.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1992_46x68_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 68 patterns found. (out of a total of 68 sites) . 1 sites without polymorphism (1.47%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6879.9877] [Alpha ][ 0.500960] . ( 0 sec) [ -6847.1051] [ 1288] [depth= 11] . ( 0 sec) [ -6765.4806] [ 1268] [depth= 10] . ( 0 sec) [ -6722.4148] [ 1268] [depth= 1] . ( 0 sec) [ -6676.5875] [ 1256] [depth= 4] . ( 1 sec) [ -6674.0115] [ 1253] [depth= 1] . ( 1 sec) [ -6635.4863] [ 1252] [depth= 3] . ( 1 sec) [ -6629.9719] [ 1240] [depth= 1] . ( 1 sec) [ -6584.2034] [ 1233] [depth= 7] . ( 1 sec) [ -6465.9200] [ 1212] [depth= 3] . ( 1 sec) [ -6426.4467] [ 1205] [depth= 2] . ( 1 sec) [ -6376.0720] [ 1198] [depth= 5] . ( 1 sec) [ -6174.3505] [ 1196] [depth= 5] . ( 2 sec) [ -6159.7111] [ 1194] [depth= 2] . ( 2 sec) [ -6128.8276] [ 1196] [depth= 1] . ( 2 sec) [ -6103.3551] [ 1195] [depth= 1] . ( 2 sec) [ -6005.9554] [ 1189] [depth= 11] . ( 2 sec) [ -5907.0139] [ 1174] [depth= 18] . ( 2 sec) [ -5684.5969] [ 1137] [depth= 5] . ( 2 sec) [ -5640.7081] [ 1138] [depth= 11] . ( 2 sec) [ -5497.4861] [ 1139] [depth= 2] . ( 3 sec) [ -5447.0314] [ 1126] [depth= 9] . ( 3 sec) [ -5361.3362] [ 1105] [depth= 9] . ( 3 sec) [ -5359.7577] [ 1105] [depth= 1] . ( 3 sec) [ -5350.7495] [ 1106] [depth= 4] . ( 3 sec) [ -5344.0550] [ 1105] [depth= 6] . ( 3 sec) [ -5134.5946] [ 1062] [depth= 5] . ( 3 sec) [ -5099.8857] [ 1049] [depth= 17] . ( 3 sec) [ -5046.8264] [ 1033] [depth= 20] . ( 3 sec) [ -5046.1287] [ 1035] [depth= 2] . ( 4 sec) [ -5045.5333] [ 1036] [depth= 1] . ( 4 sec) [ -4997.7379] [ 1013] [depth= 13] . ( 4 sec) [ -4979.0982] [ 1010] [depth= 2] . ( 5 sec) [ -4954.5756] [ 1008] [depth= 2] . ( 5 sec) [ -4843.2529] [ 1005] [depth= 13] . ( 5 sec) [ -4827.1962] [ 1001] [depth= 6] . ( 5 sec) [ -4798.6855] [ 1001] [depth= 1] . ( 5 sec) [ -4729.0399] [ 978] [depth= 22] . ( 5 sec) [ -4570.5940] [ 932] [depth= 15] . ( 5 sec) [ -4532.4556] [ 930] [depth= 9] . ( 5 sec) [ -4526.2508] [ 928] [depth= 1] . ( 6 sec) [ -4517.8954] [ 928] [depth= 2] . ( 6 sec) [ -4416.3118] [ 903] [depth= 18] . ( 6 sec) [ -4404.1432] [ 901] [depth= 6] . ( 6 sec) [ -4386.1426] [ 901] [depth= 1] . ( 6 sec) [ -4385.8151] [ 887] [depth= 6] . ( 6 sec) [ -4385.7170] [ 887] [depth= 1] . ( 7 sec) [ -4385.5891] [ 885] [depth= 5] . ( 7 sec) [ -4373.9243] [ 886] [depth= 1] . ( 7 sec) [ -4317.1121] [ 885] [depth= 3] . ( 8 sec) [ -4315.2592] [ 883] [depth= 3] . ( 8 sec) [ -4304.9718] [ 882] [depth= 1] . ( 8 sec) [ -4304.4592] [ 882] [depth= 1] . ( 8 sec) [ -4295.8623] [ 835] [depth= 12] . ( 8 sec) [ -4270.9523] [ 829] [depth= 1] . ( 8 sec) [ -4267.1401] [ 829] [depth= 1] . ( 8 sec) [ -4259.0757] [ 824] [depth= 1] . ( 9 sec) [ -4235.5582] [ 822] [depth= 1] . ( 9 sec) [ -4165.1177] [ 823] [depth= 1] . ( 9 sec) [ -4163.2250] [ 824] [depth= 1] . ( 10 sec) [ -4101.1804] [ 786] [depth= 7] . ( 10 sec) [ -4036.1071] [ 777] [depth= 2] . ( 10 sec) [ -3996.9507] [ 770] [depth= 5] . ( 10 sec) [ -3987.0608] [ 760] [depth= 2] . ( 10 sec) [ -3984.1031] [ 760] [depth= 1] . ( 10 sec) [ -3852.6464] [ 759] [depth= 1] . ( 10 sec) [ -3843.7300] [ 752] [depth= 10] . ( 10 sec) [ -3822.7938] [ 751] [depth= 1] . ( 11 sec) [ -3817.0527] [ 748] [depth= 2] . ( 11 sec) [ -3815.5392] [ 748] [depth= 1] . ( 11 sec) [ -3811.5626] [ 748] [depth= 1] . ( 11 sec) [ -3775.8662] [ 743] [depth= 2] . ( 12 sec) [ -3763.8467] [ 740] [depth= 5] . ( 12 sec) [ -3743.7418] [ 739] [depth= 1] . ( 12 sec) [ -3660.9816] [ 737] [depth= 13] . ( 12 sec) [ -3617.7673] [ 742] [depth= 3] . ( 12 sec) [ -3615.3006] [ 741] [depth= 3] . ( 13 sec) [ -3613.5236] [ 728] [depth= 1] . ( 13 sec) [ -3603.2301] [ 731] [depth= 3] . ( 13 sec) [ -3550.0820] [ 711] [depth= 3] . ( 13 sec) [ -3473.4700] [ 677] [depth= 5] . ( 14 sec) [ -3464.0542] [ 677] [depth= 1] . ( 14 sec) [ -3460.7300] [ 677] [depth= 1] . ( 14 sec) [ -3411.7011] [ 665] [depth= 15] . ( 14 sec) [ -3391.2177] [ 661] [depth= 1] . ( 14 sec) [ -3389.8453] [ 661] [depth= 1] . ( 14 sec) [ -3378.3513] [ 653] [depth= 21] . ( 14 sec) [ -3376.4725] [ 653] [depth= 1] . ( 14 sec) [ -3376.2572] [ 658] [depth= 1] . ( 15 sec) [ -3372.7223] [ 656] [depth= 1] . ( 15 sec) [ -3367.1467] [ 654] [depth= 3] . ( 15 sec) [ -3365.5673] [ 652] [depth= 5] . ( 15 sec) [ -3229.5240] [ 653] [depth= 1] . ( 15 sec) [ -3226.7479] [ 653] [depth= 1] . ( 15 sec) [ -3203.3860] [ 648] [depth= 3] . ( 16 sec) [ -3198.2416] [ 648] [depth= 1] . ( 16 sec) [ -3192.9308] [ 652] [depth= 15] . ( 16 sec) [ -3188.1326] [ 650] [depth= 2] . ( 17 sec) [ -3179.6143] [ 647] [depth= 1] . ( 17 sec) [ -3166.3393] [ 647] [depth= 1] . ( 17 sec) [ -3165.5564] [ 646] [depth= 1] . ( 18 sec) [ -3163.1137] [ 647] [depth= 1] . ( 18 sec) [ -3111.8546] [Branch lengths ] . ( 19 sec) [ -3094.6965] [Alpha ][ 1.000438] . ( 19 sec) [ -3092.1490] [ 643] [depth= 6] . ( 19 sec) [ -3091.4476] [ 646] [depth= 2] . ( 19 sec) [ -3077.8970] [ 644] [depth= 4] . ( 19 sec) [ -3076.0363] [ 643] [depth= 1] . ( 20 sec) [ -3072.4339] [ 641] [depth= 1] . ( 20 sec) [ -3014.9093] [ 612] [depth= 6] . ( 20 sec) [ -2994.6626] [ 601] [depth= 6] . ( 21 sec) [ -2994.4354] [ 601] [depth= 1] . ( 21 sec) [ -2993.5249] [ 600] [depth= 1] . ( 21 sec) [ -2987.7843] [ 598] [depth= 2] . ( 22 sec) [ -2986.3823] [ 597] [depth= 1] . ( 22 sec) [ -2984.3010] [ 597] [depth= 1] . ( 22 sec) [ -2981.4739] [ 598] [depth= 1] . ( 22 sec) [ -2975.7387] [ 596] [depth= 3] . ( 24 sec) [ -2975.6394] [ 596] [depth= 1] . ( 25 sec) [ -2975.5884] [ 596] [depth= 1] . ( 28 sec) [ -2975.4267] [ 596] [depth= 1] . ( 29 sec) [ -2970.0468] [ 594] [depth= 2] . ( 31 sec) [ -2969.7781] [ 594] [depth= 1] . ( 35 sec) [ -2968.0052] [ 594] [depth= 2] . ( 35 sec) [ -2967.6357] [ 594] [depth= 1] . ( 36 sec) [ -2966.5891] [ 592] [depth= 1] . ( 36 sec) [ -2965.7996] [ 593] [depth= 1] . ( 36 sec) [ -2965.6762] [ 595] [depth= 1] . ( 37 sec) [ -2965.3865] [ 595] [depth= 1] . ( 38 sec) [ -2965.2352] [ 593] [depth= 1] . ( 39 sec) [ -2963.8153] [ 593] [depth= 1] . ( 39 sec) [ -2963.7165] [ 593] [depth= 1] . ( 40 sec) [ -2963.6023] [ 594] [depth= 2] . ( 41 sec) [ -2962.2491] [ 595] [depth= 1] . ( 42 sec) [ -2962.1955] [ 595] [depth= 1] . ( 46 sec) [ -2961.8922] [ 596] [depth= 1] . ( 47 sec) [ -2961.2736] [ 594] [depth= 3] . ( 47 sec) [ -2959.8972] [ 597] [depth= 2] . ( 47 sec) [ -2959.5633] [ 597] [depth= 1] . ( 47 sec) [ -2958.8726] [ 596] [depth= 1] . ( 51 sec) [ -2947.9287] [Branch lengths ] . ( 51 sec) [ -2939.9133] [Alpha ][ 1.997813] . ( 51 sec) [ -2937.0531] [ 595] [depth= 1] . ( 53 sec) [ -2937.0042] [ 595] [depth= 1] . ( 54 sec) [ -2936.8962] [ 594] [depth= 1] . ( 54 sec) [ -2936.8789] [ 594] [depth= 1] . ( 61 sec) [ -2936.7599] [ 594] [depth= 1] . ( 67 sec) [ -2936.6727] [ 594] [depth= 1] . ( 74 sec) [ -2936.6625] [ 594] [depth= 1] . ( 74 sec) [ -2936.5141] [ 592] [depth= 3] . ( 74 sec) [ -2936.4373] [ 589] [depth= 1] . ( 75 sec) [ -2936.3760] [ 589] [depth= 1] . ( 77 sec) [ -2936.3525] [ 589] [depth= 1] . ( 82 sec) [ -2936.2605] [ 591] [depth= 1] . ( 84 sec) [ -2936.1406] [ 592] [depth= 1] . ( 89 sec) [ -2930.4135] [Branch lengths ] . ( 89 sec) [ -2927.7393] [Alpha ][ 3.414485] . ( 89 sec) [ -2927.6052] [ 594] [depth= 1] . ( 92 sec) [ -2927.5931] [ 594] [depth= 1] . ( 94 sec) [ -2927.5640] [ 594] [depth= 1] . ( 95 sec) [ -2927.4923] [ 594] [depth= 1] . ( 98 sec) [ -2927.4317] [ 594] [depth= 1] . ( 105 sec) [ -2927.3446] [ 594] [depth= 1] . ( 111 sec) [ -2927.3230] [ 592] [depth= 2] . ( 113 sec) [ -2927.3130] [ 592] [depth= 1] . ( 121 sec) [ -2927.3000] [ 592] [depth= 1] . ( 129 sec) [ -2925.2032] [Branch lengths ] . ( 129 sec) [ -2925.0673] [Alpha ][ 3.893835] . ( 139 sec) [ -2924.1712] [ 593] [depth= 3] . ( 146 sec) [ -2924.1576] [ 593] [depth= 1] . ( 154 sec) [ -2924.1389] [ 593] [depth= 2] . ( 170 sec) [ -2923.7058] [Branch lengths ] . ( 170 sec) [ -2923.7053] [Alpha ][ 3.860306] . ( 174 sec) [ -2923.4103] [ 591] [depth= 2] . ( 189 sec) [ -2922.3343] [ 592] [depth= 2] . ( 209 sec) [ -2921.4327] [Branch lengths ] . ( 209 sec) [ -2921.4327] [Alpha ][ 3.869232] . ( 224 sec) [ -2921.4163] [ 592] [depth= 1] . ( 232 sec) [ -2921.4051] [ 593] [depth= 11] . ( 242 sec) [ -2921.3732] [ 593] [depth= 1] . ( 250 sec) [ -2921.3491] [Branch lengths ] . ( 250 sec) [ -2921.3491] [Alpha ][ 3.869232] . ( 250 sec) [ -2921.3491] [Topology ] . ( 251 sec) [ -2921.3470] [Topology ] . ( 252 sec) [ -2921.3463] [Topology ] . ( 252 sec) [ -2921.3463] [Alpha ][ 3.865362] . ( 252 sec) [ -2921.3463] [Topology ] . ( 253 sec) [ -2921.3460] [Topology ] . ( 253 sec) [ -2921.3460] [Alpha ][ 3.865362] . Checking for NNIs, optimizing five branches... . ( 260 sec) [ -2921.2202] [Topology ] . Checking for NNIs, optimizing five branches... . ( 267 sec) [ -2921.2201] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2921.220099. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7205.4908] [Alpha ][ 0.500960] . ( 1 sec) [ -7192.3735] [ 1322] [depth= 9] . ( 1 sec) [ -7125.0498] [ 1311] [depth= 5] . ( 1 sec) [ -7031.4524] [ 1290] [depth= 3] . ( 1 sec) [ -7019.0276] [ 1289] [depth= 3] . ( 1 sec) [ -6957.3554] [ 1275] [depth= 7] . ( 2 sec) [ -6868.4360] [ 1270] [depth= 3] . ( 2 sec) [ -6698.6179] [ 1258] [depth= 1] . ( 2 sec) [ -6698.2251] [ 1253] [depth= 3] . ( 2 sec) [ -6578.2392] [ 1240] [depth= 1] . ( 2 sec) [ -6555.1054] [ 1239] [depth= 3] . ( 2 sec) [ -6517.9352] [ 1228] [depth= 5] . ( 2 sec) [ -6511.4185] [ 1231] [depth= 1] . ( 2 sec) [ -6499.2707] [ 1218] [depth= 7] . ( 3 sec) [ -6471.1157] [ 1215] [depth= 2] . ( 3 sec) [ -6462.4808] [ 1214] [depth= 1] . ( 3 sec) [ -6433.5538] [ 1202] [depth= 17] . ( 3 sec) [ -6398.4159] [ 1199] [depth= 5] . ( 3 sec) [ -6303.2620] [ 1200] [depth= 1] . ( 3 sec) [ -6301.1389] [ 1200] [depth= 1] . ( 3 sec) [ -6278.0463] [ 1196] [depth= 5] . ( 3 sec) [ -6187.2798] [ 1171] [depth= 11] . ( 4 sec) [ -6184.6595] [ 1172] [depth= 1] . ( 4 sec) [ -6068.9094] [ 1155] [depth= 13] . ( 4 sec) [ -5957.8452] [ 1122] [depth= 1] . ( 5 sec) [ -5928.2616] [ 1121] [depth= 8] . ( 5 sec) [ -5819.1347] [ 1103] [depth= 1] . ( 5 sec) [ -5748.7892] [ 1084] [depth= 16] . ( 5 sec) [ -5685.2032] [ 1088] [depth= 14] . ( 5 sec) [ -5659.4843] [ 1068] [depth= 9] . ( 5 sec) [ -5467.1983] [ 1050] [depth= 13] . ( 6 sec) [ -5458.9331] [ 1054] [depth= 2] . ( 6 sec) [ -5356.6633] [ 1040] [depth= 12] . ( 6 sec) [ -5303.3352] [ 1017] [depth= 2] . ( 6 sec) [ -5298.7025] [ 1014] [depth= 1] . ( 6 sec) [ -5296.3639] [ 1014] [depth= 3] . ( 6 sec) [ -5240.0928] [ 1006] [depth= 5] . ( 6 sec) [ -5169.4634] [ 985] [depth= 14] . ( 7 sec) [ -5168.1621] [ 985] [depth= 2] . ( 7 sec) [ -5126.6211] [ 959] [depth= 15] . ( 7 sec) [ -5024.4157] [ 949] [depth= 11] . ( 7 sec) [ -5018.5098] [ 945] [depth= 2] . ( 7 sec) [ -5015.8694] [ 942] [depth= 1] . ( 7 sec) [ -4914.0369] [ 932] [depth= 2] . ( 8 sec) [ -4894.3859] [ 954] [depth= 1] . ( 8 sec) [ -4783.5683] [ 954] [depth= 1] . ( 8 sec) [ -4749.3962] [ 908] [depth= 6] . ( 8 sec) [ -4667.2936] [ 884] [depth= 4] . ( 8 sec) [ -4518.9049] [ 880] [depth= 10] . ( 8 sec) [ -4516.8808] [ 873] [depth= 2] . ( 8 sec) [ -4508.3761] [ 874] [depth= 1] . ( 8 sec) [ -4460.9909] [ 865] [depth= 5] . ( 9 sec) [ -4453.6982] [ 868] [depth= 1] . ( 9 sec) [ -4452.7912] [ 866] [depth= 3] . ( 9 sec) [ -4420.4611] [ 863] [depth= 3] . ( 9 sec) [ -4272.2793] [ 831] [depth= 3] . ( 9 sec) [ -4192.2189] [ 820] [depth= 6] . ( 9 sec) [ -4114.6478] [ 784] [depth= 6] . ( 9 sec) [ -4090.7125] [ 782] [depth= 4] . ( 9 sec) [ -4017.3389] [ 769] [depth= 3] . ( 9 sec) [ -3939.3895] [ 772] [depth= 11] . ( 10 sec) [ -3854.1661] [ 769] [depth= 4] . ( 10 sec) [ -3691.7788] [ 724] [depth= 6] . ( 10 sec) [ -3653.4475] [ 719] [depth= 1] . ( 10 sec) [ -3652.8704] [ 719] [depth= 2] . ( 10 sec) [ -3646.1652] [ 711] [depth= 1] . ( 10 sec) [ -3613.6362] [ 703] [depth= 7] . ( 10 sec) [ -3603.4837] [ 702] [depth= 1] . ( 11 sec) [ -3600.1414] [ 705] [depth= 1] . ( 11 sec) [ -3597.5441] [ 705] [depth= 1] . ( 11 sec) [ -3589.5342] [ 704] [depth= 2] . ( 11 sec) [ -3588.2399] [ 704] [depth= 1] . ( 11 sec) [ -3583.6754] [ 703] [depth= 2] . ( 11 sec) [ -3543.0497] [ 699] [depth= 2] . ( 12 sec) [ -3519.0698] [ 697] [depth= 4] . ( 12 sec) [ -3513.6787] [ 697] [depth= 1] . ( 12 sec) [ -3509.3165] [ 698] [depth= 2] . ( 12 sec) [ -3508.6961] [ 689] [depth= 2] . ( 12 sec) [ -3475.3231] [ 669] [depth= 4] . ( 12 sec) [ -3444.3490] [ 668] [depth= 3] . ( 12 sec) [ -3442.5943] [ 670] [depth= 1] . ( 13 sec) [ -3435.9406] [ 666] [depth= 2] . ( 13 sec) [ -3403.6347] [ 665] [depth= 1] . ( 13 sec) [ -3372.6382] [ 658] [depth= 1] . ( 13 sec) [ -3298.4215] [ 653] [depth= 2] . ( 14 sec) [ -3292.7720] [ 653] [depth= 3] . ( 14 sec) [ -3284.8603] [ 649] [depth= 2] . ( 14 sec) [ -3283.9736] [ 646] [depth= 2] . ( 14 sec) [ -3281.0994] [ 644] [depth= 1] . ( 14 sec) [ -3277.6782] [ 642] [depth= 2] . ( 15 sec) [ -3239.3106] [ 616] [depth= 10] . ( 15 sec) [ -3188.2558] [ 619] [depth= 4] . ( 15 sec) [ -3170.4435] [ 618] [depth= 1] . ( 15 sec) [ -3156.6383] [ 611] [depth= 3] . ( 15 sec) [ -3092.7732] [ 608] [depth= 2] . ( 16 sec) [ -3085.6966] [ 606] [depth= 2] . ( 16 sec) [ -3082.5266] [ 607] [depth= 1] . ( 16 sec) [ -3081.9257] [ 608] [depth= 2] . ( 17 sec) [ -3079.3381] [ 608] [depth= 1] . ( 17 sec) [ -3078.5548] [ 609] [depth= 3] . ( 17 sec) [ -3076.5415] [ 610] [depth= 1] . ( 17 sec) [ -3073.2240] [ 608] [depth= 4] . ( 18 sec) [ -3073.1676] [ 608] [depth= 1] . ( 20 sec) [ -3071.4586] [ 608] [depth= 1] . ( 21 sec) [ -3015.2479] [Branch lengths ] . ( 21 sec) [ -3002.2874] [Alpha ][ 1.000690] . ( 21 sec) [ -2997.4643] [ 609] [depth= 2] . ( 21 sec) [ -2981.6103] [ 607] [depth= 2] . ( 21 sec) [ -2980.6750] [ 606] [depth= 1] . ( 22 sec) [ -2976.7135] [ 607] [depth= 1] . ( 22 sec) [ -2976.6627] [ 607] [depth= 1] . ( 23 sec) [ -2976.6088] [ 607] [depth= 1] . ( 23 sec) [ -2975.5490] [ 604] [depth= 1] . ( 24 sec) [ -2975.5121] [ 605] [depth= 2] . ( 25 sec) [ -2975.3920] [ 604] [depth= 1] . ( 25 sec) [ -2973.2029] [ 605] [depth= 5] . ( 28 sec) [ -2971.2883] [ 608] [depth= 1] . ( 28 sec) [ -2971.2524] [ 608] [depth= 1] . ( 31 sec) [ -2967.6573] [ 606] [depth= 2] . ( 32 sec) [ -2966.8441] [ 605] [depth= 6] . ( 34 sec) [ -2966.5342] [ 605] [depth= 2] . ( 34 sec) [ -2965.5195] [ 606] [depth= 1] . ( 34 sec) [ -2965.2614] [ 606] [depth= 2] . ( 34 sec) [ -2963.3242] [ 605] [depth= 1] . ( 35 sec) [ -2961.1682] [ 600] [depth= 8] . ( 36 sec) [ -2960.1224] [ 601] [depth= 1] . ( 37 sec) [ -2960.0408] [ 601] [depth= 1] . ( 39 sec) [ -2957.8771] [ 599] [depth= 2] . ( 39 sec) [ -2954.3978] [ 596] [depth= 4] . ( 43 sec) [ -2954.3035] [ 596] [depth= 1] . ( 49 sec) [ -2954.0197] [ 593] [depth= 10] . ( 49 sec) [ -2953.8798] [ 592] [depth= 3] . ( 51 sec) [ -2953.6796] [ 592] [depth= 1] . ( 53 sec) [ -2952.8541] [ 593] [depth= 3] . ( 55 sec) [ -2952.6575] [ 593] [depth= 1] . ( 56 sec) [ -2952.5428] [ 593] [depth= 1] . ( 56 sec) [ -2952.2389] [ 591] [depth= 1] . ( 56 sec) [ -2952.1503] [ 591] [depth= 1] . ( 57 sec) [ -2942.6331] [Branch lengths ] . ( 57 sec) [ -2936.1892] [Alpha ][ 1.997983] . ( 59 sec) [ -2936.1065] [ 591] [depth= 1] . ( 62 sec) [ -2936.0340] [ 593] [depth= 1] . ( 63 sec) [ -2935.9116] [ 593] [depth= 1] . ( 64 sec) [ -2935.6559] [ 592] [depth= 1] . ( 70 sec) [ -2935.6023] [ 592] [depth= 1] . ( 74 sec) [ -2935.5516] [ 592] [depth= 1] . ( 82 sec) [ -2935.5103] [ 592] [depth= 1] . ( 83 sec) [ -2935.3419] [ 592] [depth= 1] . ( 86 sec) [ -2935.3058] [ 591] [depth= 1] . ( 86 sec) [ -2934.9967] [ 592] [depth= 4] . ( 90 sec) [ -2934.9793] [ 592] [depth= 1] . ( 90 sec) [ -2934.9042] [ 592] [depth= 1] . ( 94 sec) [ -2934.7100] [ 593] [depth= 1] . ( 94 sec) [ -2934.6739] [ 593] [depth= 1] . ( 94 sec) [ -2928.3344] [Branch lengths ] . ( 94 sec) [ -2926.1514] [Alpha ][ 3.259740] . ( 97 sec) [ -2926.0891] [ 596] [depth= 1] . ( 98 sec) [ -2926.0779] [ 596] [depth= 1] . ( 101 sec) [ -2926.0672] [ 596] [depth= 1] . ( 101 sec) [ -2926.0287] [ 596] [depth= 1] . ( 102 sec) [ -2925.9922] [ 596] [depth= 1] . ( 117 sec) [ -2925.7298] [ 596] [depth= 2] . ( 123 sec) [ -2925.5705] [ 596] [depth= 1] . ( 126 sec) [ -2925.5585] [ 595] [depth= 3] . ( 127 sec) [ -2925.5440] [ 594] [depth= 5] . ( 136 sec) [ -2922.7737] [Branch lengths ] . ( 136 sec) [ -2922.6840] [Alpha ][ 3.619217] . ( 169 sec) [ -2922.6619] [ 595] [depth= 9] . ( 179 sec) [ -2922.3288] [Branch lengths ] . ( 179 sec) [ -2922.3269] [Alpha ][ 3.677159] . ( 179 sec) [ -2922.3269] [Topology ] . ( 180 sec) [ -2922.2936] [Topology ] . ( 181 sec) [ -2922.2825] [Topology ] . ( 182 sec) [ -2922.2777] [Topology ] . ( 183 sec) [ -2922.2756] [Topology ] . ( 184 sec) [ -2922.2746] [Topology ] . ( 184 sec) [ -2922.2746] [Alpha ][ 3.677159] . ( 184 sec) [ -2922.2746] [Topology ] . ( 185 sec) [ -2922.2741] [Topology ] . ( 185 sec) [ -2922.2741] [Alpha ][ 3.677159] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2922.274150. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7132.7463] [Alpha ][ 0.500960] . ( 1 sec) [ -7091.2797] [ 1305] [depth= 10] . ( 1 sec) [ -7055.6439] [ 1292] [depth= 13] . ( 1 sec) [ -6982.1597] [ 1278] [depth= 2] . ( 1 sec) [ -6839.0533] [ 1279] [depth= 8] . ( 1 sec) [ -6627.6681] [ 1250] [depth= 8] . ( 1 sec) [ -6611.6531] [ 1247] [depth= 3] . ( 1 sec) [ -6565.3078] [ 1233] [depth= 3] . ( 1 sec) [ -6521.1227] [ 1223] [depth= 4] . ( 1 sec) [ -6477.7476] [ 1210] [depth= 4] . ( 2 sec) [ -6429.6366] [ 1212] [depth= 4] . ( 2 sec) [ -6396.3656] [ 1210] [depth= 5] . ( 2 sec) [ -6260.7303] [ 1185] [depth= 6] . ( 2 sec) [ -6236.6751] [ 1184] [depth= 1] . ( 2 sec) [ -6118.7145] [ 1180] [depth= 7] . ( 2 sec) [ -6102.2637] [ 1181] [depth= 1] . ( 2 sec) [ -6082.1297] [ 1180] [depth= 1] . ( 3 sec) [ -6079.9842] [ 1180] [depth= 1] . ( 3 sec) [ -5930.7694] [ 1175] [depth= 14] . ( 3 sec) [ -5894.9661] [ 1172] [depth= 18] . ( 3 sec) [ -5806.3138] [ 1160] [depth= 14] . ( 3 sec) [ -5804.0974] [ 1148] [depth= 1] . ( 3 sec) [ -5794.9092] [ 1144] [depth= 4] . ( 3 sec) [ -5766.1751] [ 1141] [depth= 3] . ( 4 sec) [ -5747.5572] [ 1139] [depth= 2] . ( 4 sec) [ -5708.6155] [ 1137] [depth= 1] . ( 4 sec) [ -5616.5231] [ 1122] [depth= 11] . ( 4 sec) [ -5506.1517] [ 1120] [depth= 2] . ( 4 sec) [ -5488.7957] [ 1097] [depth= 3] . ( 4 sec) [ -5471.7411] [ 1078] [depth= 8] . ( 4 sec) [ -5286.0708] [ 1046] [depth= 1] . ( 4 sec) [ -5264.5095] [ 1045] [depth= 1] . ( 5 sec) [ -5236.7928] [ 1032] [depth= 9] . ( 5 sec) [ -5217.3674] [ 1029] [depth= 7] . ( 5 sec) [ -5104.6505] [ 992] [depth= 5] . ( 5 sec) [ -5085.2444] [ 988] [depth= 1] . ( 6 sec) [ -5075.6790] [ 986] [depth= 4] . ( 6 sec) [ -5070.1858] [ 988] [depth= 7] . ( 6 sec) [ -5025.3726] [ 974] [depth= 6] . ( 6 sec) [ -5020.6915] [ 966] [depth= 11] . ( 6 sec) [ -4945.9926] [ 955] [depth= 5] . ( 6 sec) [ -4941.3404] [ 959] [depth= 8] . ( 6 sec) [ -4939.1007] [ 961] [depth= 1] . ( 7 sec) [ -4802.0721] [ 930] [depth= 4] . ( 7 sec) [ -4796.4032] [ 933] [depth= 1] . ( 7 sec) [ -4754.5965] [ 934] [depth= 1] . ( 7 sec) [ -4748.6076] [ 938] [depth= 2] . ( 7 sec) [ -4700.6334] [ 917] [depth= 7] . ( 7 sec) [ -4692.1452] [ 891] [depth= 1] . ( 7 sec) [ -4614.9945] [ 878] [depth= 9] . ( 8 sec) [ -4604.7056] [ 878] [depth= 1] . ( 8 sec) [ -4572.1377] [ 876] [depth= 1] . ( 8 sec) [ -4454.1525] [ 834] [depth= 13] . ( 8 sec) [ -4447.2240] [ 830] [depth= 2] . ( 8 sec) [ -4315.4536] [ 784] [depth= 2] . ( 8 sec) [ -4309.3846] [ 781] [depth= 1] . ( 8 sec) [ -4295.6313] [ 780] [depth= 2] . ( 8 sec) [ -4089.8631] [ 749] [depth= 17] . ( 9 sec) [ -4017.5816] [ 741] [depth= 5] . ( 9 sec) [ -3990.6048] [ 736] [depth= 1] . ( 9 sec) [ -3969.1601] [ 738] [depth= 7] . ( 9 sec) [ -3957.2625] [ 730] [depth= 6] . ( 9 sec) [ -3777.9918] [ 694] [depth= 7] . ( 9 sec) [ -3771.1943] [ 693] [depth= 1] . ( 9 sec) [ -3733.3574] [ 681] [depth= 1] . ( 9 sec) [ -3719.1396] [ 679] [depth= 6] . ( 9 sec) [ -3717.7225] [ 678] [depth= 1] . ( 10 sec) [ -3715.7459] [ 679] [depth= 1] . ( 10 sec) [ -3610.9734] [ 675] [depth= 5] . ( 10 sec) [ -3591.2140] [ 673] [depth= 2] . ( 10 sec) [ -3588.3499] [ 674] [depth= 6] . ( 10 sec) [ -3588.2929] [ 674] [depth= 1] . ( 10 sec) [ -3576.5754] [ 676] [depth= 1] . ( 11 sec) [ -3575.2401] [ 678] [depth= 9] . ( 11 sec) [ -3522.6978] [ 678] [depth= 1] . ( 11 sec) [ -3486.1507] [ 677] [depth= 1] . ( 11 sec) [ -3447.7630] [ 661] [depth= 7] . ( 11 sec) [ -3440.0988] [ 660] [depth= 1] . ( 12 sec) [ -3430.7116] [ 658] [depth= 5] . ( 12 sec) [ -3395.5307] [ 646] [depth= 1] . ( 12 sec) [ -3391.7851] [ 647] [depth= 2] . ( 12 sec) [ -3362.1678] [ 636] [depth= 3] . ( 12 sec) [ -3341.5151] [ 627] [depth= 11] . ( 12 sec) [ -3334.4736] [ 624] [depth= 2] . ( 12 sec) [ -3333.3477] [ 622] [depth= 1] . ( 13 sec) [ -3312.3990] [ 619] [depth= 3] . ( 13 sec) [ -3311.8857] [ 617] [depth= 1] . ( 13 sec) [ -3296.8210] [ 617] [depth= 3] . ( 13 sec) [ -3280.4826] [ 618] [depth= 1] . ( 14 sec) [ -3276.0331] [ 622] [depth= 4] . ( 14 sec) [ -3274.6000] [ 622] [depth= 3] . ( 14 sec) [ -3260.2564] [ 621] [depth= 3] . ( 14 sec) [ -3254.2765] [ 619] [depth= 4] . ( 14 sec) [ -3251.4473] [ 618] [depth= 1] . ( 14 sec) [ -3231.6017] [ 607] [depth= 7] . ( 15 sec) [ -3229.9990] [ 607] [depth= 1] . ( 15 sec) [ -3227.7590] [ 606] [depth= 2] . ( 16 sec) [ -3165.4593] [ 603] [depth= 1] . ( 16 sec) [ -3163.4255] [ 607] [depth= 1] . ( 16 sec) [ -3158.1775] [ 605] [depth= 3] . ( 17 sec) [ -3144.5578] [ 607] [depth= 1] . ( 17 sec) [ -3140.2298] [ 606] [depth= 1] . ( 17 sec) [ -3139.0967] [ 606] [depth= 1] . ( 18 sec) [ -3041.1125] [Branch lengths ] . ( 18 sec) [ -3019.0471] [Alpha ][ 1.000841] . ( 18 sec) [ -3013.7234] [ 607] [depth= 1] . ( 19 sec) [ -3008.0805] [ 606] [depth= 2] . ( 21 sec) [ -2994.5050] [ 602] [depth= 1] . ( 21 sec) [ -2994.1747] [ 601] [depth= 2] . ( 22 sec) [ -2992.6797] [ 601] [depth= 1] . ( 23 sec) [ -2985.5435] [ 600] [depth= 3] . ( 24 sec) [ -2983.7577] [ 599] [depth= 1] . ( 25 sec) [ -2979.4598] [ 598] [depth= 1] . ( 25 sec) [ -2977.2579] [ 596] [depth= 1] . ( 26 sec) [ -2977.0320] [ 596] [depth= 1] . ( 27 sec) [ -2975.6484] [ 593] [depth= 2] . ( 27 sec) [ -2975.3541] [ 593] [depth= 1] . ( 28 sec) [ -2967.8237] [ 590] [depth= 1] . ( 28 sec) [ -2966.9693] [ 591] [depth= 1] . ( 29 sec) [ -2958.7356] [ 589] [depth= 1] . ( 30 sec) [ -2958.6462] [ 590] [depth= 1] . ( 31 sec) [ -2957.0999] [ 592] [depth= 1] . ( 31 sec) [ -2956.9980] [ 591] [depth= 1] . ( 32 sec) [ -2956.9509] [ 590] [depth= 1] . ( 32 sec) [ -2956.7364] [ 591] [depth= 4] . ( 33 sec) [ -2956.6231] [ 595] [depth= 2] . ( 34 sec) [ -2956.4963] [ 595] [depth= 1] . ( 35 sec) [ -2956.4233] [ 595] [depth= 1] . ( 37 sec) [ -2956.3713] [ 595] [depth= 1] . ( 39 sec) [ -2956.2223] [ 593] [depth= 1] . ( 42 sec) [ -2955.6942] [ 593] [depth= 1] . ( 45 sec) [ -2955.6681] [ 593] [depth= 1] . ( 49 sec) [ -2955.6443] [ 593] [depth= 1] . ( 49 sec) [ -2948.0095] [Branch lengths ] . ( 50 sec) [ -2936.0908] [Alpha ][ 1.998649] . ( 61 sec) [ -2936.0755] [ 593] [depth= 2] . ( 61 sec) [ -2936.0369] [ 595] [depth= 5] . ( 64 sec) [ -2935.7867] [ 597] [depth= 3] . ( 66 sec) [ -2934.3796] [ 599] [depth= 2] . ( 67 sec) [ -2933.3405] [ 599] [depth= 2] . ( 72 sec) [ -2933.2973] [ 599] [depth= 1] . ( 73 sec) [ -2930.9825] [ 598] [depth= 1] . ( 77 sec) [ -2930.9109] [ 597] [depth= 2] . ( 77 sec) [ -2930.8372] [ 597] [depth= 1] . ( 90 sec) [ -2928.0178] [Branch lengths ] . ( 90 sec) [ -2925.2422] [Alpha ][ 3.381241] . ( 104 sec) [ -2925.1816] [ 594] [depth= 5] . ( 104 sec) [ -2925.1716] [ 591] [depth= 3] . ( 105 sec) [ -2925.1608] [ 591] [depth= 1] . ( 130 sec) [ -2924.3007] [Branch lengths ] . ( 130 sec) [ -2924.2650] [Alpha ][ 3.606396] . ( 130 sec) [ -2924.2650] [Topology ] . ( 131 sec) [ -2924.1656] [Topology ] . ( 132 sec) [ -2924.1347] [Topology ] . ( 133 sec) [ -2924.1221] [Topology ] . ( 134 sec) [ -2924.1168] [Topology ] . ( 135 sec) [ -2924.1145] [Topology ] . ( 136 sec) [ -2924.1134] [Topology ] . ( 136 sec) [ -2924.1112] [Alpha ][ 3.668592] . ( 136 sec) [ -2924.1112] [Topology ] . ( 137 sec) [ -2924.1105] [Topology ] . ( 137 sec) [ -2924.1105] [Alpha ][ 3.668592] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -2923.9788] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2923.978789. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7077.0298] [Alpha ][ 0.500960] . ( 1 sec) [ -7054.9858] [ 1291] [depth= 6] . ( 1 sec) [ -7036.9818] [ 1284] [depth= 10] . ( 1 sec) [ -6994.8315] [ 1274] [depth= 4] . ( 1 sec) [ -6967.7091] [ 1271] [depth= 1] . ( 1 sec) [ -6894.9535] [ 1258] [depth= 7] . ( 1 sec) [ -6893.6067] [ 1270] [depth= 2] . ( 1 sec) [ -6807.9328] [ 1223] [depth= 9] . ( 1 sec) [ -6793.4309] [ 1198] [depth= 3] . ( 1 sec) [ -6756.0154] [ 1186] [depth= 8] . ( 1 sec) [ -6514.2071] [ 1184] [depth= 1] . ( 2 sec) [ -6351.6592] [ 1162] [depth= 2] . ( 2 sec) [ -6325.4749] [ 1158] [depth= 1] . ( 2 sec) [ -6248.5493] [ 1131] [depth= 7] . ( 2 sec) [ -6179.7605] [ 1120] [depth= 4] . ( 2 sec) [ -6135.0948] [ 1114] [depth= 7] . ( 2 sec) [ -6010.3100] [ 1104] [depth= 3] . ( 2 sec) [ -5954.5606] [ 1095] [depth= 9] . ( 2 sec) [ -5809.2292] [ 1087] [depth= 1] . ( 2 sec) [ -5796.7345] [ 1084] [depth= 2] . ( 3 sec) [ -5778.0418] [ 1076] [depth= 2] . ( 3 sec) [ -5757.4270] [ 1075] [depth= 2] . ( 3 sec) [ -5716.3542] [ 1073] [depth= 2] . ( 3 sec) [ -5548.2239] [ 1045] [depth= 6] . ( 3 sec) [ -5413.7612] [ 1025] [depth= 4] . ( 3 sec) [ -5402.7294] [ 1001] [depth= 1] . ( 3 sec) [ -5363.0534] [ 998] [depth= 5] . ( 3 sec) [ -5303.6405] [ 983] [depth= 5] . ( 3 sec) [ -5290.2479] [ 982] [depth= 2] . ( 4 sec) [ -5226.3134] [ 982] [depth= 1] . ( 4 sec) [ -5141.6214] [ 968] [depth= 4] . ( 4 sec) [ -5092.4637] [ 964] [depth= 5] . ( 4 sec) [ -4974.3355] [ 929] [depth= 16] . ( 4 sec) [ -4865.4130] [ 927] [depth= 5] . ( 4 sec) [ -4669.8997] [ 921] [depth= 6] . ( 4 sec) [ -4506.9064] [ 871] [depth= 12] . ( 4 sec) [ -4385.7744] [ 873] [depth= 2] . ( 5 sec) [ -4314.4442] [ 864] [depth= 8] . ( 5 sec) [ -4305.6849] [ 856] [depth= 3] . ( 5 sec) [ -4261.3001] [ 849] [depth= 6] . ( 5 sec) [ -4260.6150] [ 851] [depth= 1] . ( 5 sec) [ -4258.9370] [ 852] [depth= 1] . ( 5 sec) [ -4225.6404] [ 846] [depth= 3] . ( 5 sec) [ -4125.6536] [ 827] [depth= 13] . ( 5 sec) [ -4120.3122] [ 827] [depth= 1] . ( 6 sec) [ -4118.9394] [ 827] [depth= 1] . ( 6 sec) [ -4102.5101] [ 825] [depth= 1] . ( 6 sec) [ -4061.5244] [ 827] [depth= 1] . ( 6 sec) [ -4041.3898] [ 825] [depth= 1] . ( 6 sec) [ -4029.4097] [ 822] [depth= 4] . ( 6 sec) [ -3938.8562] [ 799] [depth= 14] . ( 7 sec) [ -3906.1877] [ 785] [depth= 9] . ( 7 sec) [ -3900.1589] [ 785] [depth= 1] . ( 7 sec) [ -3863.6322] [ 779] [depth= 4] . ( 7 sec) [ -3850.9555] [ 776] [depth= 5] . ( 8 sec) [ -3818.2793] [ 775] [depth= 1] . ( 8 sec) [ -3808.5402] [ 770] [depth= 2] . ( 8 sec) [ -3795.5374] [ 769] [depth= 2] . ( 8 sec) [ -3789.7788] [ 767] [depth= 1] . ( 8 sec) [ -3788.8600] [ 768] [depth= 1] . ( 8 sec) [ -3711.0045] [ 738] [depth= 14] . ( 8 sec) [ -3710.8575] [ 736] [depth= 1] . ( 8 sec) [ -3708.1572] [ 737] [depth= 1] . ( 9 sec) [ -3682.6881] [ 733] [depth= 3] . ( 9 sec) [ -3602.2963] [ 737] [depth= 2] . ( 9 sec) [ -3468.2688] [ 693] [depth= 11] . ( 10 sec) [ -3416.0637] [ 697] [depth= 3] . ( 10 sec) [ -3414.9337] [ 697] [depth= 1] . ( 10 sec) [ -3411.3368] [ 697] [depth= 1] . ( 10 sec) [ -3360.4895] [ 697] [depth= 1] . ( 11 sec) [ -3334.0117] [ 686] [depth= 4] . ( 11 sec) [ -3296.1173] [ 681] [depth= 2] . ( 11 sec) [ -3276.9174] [ 678] [depth= 4] . ( 11 sec) [ -3252.4925] [ 677] [depth= 4] . ( 11 sec) [ -3248.8184] [ 676] [depth= 1] . ( 11 sec) [ -3244.7463] [ 673] [depth= 4] . ( 11 sec) [ -3231.6483] [ 671] [depth= 3] . ( 11 sec) [ -3212.6391] [ 665] [depth= 1] . ( 12 sec) [ -3206.8185] [ 665] [depth= 2] . ( 12 sec) [ -3204.0794] [ 665] [depth= 1] . ( 12 sec) [ -3200.2716] [ 665] [depth= 1] . ( 13 sec) [ -3198.3156] [ 665] [depth= 1] . ( 14 sec) [ -3197.7157] [ 667] [depth= 2] . ( 14 sec) [ -3196.6308] [ 666] [depth= 1] . ( 14 sec) [ -3127.1442] [ 627] [depth= 14] . ( 14 sec) [ -3121.2820] [ 627] [depth= 3] . ( 16 sec) [ -3118.5387] [ 626] [depth= 1] . ( 16 sec) [ -3117.9468] [ 631] [depth= 3] . ( 16 sec) [ -3117.1612] [ 633] [depth= 2] . ( 17 sec) [ -3113.9098] [ 633] [depth= 1] . ( 17 sec) [ -3111.6875] [ 631] [depth= 2] . ( 18 sec) [ -3111.3020] [ 631] [depth= 1] . ( 18 sec) [ -3092.9077] [ 633] [depth= 1] . ( 18 sec) [ -3092.2842] [ 634] [depth= 1] . ( 18 sec) [ -3038.0485] [ 604] [depth= 22] . ( 19 sec) [ -3024.9248] [ 604] [depth= 1] . ( 19 sec) [ -3021.3983] [ 604] [depth= 1] . ( 19 sec) [ -3016.2356] [ 603] [depth= 1] . ( 20 sec) [ -3013.3443] [ 601] [depth= 2] . ( 21 sec) [ -2977.4591] [Branch lengths ] . ( 22 sec) [ -2954.9894] [Alpha ][ 1.000401] . ( 22 sec) [ -2951.7457] [ 599] [depth= 2] . ( 22 sec) [ -2950.7049] [ 598] [depth= 1] . ( 25 sec) [ -2950.6836] [ 597] [depth= 6] . ( 25 sec) [ -2950.5778] [ 592] [depth= 5] . ( 27 sec) [ -2949.7979] [ 591] [depth= 1] . ( 28 sec) [ -2949.6505] [ 591] [depth= 1] . ( 30 sec) [ -2948.2844] [ 591] [depth= 1] . ( 36 sec) [ -2946.3990] [ 588] [depth= 1] . ( 36 sec) [ -2945.7066] [ 591] [depth= 1] . ( 38 sec) [ -2945.5148] [ 591] [depth= 1] . ( 42 sec) [ -2945.4973] [ 591] [depth= 1] . ( 43 sec) [ -2945.2996] [ 593] [depth= 1] . ( 52 sec) [ -2945.0964] [ 592] [depth= 1] . ( 53 sec) [ -2944.9775] [ 593] [depth= 1] . ( 58 sec) [ -2944.9456] [ 592] [depth= 2] . ( 58 sec) [ -2944.9185] [ 592] [depth= 2] . ( 61 sec) [ -2941.4031] [Branch lengths ] . ( 62 sec) [ -2930.1533] [Alpha ][ 1.997772] . ( 94 sec) [ -2928.7466] [ 593] [depth= 2] . ( 98 sec) [ -2928.5103] [ 593] [depth= 1] . ( 98 sec) [ -2928.3940] [ 593] [depth= 1] . ( 99 sec) [ -2928.3548] [ 595] [depth= 4] . ( 99 sec) [ -2928.3382] [ 592] [depth= 2] . ( 102 sec) [ -2926.4452] [Branch lengths ] . ( 102 sec) [ -2923.9154] [Alpha ][ 3.316394] . ( 103 sec) [ -2923.8610] [ 594] [depth= 1] . ( 105 sec) [ -2923.7642] [ 597] [depth= 1] . ( 106 sec) [ -2923.7458] [ 597] [depth= 1] . ( 116 sec) [ -2923.7237] [ 596] [depth= 1] . ( 119 sec) [ -2923.6839] [ 596] [depth= 1] . ( 121 sec) [ -2923.6704] [ 596] [depth= 1] . ( 133 sec) [ -2923.6514] [ 596] [depth= 1] . ( 135 sec) [ -2923.6398] [ 596] [depth= 1] . ( 146 sec) [ -2922.5956] [Branch lengths ] . ( 147 sec) [ -2922.5359] [Alpha ][ 3.607584] . ( 149 sec) [ -2922.5181] [ 594] [depth= 1] . ( 189 sec) [ -2922.3135] [Branch lengths ] . ( 189 sec) [ -2922.3117] [Alpha ][ 3.663844] . ( 189 sec) [ -2922.3117] [Topology ] . ( 190 sec) [ -2922.2873] [Topology ] . ( 191 sec) [ -2922.2793] [Topology ] . ( 192 sec) [ -2922.2761] [Topology ] . ( 193 sec) [ -2922.2747] [Topology ] . ( 194 sec) [ -2922.2741] [Topology ] . ( 194 sec) [ -2922.2741] [Alpha ][ 3.673968] . ( 194 sec) [ -2922.2741] [Topology ] . ( 195 sec) [ -2922.2738] [Topology ] . ( 196 sec) [ -2922.2738] [Alpha ][ 3.673968] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2922.273822. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7237.5516] [Alpha ][ 0.500960] . ( 0 sec) [ -7160.2990] [ 1341] [depth= 7] . ( 1 sec) [ -7059.3055] [ 1319] [depth= 7] . ( 1 sec) [ -6972.6285] [ 1319] [depth= 1] . ( 1 sec) [ -6793.4640] [ 1317] [depth= 11] . ( 1 sec) [ -6619.0763] [ 1276] [depth= 3] . ( 1 sec) [ -6536.1818] [ 1273] [depth= 3] . ( 1 sec) [ -6423.5618] [ 1253] [depth= 8] . ( 1 sec) [ -6409.2730] [ 1228] [depth= 1] . ( 1 sec) [ -6353.9142] [ 1212] [depth= 12] . ( 1 sec) [ -6259.5021] [ 1211] [depth= 1] . ( 2 sec) [ -6247.4216] [ 1208] [depth= 5] . ( 2 sec) [ -6170.7540] [ 1175] [depth= 2] . ( 2 sec) [ -6100.2610] [ 1172] [depth= 8] . ( 2 sec) [ -5998.0061] [ 1165] [depth= 2] . ( 2 sec) [ -5893.9026] [ 1155] [depth= 4] . ( 2 sec) [ -5707.1710] [ 1122] [depth= 1] . ( 3 sec) [ -5672.9460] [ 1119] [depth= 2] . ( 3 sec) [ -5658.3868] [ 1076] [depth= 6] . ( 3 sec) [ -5626.1493] [ 1075] [depth= 2] . ( 3 sec) [ -5530.5080] [ 1054] [depth= 4] . ( 3 sec) [ -5473.8282] [ 1043] [depth= 15] . ( 3 sec) [ -5426.0933] [ 1039] [depth= 3] . ( 3 sec) [ -5371.0905] [ 1040] [depth= 1] . ( 3 sec) [ -5358.7935] [ 1040] [depth= 2] . ( 3 sec) [ -5342.9118] [ 1039] [depth= 1] . ( 4 sec) [ -5225.0150] [ 994] [depth= 11] . ( 4 sec) [ -5212.8205] [ 995] [depth= 1] . ( 4 sec) [ -5201.2509] [ 992] [depth= 1] . ( 4 sec) [ -5200.3743] [ 991] [depth= 3] . ( 4 sec) [ -5200.2793] [ 990] [depth= 1] . ( 4 sec) [ -5181.4185] [ 982] [depth= 5] . ( 5 sec) [ -5132.0748] [ 981] [depth= 2] . ( 5 sec) [ -5089.5674] [ 982] [depth= 17] . ( 5 sec) [ -5024.9932] [ 977] [depth= 1] . ( 5 sec) [ -4879.2689] [ 946] [depth= 9] . ( 5 sec) [ -4747.4365] [ 901] [depth= 3] . ( 5 sec) [ -4720.7842] [ 898] [depth= 1] . ( 5 sec) [ -4569.4553] [ 882] [depth= 11] . ( 6 sec) [ -4485.9087] [ 883] [depth= 2] . ( 6 sec) [ -4482.1060] [ 883] [depth= 5] . ( 6 sec) [ -4452.0407] [ 883] [depth= 2] . ( 6 sec) [ -4413.5374] [ 881] [depth= 1] . ( 6 sec) [ -4383.4831] [ 879] [depth= 5] . ( 6 sec) [ -4294.3464] [ 859] [depth= 3] . ( 6 sec) [ -4257.8102] [ 846] [depth= 3] . ( 6 sec) [ -4223.5733] [ 842] [depth= 5] . ( 7 sec) [ -4211.5950] [ 841] [depth= 1] . ( 7 sec) [ -4154.1102] [ 839] [depth= 2] . ( 7 sec) [ -4135.5438] [ 822] [depth= 13] . ( 7 sec) [ -4111.9551] [ 794] [depth= 10] . ( 7 sec) [ -4110.2753] [ 793] [depth= 1] . ( 7 sec) [ -4105.8534] [ 790] [depth= 2] . ( 7 sec) [ -4039.6947] [ 785] [depth= 4] . ( 8 sec) [ -4023.9384] [ 783] [depth= 6] . ( 8 sec) [ -3981.7851] [ 780] [depth= 1] . ( 8 sec) [ -3964.3690] [ 774] [depth= 14] . ( 8 sec) [ -3962.5975] [ 776] [depth= 1] . ( 8 sec) [ -3960.8460] [ 778] [depth= 1] . ( 8 sec) [ -3949.0501] [ 776] [depth= 1] . ( 8 sec) [ -3946.8296] [ 774] [depth= 6] . ( 8 sec) [ -3944.2064] [ 774] [depth= 2] . ( 9 sec) [ -3939.0742] [ 776] [depth= 1] . ( 9 sec) [ -3937.9563] [ 773] [depth= 1] . ( 9 sec) [ -3930.9173] [ 774] [depth= 3] . ( 9 sec) [ -3910.7707] [ 767] [depth= 3] . ( 9 sec) [ -3900.4369] [ 766] [depth= 9] . ( 10 sec) [ -3817.2374] [ 744] [depth= 10] . ( 10 sec) [ -3816.7553] [ 745] [depth= 1] . ( 10 sec) [ -3814.8669] [ 744] [depth= 1] . ( 10 sec) [ -3766.5514] [ 723] [depth= 3] . ( 11 sec) [ -3766.1689] [ 722] [depth= 2] . ( 11 sec) [ -3744.4264] [ 710] [depth= 2] . ( 11 sec) [ -3711.8278] [ 708] [depth= 6] . ( 11 sec) [ -3702.5192] [ 705] [depth= 2] . ( 11 sec) [ -3700.0721] [ 708] [depth= 2] . ( 11 sec) [ -3697.6243] [ 711] [depth= 1] . ( 11 sec) [ -3689.7505] [ 706] [depth= 4] . ( 12 sec) [ -3687.3917] [ 704] [depth= 2] . ( 12 sec) [ -3682.4182] [ 702] [depth= 1] . ( 12 sec) [ -3679.1320] [ 702] [depth= 3] . ( 12 sec) [ -3616.1846] [ 687] [depth= 11] . ( 12 sec) [ -3604.0808] [ 685] [depth= 1] . ( 13 sec) [ -3602.0446] [ 688] [depth= 2] . ( 13 sec) [ -3601.6335] [ 690] [depth= 2] . ( 14 sec) [ -3579.1683] [ 691] [depth= 2] . ( 14 sec) [ -3574.9906] [ 688] [depth= 2] . ( 14 sec) [ -3573.2409] [ 689] [depth= 1] . ( 14 sec) [ -3569.0204] [ 684] [depth= 2] . ( 14 sec) [ -3565.0587] [ 682] [depth= 2] . ( 14 sec) [ -3304.7940] [ 681] [depth= 13] . ( 14 sec) [ -3300.9809] [ 681] [depth= 1] . ( 14 sec) [ -3289.7147] [ 678] [depth= 3] . ( 15 sec) [ -3280.8073] [ 675] [depth= 4] . ( 15 sec) [ -3280.0378] [ 676] [depth= 1] . ( 15 sec) [ -3264.9766] [ 674] [depth= 12] . ( 15 sec) [ -3262.4538] [ 673] [depth= 1] . ( 16 sec) [ -3259.1082] [ 674] [depth= 1] . ( 16 sec) [ -3236.5950] [ 667] [depth= 8] . ( 16 sec) [ -3233.9292] [ 664] [depth= 4] . ( 16 sec) [ -3230.9251] [ 668] [depth= 3] . ( 16 sec) [ -3219.2648] [ 666] [depth= 3] . ( 17 sec) [ -3200.2759] [ 664] [depth= 12] . ( 18 sec) [ -3199.5556] [ 668] [depth= 4] . ( 18 sec) [ -3186.2516] [ 660] [depth= 2] . ( 19 sec) [ -3161.0655] [Branch lengths ] . ( 19 sec) [ -3151.1106] [Alpha ][ 1.000156] . ( 19 sec) [ -3150.1592] [ 658] [depth= 1] . ( 20 sec) [ -3149.9769] [ 657] [depth= 2] . ( 20 sec) [ -3147.5518] [ 657] [depth= 3] . ( 20 sec) [ -3045.6624] [ 625] [depth= 8] . ( 20 sec) [ -3045.0375] [ 609] [depth= 6] . ( 20 sec) [ -3044.2825] [ 602] [depth= 2] . ( 21 sec) [ -3043.6217] [ 605] [depth= 2] . ( 22 sec) [ -3043.0042] [ 604] [depth= 1] . ( 22 sec) [ -3042.7111] [ 604] [depth= 2] . ( 22 sec) [ -3042.1341] [ 608] [depth= 2] . ( 22 sec) [ -3039.5022] [ 608] [depth= 1] . ( 22 sec) [ -2982.8991] [ 607] [depth= 1] . ( 25 sec) [ -2974.1635] [ 602] [depth= 3] . ( 27 sec) [ -2972.8791] [ 601] [depth= 1] . ( 28 sec) [ -2971.1488] [ 602] [depth= 1] . ( 28 sec) [ -2971.0679] [ 606] [depth= 2] . ( 32 sec) [ -2970.7800] [ 606] [depth= 1] . ( 33 sec) [ -2970.1324] [ 600] [depth= 7] . ( 33 sec) [ -2970.0205] [ 600] [depth= 2] . ( 33 sec) [ -2968.4509] [ 600] [depth= 1] . ( 36 sec) [ -2968.1732] [ 595] [depth= 2] . ( 36 sec) [ -2967.4517] [ 595] [depth= 1] . ( 38 sec) [ -2967.4261] [ 595] [depth= 1] . ( 38 sec) [ -2966.9835] [ 595] [depth= 1] . ( 40 sec) [ -2966.8799] [ 595] [depth= 1] . ( 40 sec) [ -2966.7906] [ 592] [depth= 1] . ( 40 sec) [ -2966.6470] [ 592] [depth= 1] . ( 48 sec) [ -2963.9825] [ 592] [depth= 1] . ( 48 sec) [ -2961.9896] [ 592] [depth= 1] . ( 53 sec) [ -2960.8531] [ 592] [depth= 1] . ( 54 sec) [ -2958.7965] [ 590] [depth= 3] . ( 55 sec) [ -2945.3241] [Branch lengths ] . ( 55 sec) [ -2938.6205] [Alpha ][ 1.996666] . ( 56 sec) [ -2938.5284] [ 590] [depth= 1] . ( 57 sec) [ -2938.0957] [ 593] [depth= 1] . ( 57 sec) [ -2937.6562] [ 595] [depth= 1] . ( 59 sec) [ -2937.6382] [ 593] [depth= 3] . ( 59 sec) [ -2937.5687] [ 592] [depth= 5] . ( 71 sec) [ -2937.4750] [ 595] [depth= 1] . ( 75 sec) [ -2937.4627] [ 595] [depth= 1] . ( 76 sec) [ -2937.3350] [ 595] [depth= 1] . ( 79 sec) [ -2937.3151] [ 595] [depth= 1] . ( 81 sec) [ -2937.1403] [ 595] [depth= 1] . ( 87 sec) [ -2937.1174] [ 595] [depth= 1] . ( 94 sec) [ -2931.8039] [Branch lengths ] . ( 94 sec) [ -2929.7867] [Alpha ][ 3.171205] . ( 96 sec) [ -2929.7623] [ 595] [depth= 1] . ( 97 sec) [ -2929.7355] [ 595] [depth= 1] . ( 98 sec) [ -2929.6956] [ 595] [depth= 1] . ( 98 sec) [ -2929.5486] [ 594] [depth= 1] . ( 99 sec) [ -2929.4882] [ 594] [depth= 1] . ( 102 sec) [ -2929.4769] [ 591] [depth= 4] . ( 102 sec) [ -2929.3872] [ 593] [depth= 4] . ( 112 sec) [ -2929.3416] [ 595] [depth= 1] . ( 120 sec) [ -2929.3228] [ 594] [depth= 1] . ( 120 sec) [ -2929.3095] [ 594] [depth= 1] . ( 120 sec) [ -2929.2937] [ 594] [depth= 1] . ( 136 sec) [ -2927.2412] [Branch lengths ] . ( 136 sec) [ -2927.1000] [Alpha ][ 3.616330] . ( 140 sec) [ -2927.0879] [ 594] [depth= 1] . ( 144 sec) [ -2927.0658] [ 592] [depth= 3] . ( 176 sec) [ -2926.6181] [Branch lengths ] . ( 177 sec) [ -2926.6116] [Alpha ][ 3.721071] . ( 177 sec) [ -2926.6116] [Topology ] . ( 178 sec) [ -2926.5702] [Topology ] . ( 179 sec) [ -2926.5584] [Topology ] . ( 180 sec) [ -2926.5538] [Topology ] . ( 181 sec) [ -2926.5519] [Topology ] . ( 181 sec) [ -2926.5511] [Topology ] . ( 182 sec) [ -2926.5511] [Alpha ][ 3.728635] . ( 182 sec) [ -2926.5511] [Topology ] . ( 183 sec) [ -2926.5507] [Topology ] . ( 183 sec) [ -2926.5507] [Alpha ][ 3.728635] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2926.550710. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3015.2739] [Alpha ][ 1.996970] . ( 1 sec) [ -3015.2739] [Topology ] . ( 2 sec) [ -2947.5324] [Topology ] . ( 3 sec) [ -2935.3074] [Topology ] . ( 4 sec) [ -2930.3388] [Topology ] . ( 5 sec) [ -2927.4368] [Topology ] . ( 6 sec) [ -2926.9560] [Topology ] . ( 6 sec) [ -2926.8177] [Topology ] . ( 7 sec) [ -2926.7584] [Topology ] . ( 8 sec) [ -2926.7265] [Topology ] . ( 9 sec) [ -2926.7072] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -2926.5115] [Topology ] . ( 17 sec) [ -2922.8546] [Alpha ][ 3.815477] . ( 17 sec) [ -2922.8546] [Topology ] . ( 18 sec) [ -2921.6808] [Topology ] . ( 19 sec) [ -2921.4624] [Topology ] . ( 20 sec) [ -2921.4165] [Topology ] . ( 21 sec) [ -2921.4036] [Topology ] . ( 22 sec) [ -2921.3998] [Topology ] . ( 23 sec) [ -2921.3987] [Topology ] . ( 24 sec) [ -2921.3983] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -2921.3961] [Alpha ][ 3.883619] . ( 31 sec) [ -2921.3961] [Topology ] . ( 31 sec) [ -2921.3960] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -2921.3960] [Alpha ][ 3.883619] . ( 38 sec) [ -2921.3960] [Topology ] . ( 39 sec) [ -2921.3959] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -3015.2739] [Alpha ][ 1.996970] . ( 54 sec) [ -3009.8145] [ 596] [depth= 1] . ( 55 sec) [ -3008.6553] [ 596] [depth= 1] . ( 55 sec) [ -3008.0825] [ 596] [depth= 1] . ( 55 sec) [ -3007.9894] [ 596] [depth= 1] . ( 55 sec) [ -3007.8324] [ 596] [depth= 1] . ( 56 sec) [ -2984.1112] [ 596] [depth= 4] . ( 57 sec) [ -2970.8096] [ 596] [depth= 3] . ( 57 sec) [ -2969.9180] [ 594] [depth= 3] . ( 57 sec) [ -2968.9224] [ 593] [depth= 4] . ( 57 sec) [ -2968.5292] [ 594] [depth= 2] . ( 57 sec) [ -2960.2240] [ 594] [depth= 1] . ( 59 sec) [ -2958.9926] [ 597] [depth= 2] . ( 60 sec) [ -2957.9119] [ 597] [depth= 1] . ( 60 sec) [ -2956.0693] [ 593] [depth= 1] . ( 61 sec) [ -2955.2325] [ 597] [depth= 1] . ( 61 sec) [ -2954.5183] [ 597] [depth= 1] . ( 62 sec) [ -2954.1297] [ 597] [depth= 1] . ( 62 sec) [ -2954.0281] [ 597] [depth= 1] . ( 62 sec) [ -2953.9961] [ 597] [depth= 1] . ( 64 sec) [ -2953.9681] [ 593] [depth= 1] . ( 64 sec) [ -2953.6735] [ 595] [depth= 2] . ( 64 sec) [ -2953.3501] [ 595] [depth= 1] . ( 65 sec) [ -2952.7980] [ 595] [depth= 1] . ( 68 sec) [ -2951.9097] [ 597] [depth= 2] . ( 69 sec) [ -2950.5572] [ 597] [depth= 1] . ( 70 sec) [ -2948.1402] [ 596] [depth= 1] . ( 72 sec) [ -2947.0059] [ 595] [depth= 3] . ( 73 sec) [ -2946.6394] [ 593] [depth= 2] . ( 73 sec) [ -2945.1957] [ 595] [depth= 1] . ( 73 sec) [ -2943.6144] [ 595] [depth= 1] . ( 74 sec) [ -2943.2339] [ 596] [depth= 1] . ( 76 sec) [ -2942.6632] [ 597] [depth= 2] . ( 76 sec) [ -2942.6429] [ 597] [depth= 1] . ( 76 sec) [ -2942.5838] [ 597] [depth= 1] . ( 76 sec) [ -2942.4906] [ 597] [depth= 1] . ( 77 sec) [ -2942.4054] [ 597] [depth= 1] . ( 78 sec) [ -2942.3926] [ 598] [depth= 1] . ( 78 sec) [ -2941.8188] [ 599] [depth= 1] . ( 78 sec) [ -2937.6111] [ 599] [depth= 1] . ( 82 sec) [ -2937.3528] [ 597] [depth= 1] . ( 83 sec) [ -2935.4339] [ 597] [depth= 1] . ( 85 sec) [ -2926.7740] [Branch lengths ] . ( 85 sec) [ -2923.7857] [Alpha ][ 3.533893] . ( 91 sec) [ -2923.0855] [ 597] [depth= 1] . ( 100 sec) [ -2922.9826] [ 597] [depth= 3] . ( 100 sec) [ -2922.9582] [ 592] [depth= 13] . ( 125 sec) [ -2922.3548] [Branch lengths ] . ( 125 sec) [ -2922.3434] [Alpha ][ 3.670174] . ( 135 sec) [ -2922.3323] [ 594] [depth= 1] . ( 165 sec) [ -2922.2811] [Branch lengths ] . ( 165 sec) [ -2922.2811] [Alpha ][ 3.675766] . ( 165 sec) [ -2922.2811] [Topology ] . ( 166 sec) [ -2922.2760] [Topology ] . ( 167 sec) [ -2922.2745] [Topology ] . ( 168 sec) [ -2922.2739] [Topology ] . ( 168 sec) [ -2922.2739] [Alpha ][ 3.675766] . ( 168 sec) [ -2922.2739] [Topology ] . ( 169 sec) [ -2922.2737] [Topology ] . ( 169 sec) [ -2922.2737] [Alpha ][ 3.675766] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2921.395934 . Log likelihood obtained after SPR moves : -2922.273687 . Log likelihood of the current tree: -2921.395934. . Printing the most likely tree in file 'proteic_M1992_46x68_2004.phy_phyml_tree.txt'... . Best log likelihood : -2921.220099 . Time used 0h2m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1184.72user 0.00system 19:46.80elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps