) [ -20988.6537] [ 4049] [depth= 1] . ( 31 sec) [ -20986.6100] [ 4049] [depth= 2] . ( 31 sec) [ -20986.3305] [ 4049] [depth= 1] . ( 32 sec) [ -20986.1876] [ 4049] [depth= 1] . ( 32 sec) [ -20986.0387] [ 4049] [depth= 1] . ( 33 sec) [ -20982.4180] [ 4049] [depth= 2] . ( 35 sec) [ -20982.3947] [ 4049] [depth= 1] . ( 35 sec) [ -20981.1939] [ 4048] [depth= 1] . ( 37 sec) [ -20978.0299] [ 4047] [depth= 1] . ( 37 sec) [ -20976.6007] [ 4047] [depth= 1] . ( 37 sec) [ -20975.7685] [ 4049] [depth= 1] . ( 40 sec) [ -20973.6598] [ 4049] [depth= 2] . ( 41 sec) [ -20972.9838] [ 4049] [depth= 1] . ( 42 sec) [ -20972.7004] [ 4050] [depth= 2] . ( 43 sec) [ -20971.6490] [ 4050] [depth= 1] . ( 44 sec) [ -20971.6227] [ 4050] [depth= 1] . ( 45 sec) [ -20971.5535] [ 4050] [depth= 1] . ( 46 sec) [ -20971.1680] [ 4050] [depth= 1] . ( 47 sec) [ -20970.2555] [ 4050] [depth= 1] . ( 47 sec) [ -20968.2969] [ 4050] [depth= 1] . ( 48 sec) [ -20964.4217] [ 4054] [depth= 2] . ( 49 sec) [ -20964.3855] [ 4054] [depth= 1] . ( 50 sec) [ -20964.1064] [ 4054] [depth= 1] . ( 50 sec) [ -20962.6941] [ 4054] [depth= 2] . ( 50 sec) [ -20961.8045] [ 4053] [depth= 2] . ( 51 sec) [ -20955.3797] [ 4052] [depth= 1] . ( 54 sec) [ -20947.6213] [ 4052] [depth= 1] . ( 54 sec) [ -20943.6993] [ 4051] [depth= 4] . ( 55 sec) [ -20940.9382] [ 4050] [depth= 1] . ( 55 sec) [ -20939.1549] [ 4052] [depth= 2] . ( 55 sec) [ -20934.4192] [ 4051] [depth= 2] . ( 57 sec) [ -20930.7010] [ 4050] [depth= 1] . ( 57 sec) [ -20928.0828] [ 4050] [depth= 1] . ( 59 sec) [ -20926.6514] [ 4052] [depth= 1] . ( 60 sec) [ -20926.4194] [ 4052] [depth= 1] . ( 60 sec) [ -20926.2712] [ 4052] [depth= 1] . ( 60 sec) [ -20922.4197] [ 4052] [depth= 1] . ( 62 sec) [ -20916.7962] [ 4048] [depth= 1] . ( 63 sec) [ -20915.0047] [ 4046] [depth= 1] . ( 64 sec) [ -20914.5614] [ 4047] [depth= 1] . ( 64 sec) [ -20913.6571] [ 4050] [depth= 6] . ( 64 sec) [ -20912.5885] [ 4048] [depth= 6] . ( 67 sec) [ -20906.4585] [ 4046] [depth= 2] . ( 67 sec) [ -20904.2149] [ 4047] [depth= 2] . ( 70 sec) [ -20903.0832] [ 4047] [depth= 4] . ( 70 sec) [ -20902.7264] [ 4047] [depth= 1] . ( 70 sec) [ -20901.9673] [ 4048] [depth= 4] . ( 71 sec) [ -20901.3728] [ 4048] [depth= 5] . ( 73 sec) [ -20897.3744] [ 4046] [depth= 1] . ( 74 sec) [ -20890.1952] [ 4044] [depth= 2] . ( 76 sec) [ -20885.8106] [ 4043] [depth= 3] . ( 77 sec) [ -20885.6405] [ 4042] [depth= 1] . ( 77 sec) [ -20884.1416] [ 4041] [depth= 1] . ( 77 sec) [ -20882.4861] [ 4041] [depth= 1] . ( 78 sec) [ -20881.9137] [ 4041] [depth= 1] . ( 78 sec) [ -20881.7611] [ 4041] [depth= 2] . ( 82 sec) [ -20881.5728] [ 4042] [depth= 1] . ( 82 sec) [ -20880.4098] [ 4041] [depth= 1] . ( 83 sec) [ -20878.5892] [ 4040] [depth= 1] . ( 83 sec) [ -20876.4135] [ 4040] [depth= 1] . ( 84 sec) [ -20874.8255] [ 4042] [depth= 1] . ( 84 sec) [ -20873.5721] [ 4042] [depth= 1] . ( 86 sec) [ -20873.2351] [ 4043] [depth= 1] . ( 92 sec) [ -20871.0193] [ 4042] [depth= 2] . ( 93 sec) [ -20870.5950] [ 4041] [depth= 1] . ( 96 sec) [ -20870.4229] [ 4041] [depth= 1] . ( 96 sec) [ -20869.3466] [ 4042] [depth= 3] . ( 96 sec) [ -20869.0344] [ 4041] [depth= 1] . ( 98 sec) [ -20868.7014] [ 4043] [depth= 2] . ( 99 sec) [ -20868.3841] [ 4043] [depth= 1] . ( 100 sec) [ -20867.7246] [ 4042] [depth= 2] . ( 102 sec) [ -20679.7226] [Branch lengths ] . ( 103 sec) [ -20677.4652] [Ts/ts ratio ][ 2.405102] . ( 105 sec) [ -20676.0254] [ 4047] [depth= 1] . ( 109 sec) [ -20673.1224] [ 4050] [depth= 1] . ( 111 sec) [ -20672.1297] [ 4052] [depth= 1] . ( 112 sec) [ -20670.3509] [ 4051] [depth= 1] . ( 112 sec) [ -20669.8314] [ 4050] [depth= 1] . ( 112 sec) [ -20668.6480] [ 4049] [depth= 1] . ( 116 sec) [ -20668.1854] [ 4049] [depth= 1] . ( 118 sec) [ -20668.0667] [ 4047] [depth= 1] . ( 119 sec) [ -20667.3701] [ 4052] [depth= 1] . ( 124 sec) [ -20660.9647] [ 4053] [depth= 10] . ( 126 sec) [ -20659.7655] [ 4051] [depth= 1] . ( 128 sec) [ -20657.6793] [ 4044] [depth= 6] . ( 129 sec) [ -20654.8121] [ 4045] [depth= 3] . ( 129 sec) [ -20653.8132] [ 4045] [depth= 4] . ( 140 sec) [ -20652.6884] [ 4045] [depth= 1] . ( 140 sec) [ -20652.2220] [ 4046] [depth= 1] . ( 142 sec) [ -20651.5104] [ 4045] [depth= 1] . ( 147 sec) [ -20651.3534] [ 4045] [depth= 1] . ( 149 sec) [ -20651.3078] [ 4045] [depth= 1] . ( 149 sec) [ -20651.1917] [ 4045] [depth= 1] . ( 150 sec) [ -20650.8254] [ 4046] [depth= 1] . ( 154 sec) [ -20650.7680] [ 4046] [depth= 1] . ( 181 sec) [ -20650.7126] [ 4046] [depth= 1] . ( 181 sec) [ -20650.5890] [ 4046] [depth= 1] . ( 183 sec) [ -20649.7077] [ 4047] [depth= 3] . ( 187 sec) [ -20649.5180] [ 4047] [depth= 1] . ( 193 sec) [ -20649.4871] [ 4047] [depth= 1] . ( 194 sec) [ -20649.2917] [ 4047] [depth= 1] . ( 194 sec) [ -20649.1956] [ 4047] [depth= 1] . ( 200 sec) [ -20648.9856] [ 4047] [depth= 1] . ( 202 sec) [ -20648.4360] [ 4044] [depth= 3] . ( 202 sec) [ -20646.5095] [ 4042] [depth= 3] . ( 204 sec) [ -20646.4197] [ 4042] [depth= 1] . ( 207 sec) [ -20646.2278] [ 4042] [depth= 1] . ( 209 sec) [ -20646.0906] [ 4042] [depth= 1] . ( 216 sec) [ -20643.2319] [ 4041] [depth= 2] . ( 220 sec) [ -20642.6452] [ 4041] [depth= 2] . ( 222 sec) [ -20609.0276] [Branch lengths ] . ( 222 sec) [ -20608.8900] [Ts/ts ratio ][ 2.448300] . ( 267 sec) [ -20608.8629] [ 4041] [depth= 1] . ( 269 sec) [ -20608.8296] [ 4041] [depth= 1] . ( 271 sec) [ -20608.8182] [ 4041] [depth= 1] . ( 276 sec) [ -20608.8001] [ 4041] [depth= 1] . ( 329 sec) [ -20608.1364] [ 4042] [depth= 7] . ( 334 sec) [ -20607.7889] [ 4042] [depth= 1] . ( 335 sec) [ -20607.7060] [ 4042] [depth= 1] . ( 354 sec) [ -20601.8135] [Branch lengths ] . ( 354 sec) [ -20601.7936] [Ts/ts ratio ][ 2.465514] . ( 429 sec) [ -20601.5408] [ 4046] [depth= 4] . ( 495 sec) [ -20599.4820] [Branch lengths ] . ( 496 sec) [ -20599.4784] [Ts/ts ratio ][ 2.472897] . ( 557 sec) [ -20599.4477] [ 4046] [depth= 1] . ( 580 sec) [ -20599.3553] [ 4045] [depth= 1] . ( 591 sec) [ -20597.9561] [ 4046] [depth= 1] . ( 593 sec) [ -20597.6697] [ 4047] [depth= 1] . ( 623 sec) [ -20596.8443] [ 4046] [depth= 1] . ( 633 sec) [ -20594.6764] [Branch lengths ] . ( 634 sec) [ -20594.6764] [Ts/ts ratio ][ 2.472897] . ( 718 sec) [ -20593.4594] [ 4045] [depth= 5] . ( 773 sec) [ -20589.9549] [Branch lengths ] . ( 773 sec) [ -20589.9549] [Ts/ts ratio ][ 2.472897] . ( 914 sec) [ -20585.2959] [Branch lengths ] . ( 951 sec) [ -20583.1566] [ 4051] [depth= 2] . ( 957 sec) [ -20583.0532] [ 4045] [depth= 1] . ( 1038 sec) [ -20582.6787] [ 4054] [depth= 6] . ( 1171 sec) [ -20574.5078] [Branch lengths ] . ( 1171 sec) [ -20574.5078] [Ts/ts ratio ][ 2.475370] . ( 1204 sec) [ -20574.3771] [ 4059] [depth= 2] . ( 1204 sec) [ -20573.6265] [ 4058] [depth= 1] . ( 1380 sec) [ -20573.6152] [ 4058] [depth= 1] . ( 1428 sec) [ -20563.9329] [Branch lengths ] . ( 1428 sec) [ -20563.9290] [Ts/ts ratio ][ 2.467805] . ( 1688 sec) [ -20562.9911] [Branch lengths ] . ( 1688 sec) [ -20562.9911] [Topology ] . ( 1693 sec) [ -20562.9738] [Topology ] . ( 1698 sec) [ -20562.9710] [Topology ] . ( 1703 sec) [ -20562.9703] [Topology ] . ( 1704 sec) [ -20562.9703] [Ts/ts ratio ][ 2.467805] . ( 1704 sec) [ -20562.9703] [Topology ] . ( 1709 sec) [ -20562.9701] [Topology ] . ( 1710 sec) [ -20562.9701] [Ts/ts ratio ][ 2.467805] . Checking for NNIs, optimizing five branches... . ( 1746 sec) [ -20562.8848] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1782 sec) [ -20562.8181] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1819 sec) [ -20562.7743] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1855 sec) [ -20562.7740] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20562.773970. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 55 9.203956 0.695000 0.013081 90 19.749751 0.919000 0.025052 96 34.590626 0.957000 0.042968 47 0.133479 0.000000 0.032619 100 397.847908 1.000000 0.424714 83 36.599257 0.981000 0.090808 100 84.019762 1.000000 0.142060 94 42.149175 0.986000 0.094594 90 26.182918 0.959000 0.056554 11 0.346165 0.155000 0.005736 13 2.235812 0.770000 0.012242 44 0.967717 0.347000 0.006102 99 104.966806 1.000000 0.095947 45 5.097060 0.748000 0.018158 97 41.865541 0.994000 0.071840 100 60.005394 0.992000 0.057635 70 5.486568 0.816000 0.017955 69 8.523574 0.836000 0.018387 100 42.350124 0.993000 0.050480 15 9.171620 0.843000 0.009423 57 51.248332 0.985000 0.042607 58 4.040718 0.809000 0.020505 71 12.774572 0.896000 0.035014 100 50.392652 0.993000 0.058127 65 22.645316 0.948000 0.049120 51 4.797522 0.831000 0.030330 70 16.523130 0.939000 0.030233 99 124.714528 1.000000 0.099814 88 40.042844 0.981000 0.049399 22 0.866236 0.113000 0.013995 98 56.540009 0.992000 0.048282 69 0.613656 0.106000 0.008740 70 3.077814 0.282000 0.019207 40 16.449192 0.912000 0.027845 6 0.885451 0.647000 0.005866 6 17.296309 0.913000 0.016425 14 4.025543 0.721000 0.003924 93 59.315045 0.993000 0.027800 73 43.504263 0.987000 0.021560 36 0.194485 0.000000 0.002647 100 246.316790 1.000000 0.113317 1 8.309211 0.790000 0.007678 4 8.966411 0.853000 0.008664 3 1.979820 0.671000 0.009168 7 0.085881 0.000000 0.001509 53 17.079604 0.933000 0.021497 27 10.132381 0.822000 0.009574 26 1.517934 0.213000 0.003146 22 8.770253 0.879000 0.011857 96 97.002659 1.000000 0.039156 70 4.144580 0.805000 0.005892 100 111.918801 1.000000 0.045637 96 68.618829 0.998000 0.031553 10 0.541941 0.061000 0.007612 14 11.092193 0.873000 0.007598 1 4.562502 0.774000 0.003492 3 0.141344 0.000000 0.003224 62 24.185554 0.940000 0.013702 98 48.256720 0.990000 0.025953 83 27.817880 0.963000 0.017212 100 27.452740 0.958000 0.017859 17 5.122908 0.577000 0.011033 100 105.703042 0.999000 0.040353 26 0.435540 0.070000 0.004968 3 17.211361 0.892000 0.007477 6 0.011338 0.000000 0.000003 49 25.592144 0.935000 0.010719 32 0.267106 0.050000 0.002003 100 70.627337 0.999000 0.023514 2 8.293526 0.769000 0.002373 13 16.887893 0.899000 0.004615 60 21.909322 0.923000 0.007406 96 24.941167 0.914000 0.009785 92 6.942537 0.839000 0.004411 5 -1.000000 0.000000 0.000000 100 72.123559 0.999000 0.020925 37 14.525080 0.934000 0.007885 54 19.222944 0.904000 0.009898 88 15.657127 0.938000 0.010129 100 27.139827 0.937000 0.017962 100 29.947187 0.941000 0.010460 54 6.701776 0.847000 0.005743 74 10.576021 0.876000 0.013561 58 3.539234 0.664000 0.006444 6 0.270486 0.025000 0.001707 98 49.459858 0.988000 0.013575 64 -1.000000 0.000000 0.000000 71 34.297662 0.957000 0.014944 78 31.493052 0.964000 0.014111 43 10.566426 0.832000 0.002589 10 -1.000000 0.000000 0.000000 40 7.151671 0.755000 0.002579 13 -1.000000 0.000000 0.000000 56 20.975918 0.926000 0.007107 82 4.213485 0.783000 0.007545 73 10.604218 0.870000 0.005015 36 3.998947 0.748000 0.001760 0 8.209920 0.858000 0.005253 36 31.908568 0.958000 0.011485 95 21.904944 0.943000 0.010424 35 16.160080 0.930000 0.007607 19 2.457799 0.725000 0.001848 21 7.615498 0.831000 0.003517 1 4.664105 0.625000 0.005013 44 7.469163 0.858000 0.006414 100 73.815298 0.998000 0.028205 0 6.927283 0.843000 0.007813 0 2.464487 0.731000 0.001965 3 7.071706 0.854000 0.003855 5 2.017584 0.762000 0.002570 14 4.992587 0.809000 0.003473 29 8.277006 0.830000 0.005842 100 103.232793 0.999000 0.039471 99 26.654372 0.962000 0.013520 100 38.779076 0.963000 0.017066 0 3.543391 0.723000 0.001837 17 11.036654 0.889000 0.009833 0 0.256428 0.565000 0.000934 26 17.665048 0.937000 0.013345 92 60.782978 0.997000 0.024268 63 5.077017 0.799000 0.004080 43 2.170403 0.764000 0.002243 32 1.143137 0.699000 0.001522 93 45.890863 0.980000 0.016525 92 24.411903 0.965000 0.022184 97 7.844102 0.854000 0.009452 1 4.771353 0.730000 0.002328 4 3.580147 0.748000 0.003056 12 1.930077 0.760000 0.002959 99 236.268628 1.000000 0.062900 55 2.086164 0.396000 0.003283 45 6.604909 0.840000 0.004237 87 30.135455 0.937000 0.007189 9 -1.000000 0.000000 0.000000 55 5.093539 0.740000 0.001980 46 6.421187 0.777000 0.002444 9 4.496190 0.738000 0.003635 77 54.308310 0.979000 0.017009 95 20.955241 0.949000 0.013644 . Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'... . Time used 29h31m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo