.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data44.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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... . 285 patterns found. (out of a total of 500 sites) . 201 sites without polymorphism (40.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9071.8620] [GTR parameters ] . ( 1 sec) [ -8919.9530] [Alpha ][ 0.500960] . ( 1 sec) [ -8535.8259] [ 1504] [depth= 8] . ( 1 sec) [ -8407.7138] [ 1483] [depth= 6] . ( 1 sec) [ -8310.4575] [ 1477] [depth= 4] . ( 1 sec) [ -8269.0300] [ 1476] [depth= 5] . ( 1 sec) [ -8187.9759] [ 1445] [depth= 4] . ( 1 sec) [ -8175.7369] [ 1443] [depth= 8] . ( 1 sec) [ -8166.4017] [ 1442] [depth= 4] . ( 1 sec) [ -8151.8057] [ 1449] [depth= 1] . ( 1 sec) [ -8067.9278] [ 1442] [depth= 11] . ( 1 sec) [ -8027.1191] [ 1429] [depth= 5] . ( 1 sec) [ -7969.3798] [ 1410] [depth= 1] . ( 1 sec) [ -7889.1773] [ 1397] [depth= 7] . ( 1 sec) [ -7842.6206] [ 1396] [depth= 1] . ( 1 sec) [ -7829.3524] [ 1395] [depth= 2] . ( 1 sec) [ -7808.5910] [ 1391] [depth= 3] . ( 1 sec) [ -7776.4004] [ 1390] [depth= 1] . ( 1 sec) [ -7710.4563] [ 1389] [depth= 2] . ( 1 sec) [ -7659.3042] [ 1388] [depth= 2] . ( 1 sec) [ -7543.4115] [ 1355] [depth= 3] . ( 1 sec) [ -7514.3005] [ 1335] [depth= 3] . ( 1 sec) [ -7421.8334] [ 1335] [depth= 4] . ( 1 sec) [ -7300.1519] [ 1324] [depth= 3] . ( 1 sec) [ -7187.0468] [ 1299] [depth= 10] . ( 1 sec) [ -7155.1025] [ 1278] [depth= 3] . ( 1 sec) [ -6989.7734] [ 1254] [depth= 9] . ( 2 sec) [ -6974.8316] [ 1243] [depth= 5] . ( 2 sec) [ -6915.2275] [ 1228] [depth= 5] . ( 2 sec) [ -6854.0862] [ 1207] [depth= 7] . ( 2 sec) [ -6853.6342] [ 1212] [depth= 1] . ( 2 sec) [ -6841.8027] [ 1206] [depth= 1] . ( 2 sec) [ -6837.1388] [ 1205] [depth= 1] . ( 2 sec) [ -6813.9974] [ 1201] [depth= 1] . ( 2 sec) [ -6755.1338] [ 1185] [depth= 1] . ( 2 sec) [ -6727.5668] [ 1181] [depth= 7] . ( 2 sec) [ -6656.1511] [ 1150] [depth= 1] . ( 2 sec) [ -6598.0749] [ 1140] [depth= 5] . ( 2 sec) [ -6552.8824] [ 1128] [depth= 2] . ( 2 sec) [ -6547.8442] [ 1127] [depth= 4] . ( 2 sec) [ -6363.0289] [ 1087] [depth= 5] . ( 2 sec) [ -6284.8958] [ 1052] [depth= 5] . ( 2 sec) [ -6261.6352] [ 1043] [depth= 9] . ( 2 sec) [ -6243.2867] [ 1054] [depth= 1] . ( 2 sec) [ -6164.6958] [ 1027] [depth= 8] . ( 2 sec) [ -6049.6512] [ 1018] [depth= 11] . ( 2 sec) [ -5969.0542] [ 996] [depth= 9] . ( 2 sec) [ -5895.7462] [ 967] [depth= 13] . ( 2 sec) [ -5752.9143] [ 967] [depth= 1] . ( 2 sec) [ -5650.1233] [ 943] [depth= 3] . ( 2 sec) [ -5593.7277] [ 933] [depth= 3] . ( 2 sec) [ -5583.6416] [ 932] [depth= 2] . ( 2 sec) [ -5576.6390] [ 931] [depth= 4] . ( 2 sec) [ -5426.5894] [ 888] [depth= 8] . ( 2 sec) [ -5426.0625] [ 887] [depth= 5] . ( 2 sec) [ -5425.5777] [ 889] [depth= 1] . ( 2 sec) [ -5382.2257] [ 872] [depth= 4] . ( 2 sec) [ -5210.9066] [ 843] [depth= 2] . ( 2 sec) [ -5169.3402] [ 832] [depth= 3] . ( 3 sec) [ -5086.3657] [ 803] [depth= 6] . ( 3 sec) [ -5063.0644] [ 799] [depth= 4] . ( 3 sec) [ -5032.7378] [ 787] [depth= 5] . ( 3 sec) [ -5026.8721] [ 790] [depth= 1] . ( 3 sec) [ -4992.2120] [ 782] [depth= 2] . ( 3 sec) [ -4965.4483] [ 778] [depth= 2] . ( 3 sec) [ -4958.9476] [ 779] [depth= 1] . ( 3 sec) [ -4945.4147] [ 775] [depth= 3] . ( 3 sec) [ -4924.7276] [ 767] [depth= 2] . ( 3 sec) [ -4919.7787] [ 767] [depth= 6] . ( 3 sec) [ -4919.1914] [ 767] [depth= 1] . ( 3 sec) [ -4872.7764] [ 752] [depth= 2] . ( 3 sec) [ -4816.1922] [ 742] [depth= 2] . ( 3 sec) [ -4812.8846] [ 741] [depth= 2] . ( 3 sec) [ -4790.2040] [ 735] [depth= 1] . ( 3 sec) [ -4777.4158] [ 735] [depth= 1] . ( 3 sec) [ -4777.2458] [ 737] [depth= 2] . ( 3 sec) [ -4772.4048] [ 734] [depth= 1] . ( 4 sec) [ -4737.4285] [Branch lengths ] . ( 4 sec) [ -4736.0349] [GTR parameters ] . ( 4 sec) [ -4724.6563] [Alpha ][ 0.839621] . ( 4 sec) [ -4707.5041] [ 731] [depth= 2] . ( 4 sec) [ -4705.0499] [ 729] [depth= 1] . ( 4 sec) [ -4705.0148] [ 730] [depth= 1] . ( 4 sec) [ -4704.9473] [ 730] [depth= 1] . ( 4 sec) [ -4704.5613] [ 730] [depth= 1] . ( 5 sec) [ -4704.4229] [ 730] [depth= 1] . ( 6 sec) [ -4704.3799] [ 729] [depth= 1] . ( 6 sec) [ -4704.3625] [ 729] [depth= 1] . ( 6 sec) [ -4682.9532] [ 720] [depth= 1] . ( 6 sec) [ -4679.7997] [ 718] [depth= 1] . ( 7 sec) [ -4676.5617] [Branch lengths ] . ( 8 sec) [ -4676.5109] [GTR parameters ] . ( 8 sec) [ -4676.3233] [Alpha ][ 0.902651] . ( 11 sec) [ -4676.3078] [Branch lengths ] . ( 28 sec) [ -4676.3071] [Branch lengths ] . ( 28 sec) [ -4676.3071] [Topology ] . ( 29 sec) [ -4676.3070] [Topology ] . ( 29 sec) [ -4676.3068] [GTR parameters ] . ( 29 sec) [ -4676.3066] [Alpha ][ 0.904845] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4676.306565. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8914.2500] [GTR parameters ] . ( 1 sec) [ -8765.9898] [Alpha ][ 0.500960] . ( 1 sec) [ -8519.0963] [ 1501] [depth= 3] . ( 1 sec) [ -8372.0514] [ 1474] [depth= 3] . ( 1 sec) [ -8330.7484] [ 1464] [depth= 4] . ( 1 sec) [ -8256.6489] [ 1460] [depth= 6] . ( 1 sec) [ -8241.4584] [ 1450] [depth= 1] . ( 1 sec) [ -8150.9428] [ 1439] [depth= 4] . ( 1 sec) [ -8044.8442] [ 1440] [depth= 1] . ( 1 sec) [ -8030.6124] [ 1440] [depth= 1] . ( 1 sec) [ -8023.1988] [ 1440] [depth= 3] . ( 1 sec) [ -7969.1105] [ 1439] [depth= 4] . ( 1 sec) [ -7902.5785] [ 1406] [depth= 4] . ( 1 sec) [ -7835.5847] [ 1404] [depth= 3] . ( 1 sec) [ -7799.5336] [ 1378] [depth= 1] . ( 1 sec) [ -7647.7560] [ 1376] [depth= 4] . ( 1 sec) [ -7357.2444] [ 1305] [depth= 9] . ( 1 sec) [ -7317.7190] [ 1303] [depth= 4] . ( 1 sec) [ -7256.7794] [ 1287] [depth= 3] . ( 1 sec) [ -7168.9942] [ 1287] [depth= 3] . ( 1 sec) [ -7167.5340] [ 1288] [depth= 1] . ( 1 sec) [ -7064.6714] [ 1262] [depth= 2] . ( 1 sec) [ -7037.8152] [ 1258] [depth= 1] . ( 1 sec) [ -6864.5450] [ 1226] [depth= 4] . ( 1 sec) [ -6804.3055] [ 1213] [depth= 12] . ( 1 sec) [ -6774.0383] [ 1211] [depth= 3] . ( 1 sec) [ -6648.5109] [ 1177] [depth= 4] . ( 1 sec) [ -6570.0937] [ 1168] [depth= 2] . ( 1 sec) [ -6548.0001] [ 1160] [depth= 1] . ( 1 sec) [ -6454.4799] [ 1128] [depth= 1] . ( 1 sec) [ -6307.0651] [ 1106] [depth= 7] . ( 1 sec) [ -6126.8959] [ 1070] [depth= 10] . ( 1 sec) [ -5989.3314] [ 1029] [depth= 7] . ( 1 sec) [ -5981.3110] [ 1029] [depth= 1] . ( 2 sec) [ -5965.7158] [ 1027] [depth= 8] . ( 2 sec) [ -5844.1089] [ 1019] [depth= 2] . ( 2 sec) [ -5780.3546] [ 1005] [depth= 7] . ( 2 sec) [ -5780.1623] [ 1008] [depth= 1] . ( 2 sec) [ -5763.2842] [ 1006] [depth= 3] . ( 2 sec) [ -5752.4437] [ 1004] [depth= 5] . ( 2 sec) [ -5713.1963] [ 1003] [depth= 1] . ( 2 sec) [ -5655.8578] [ 981] [depth= 9] . ( 2 sec) [ -5570.8390] [ 961] [depth= 5] . ( 2 sec) [ -5525.0629] [ 946] [depth= 4] . ( 2 sec) [ -5480.2145] [ 935] [depth= 7] . ( 2 sec) [ -5452.4294] [ 927] [depth= 1] . ( 2 sec) [ -5444.7930] [ 926] [depth= 3] . ( 2 sec) [ -5435.8806] [ 923] [depth= 1] . ( 2 sec) [ -5418.4969] [ 918] [depth= 9] . ( 2 sec) [ -5390.2638] [ 915] [depth= 1] . ( 2 sec) [ -5388.1068] [ 914] [depth= 2] . ( 2 sec) [ -5376.2163] [ 914] [depth= 2] . ( 2 sec) [ -5351.7703] [ 913] [depth= 2] . ( 2 sec) [ -5332.3906] [ 914] [depth= 1] . ( 2 sec) [ -5309.0104] [ 902] [depth= 7] . ( 2 sec) [ -5308.6847] [ 901] [depth= 1] . ( 2 sec) [ -5283.4978] [ 887] [depth= 3] . ( 2 sec) [ -5279.8637] [ 887] [depth= 3] . ( 2 sec) [ -5276.7981] [ 889] [depth= 1] . ( 2 sec) [ -5219.9681] [ 866] [depth= 4] . ( 2 sec) [ -5215.3967] [ 864] [depth= 1] . ( 2 sec) [ -5191.9351] [ 850] [depth= 1] . ( 2 sec) [ -5132.7528] [ 839] [depth= 3] . ( 3 sec) [ -5130.3797] [ 836] [depth= 1] . ( 3 sec) [ -5124.3978] [ 833] [depth= 1] . ( 3 sec) [ -5086.3124] [ 811] [depth= 1] . ( 3 sec) [ -5070.7731] [ 808] [depth= 1] . ( 3 sec) [ -5047.0779] [ 806] [depth= 6] . ( 3 sec) [ -5025.5827] [ 804] [depth= 2] . ( 3 sec) [ -4974.8306] [ 781] [depth= 7] . ( 3 sec) [ -4970.4409] [ 780] [depth= 1] . ( 3 sec) [ -4968.8519] [ 780] [depth= 2] . ( 3 sec) [ -4923.6539] [ 768] [depth= 1] . ( 3 sec) [ -4879.1350] [ 766] [depth= 3] . ( 3 sec) [ -4863.9468] [ 759] [depth= 2] . ( 3 sec) [ -4828.6077] [ 751] [depth= 2] . ( 3 sec) [ -4812.6384] [ 751] [depth= 1] . ( 3 sec) [ -4811.4946] [ 751] [depth= 1] . ( 4 sec) [ -4783.1460] [Branch lengths ] . ( 4 sec) [ -4781.2152] [GTR parameters ] . ( 4 sec) [ -4770.5455] [Alpha ][ 0.820442] . ( 4 sec) [ -4768.2269] [ 749] [depth= 1] . ( 5 sec) [ -4763.8244] [ 744] [depth= 1] . ( 5 sec) [ -4755.1806] [ 742] [depth= 2] . ( 6 sec) [ -4744.5660] [ 733] [depth= 2] . ( 6 sec) [ -4740.5100] [ 732] [depth= 1] . ( 6 sec) [ -4740.3851] [ 732] [depth= 1] . ( 6 sec) [ -4739.6033] [ 737] [depth= 2] . ( 6 sec) [ -4739.2234] [ 738] [depth= 1] . ( 6 sec) [ -4731.5456] [ 733] [depth= 1] . ( 6 sec) [ -4694.9465] [ 724] [depth= 1] . ( 6 sec) [ -4691.5954] [ 724] [depth= 1] . ( 7 sec) [ -4691.5329] [ 724] [depth= 1] . ( 7 sec) [ -4679.8736] [ 719] [depth= 1] . ( 7 sec) [ -4676.8686] [Branch lengths ] . ( 8 sec) [ -4676.8174] [GTR parameters ] . ( 8 sec) [ -4676.5236] [Alpha ][ 0.898123] . ( 8 sec) [ -4676.4964] [ 718] [depth= 1] . ( 11 sec) [ -4676.3148] [Branch lengths ] . ( 11 sec) [ -4676.3136] [GTR parameters ] . ( 11 sec) [ -4676.3123] [Alpha ][ 0.903643] . ( 29 sec) [ -4676.3069] [Branch lengths ] . ( 29 sec) [ -4676.3069] [Topology ] . ( 29 sec) [ -4676.3067] [Topology ] . ( 29 sec) [ -4676.3067] [GTR parameters ] . ( 29 sec) [ -4676.3066] [Alpha ][ 0.904710] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4676.306626. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9386.7813] [GTR parameters ] . ( 1 sec) [ -9229.6912] [Alpha ][ 0.500960] . ( 1 sec) [ -8979.7181] [ 1528] [depth= 8] . ( 1 sec) [ -8873.9962] [ 1509] [depth= 8] . ( 1 sec) [ -8828.5719] [ 1507] [depth= 4] . ( 1 sec) [ -8788.0023] [ 1506] [depth= 3] . ( 1 sec) [ -8683.8809] [ 1490] [depth= 2] . ( 1 sec) [ -8676.9805] [ 1489] [depth= 3] . ( 1 sec) [ -8436.0380] [ 1448] [depth= 14] . ( 1 sec) [ -8260.9196] [ 1441] [depth= 6] . ( 1 sec) [ -8090.9905] [ 1397] [depth= 15] . ( 1 sec) [ -7947.8848] [ 1377] [depth= 6] . ( 1 sec) [ -7824.2134] [ 1373] [depth= 8] . ( 1 sec) [ -7790.8466] [ 1372] [depth= 1] . ( 1 sec) [ -7664.6008] [ 1368] [depth= 1] . ( 1 sec) [ -7515.4894] [ 1326] [depth= 2] . ( 1 sec) [ -7318.0874] [ 1323] [depth= 10] . ( 2 sec) [ -7265.1713] [ 1321] [depth= 11] . ( 2 sec) [ -7262.2532] [ 1321] [depth= 1] . ( 2 sec) [ -7218.0801] [ 1317] [depth= 10] . ( 2 sec) [ -7138.5674] [ 1308] [depth= 1] . ( 2 sec) [ -7104.8678] [ 1292] [depth= 7] . ( 2 sec) [ -7060.4754] [ 1282] [depth= 6] . ( 2 sec) [ -6935.6950] [ 1246] [depth= 2] . ( 2 sec) [ -6901.1686] [ 1240] [depth= 3] . ( 2 sec) [ -6739.6772] [ 1194] [depth= 11] . ( 2 sec) [ -6653.4335] [ 1157] [depth= 7] . ( 2 sec) [ -6590.8107] [ 1132] [depth= 1] . ( 2 sec) [ -6575.8994] [ 1132] [depth= 1] . ( 2 sec) [ -6541.0325] [ 1132] [depth= 1] . ( 2 sec) [ -6494.7052] [ 1111] [depth= 8] . ( 2 sec) [ -6439.2273] [ 1092] [depth= 8] . ( 2 sec) [ -6397.4422] [ 1093] [depth= 3] . ( 2 sec) [ -6367.9156] [ 1092] [depth= 1] . ( 2 sec) [ -6345.4529] [ 1088] [depth= 10] . ( 2 sec) [ -6325.4826] [ 1083] [depth= 3] . ( 2 sec) [ -6310.6846] [ 1071] [depth= 2] . ( 2 sec) [ -6232.4217] [ 1056] [depth= 1] . ( 2 sec) [ -6141.9295] [ 1019] [depth= 9] . ( 2 sec) [ -6084.3182] [ 1006] [depth= 5] . ( 2 sec) [ -5998.5593] [ 1007] [depth= 10] . ( 2 sec) [ -5960.6789] [ 1006] [depth= 1] . ( 2 sec) [ -5898.8505] [ 987] [depth= 3] . ( 2 sec) [ -5892.5865] [ 985] [depth= 2] . ( 2 sec) [ -5854.0125] [ 983] [depth= 2] . ( 2 sec) [ -5836.3673] [ 978] [depth= 5] . ( 2 sec) [ -5805.0582] [ 975] [depth= 1] . ( 2 sec) [ -5802.6792] [ 975] [depth= 1] . ( 3 sec) [ -5780.7079] [ 970] [depth= 2] . ( 3 sec) [ -5764.0373] [ 962] [depth= 5] . ( 3 sec) [ -5745.5247] [ 956] [depth= 2] . ( 3 sec) [ -5519.8307] [ 948] [depth= 4] . ( 3 sec) [ -5376.1695] [ 913] [depth= 1] . ( 3 sec) [ -5364.5275] [ 912] [depth= 7] . ( 3 sec) [ -5357.7809] [ 908] [depth= 6] . ( 3 sec) [ -5355.5686] [ 911] [depth= 1] . ( 3 sec) [ -5309.7641] [ 899] [depth= 3] . ( 3 sec) [ -5305.6263] [ 896] [depth= 1] . ( 3 sec) [ -5282.9645] [ 894] [depth= 5] . ( 3 sec) [ -5229.7515] [ 886] [depth= 6] . ( 3 sec) [ -5194.7408] [ 880] [depth= 1] . ( 3 sec) [ -5190.8361] [ 878] [depth= 1] . ( 3 sec) [ -5154.9221] [ 866] [depth= 2] . ( 3 sec) [ -5148.0701] [ 859] [depth= 3] . ( 3 sec) [ -5127.9186] [ 853] [depth= 2] . ( 3 sec) [ -5117.1927] [ 854] [depth= 1] . ( 3 sec) [ -5097.0572] [ 846] [depth= 1] . ( 3 sec) [ -5096.6394] [ 847] [depth= 1] . ( 3 sec) [ -5072.0773] [ 837] [depth= 3] . ( 3 sec) [ -5065.9700] [ 837] [depth= 1] . ( 4 sec) [ -5050.9711] [ 835] [depth= 4] . ( 4 sec) [ -5050.6453] [ 836] [depth= 1] . ( 4 sec) [ -4989.8860] [ 817] [depth= 8] . ( 4 sec) [ -4989.3239] [ 816] [depth= 1] . ( 4 sec) [ -4986.7246] [ 816] [depth= 1] . ( 4 sec) [ -4980.9465] [ 812] [depth= 1] . ( 4 sec) [ -4980.7162] [ 812] [depth= 2] . ( 4 sec) [ -4948.1766] [Branch lengths ] . ( 4 sec) [ -4946.4306] [GTR parameters ] . ( 4 sec) [ -4939.9499] [Alpha ][ 0.717704] . ( 4 sec) [ -4938.4067] [ 809] [depth= 1] . ( 5 sec) [ -4910.9951] [ 804] [depth= 3] . ( 5 sec) [ -4905.8884] [ 803] [depth= 4] . ( 5 sec) [ -4860.3087] [ 779] [depth= 3] . ( 5 sec) [ -4849.0321] [ 779] [depth= 1] . ( 5 sec) [ -4809.7274] [ 765] [depth= 1] . ( 5 sec) [ -4799.4442] [ 760] [depth= 1] . ( 5 sec) [ -4784.6609] [ 754] [depth= 2] . ( 5 sec) [ -4784.5290] [ 754] [depth= 1] . ( 5 sec) [ -4749.5643] [ 742] [depth= 1] . ( 5 sec) [ -4741.7326] [ 738] [depth= 2] . ( 5 sec) [ -4734.4642] [ 732] [depth= 2] . ( 6 sec) [ -4731.0151] [ 732] [depth= 1] . ( 6 sec) [ -4730.4186] [ 730] [depth= 2] . ( 6 sec) [ -4706.3963] [ 721] [depth= 1] . ( 6 sec) [ -4703.4586] [ 718] [depth= 1] . ( 6 sec) [ -4703.4391] [ 718] [depth= 1] . ( 6 sec) [ -4694.5110] [ 718] [depth= 1] . ( 6 sec) [ -4694.3778] [ 718] [depth= 1] . ( 6 sec) [ -4688.2087] [ 718] [depth= 1] . ( 6 sec) [ -4686.1796] [ 720] [depth= 1] . ( 7 sec) [ -4683.1523] [ 718] [depth= 1] . ( 8 sec) [ -4679.1949] [Branch lengths ] . ( 8 sec) [ -4678.8893] [GTR parameters ] . ( 8 sec) [ -4677.0572] [Alpha ][ 0.896199] . ( 8 sec) [ -4676.6180] [ 718] [depth= 1] . ( 11 sec) [ -4676.3266] [Branch lengths ] . ( 11 sec) [ -4676.3201] [GTR parameters ] . ( 11 sec) [ -4676.3183] [Alpha ][ 0.902789] . ( 29 sec) [ -4676.3075] [Branch lengths ] . ( 29 sec) [ -4676.3075] [Topology ] . ( 29 sec) [ -4676.3069] [Topology ] . ( 30 sec) [ -4676.3068] [GTR parameters ] . ( 30 sec) [ -4676.3067] [Alpha ][ 0.904561] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4676.306685. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8722.9947] [GTR parameters ] . ( 1 sec) [ -8574.9782] [Alpha ][ 0.500960] . ( 1 sec) [ -8274.3129] [ 1471] [depth= 8] . ( 1 sec) [ -8128.3877] [ 1433] [depth= 9] . ( 1 sec) [ -7978.3283] [ 1415] [depth= 8] . ( 1 sec) [ -7888.3112] [ 1386] [depth= 1] . ( 1 sec) [ -7786.5470] [ 1363] [depth= 3] . ( 1 sec) [ -7735.7611] [ 1357] [depth= 1] . ( 1 sec) [ -7684.3823] [ 1357] [depth= 3] . ( 1 sec) [ -7673.1626] [ 1349] [depth= 5] . ( 1 sec) [ -7625.8261] [ 1348] [depth= 5] . ( 1 sec) [ -7592.4988] [ 1348] [depth= 4] . ( 1 sec) [ -7588.5404] [ 1351] [depth= 1] . ( 1 sec) [ -7450.6870] [ 1333] [depth= 7] . ( 1 sec) [ -7237.4333] [ 1300] [depth= 16] . ( 1 sec) [ -7231.4068] [ 1299] [depth= 2] . ( 1 sec) [ -7227.8351] [ 1300] [depth= 1] . ( 1 sec) [ -7209.8918] [ 1296] [depth= 11] . ( 2 sec) [ -7086.0668] [ 1272] [depth= 2] . ( 2 sec) [ -6988.6698] [ 1242] [depth= 7] . ( 2 sec) [ -6974.7560] [ 1240] [depth= 1] . ( 2 sec) [ -6913.4081] [ 1217] [depth= 17] . ( 2 sec) [ -6756.7614] [ 1181] [depth= 11] . ( 2 sec) [ -6631.0137] [ 1152] [depth= 10] . ( 2 sec) [ -6630.5112] [ 1152] [depth= 1] . ( 2 sec) [ -6592.7184] [ 1144] [depth= 2] . ( 2 sec) [ -6588.5032] [ 1144] [depth= 1] . ( 2 sec) [ -6470.1300] [ 1130] [depth= 6] . ( 2 sec) [ -6444.2950] [ 1129] [depth= 1] . ( 2 sec) [ -6391.3285] [ 1114] [depth= 1] . ( 2 sec) [ -6383.2550] [ 1115] [depth= 1] . ( 2 sec) [ -6220.7406] [ 1095] [depth= 5] . ( 2 sec) [ -6213.3188] [ 1096] [depth= 1] . ( 2 sec) [ -6212.0213] [ 1096] [depth= 2] . ( 2 sec) [ -6173.5079] [ 1094] [depth= 6] . ( 2 sec) [ -6167.2115] [ 1091] [depth= 2] . ( 2 sec) [ -6008.1490] [ 1051] [depth= 8] . ( 2 sec) [ -5985.0017] [ 1037] [depth= 1] . ( 2 sec) [ -5938.4660] [ 1023] [depth= 9] . ( 2 sec) [ -5908.6684] [ 1021] [depth= 7] . ( 2 sec) [ -5901.2186] [ 1033] [depth= 1] . ( 2 sec) [ -5795.4429] [ 989] [depth= 7] . ( 2 sec) [ -5741.8908] [ 966] [depth= 8] . ( 2 sec) [ -5741.4824] [ 968] [depth= 1] . ( 2 sec) [ -5681.4978] [ 965] [depth= 6] . ( 2 sec) [ -5644.0738] [ 950] [depth= 1] . ( 2 sec) [ -5638.1808] [ 948] [depth= 1] . ( 2 sec) [ -5631.4059] [ 947] [depth= 1] . ( 3 sec) [ -5611.4341] [ 946] [depth= 3] . ( 3 sec) [ -5597.4949] [ 930] [depth= 2] . ( 3 sec) [ -5492.3460] [ 908] [depth= 3] . ( 3 sec) [ -5481.0893] [ 908] [depth= 1] . ( 3 sec) [ -5469.6674] [ 906] [depth= 2] . ( 3 sec) [ -5424.5126] [ 901] [depth= 9] . ( 3 sec) [ -5408.0610] [ 896] [depth= 1] . ( 3 sec) [ -5352.3399] [ 869] [depth= 12] . ( 3 sec) [ -5313.8682] [ 852] [depth= 9] . ( 3 sec) [ -5200.9314] [ 831] [depth= 1] . ( 3 sec) [ -5195.6297] [ 836] [depth= 1] . ( 3 sec) [ -5127.6544] [ 825] [depth= 1] . ( 3 sec) [ -5069.4217] [ 809] [depth= 1] . ( 3 sec) [ -5031.2178] [ 807] [depth= 1] . ( 3 sec) [ -5029.5267] [ 809] [depth= 1] . ( 3 sec) [ -5028.7590] [ 808] [depth= 1] . ( 3 sec) [ -4973.5266] [ 786] [depth= 3] . ( 3 sec) [ -4960.1314] [ 783] [depth= 1] . ( 3 sec) [ -4903.0199] [ 768] [depth= 3] . ( 3 sec) [ -4902.9062] [ 768] [depth= 1] . ( 3 sec) [ -4878.9065] [ 759] [depth= 1] . ( 3 sec) [ -4878.6281] [ 759] [depth= 1] . ( 4 sec) [ -4874.8526] [ 756] [depth= 1] . ( 4 sec) [ -4837.7005] [ 744] [depth= 3] . ( 4 sec) [ -4836.5186] [ 745] [depth= 1] . ( 4 sec) [ -4829.5660] [ 745] [depth= 1] . ( 4 sec) [ -4824.8390] [ 743] [depth= 1] . ( 4 sec) [ -4791.6405] [ 744] [depth= 1] . ( 4 sec) [ -4791.4847] [ 744] [depth= 1] . ( 4 sec) [ -4762.2744] [Branch lengths ] . ( 4 sec) [ -4760.5703] [GTR parameters ] . ( 4 sec) [ -4750.9898] [Alpha ][ 0.805942] . ( 5 sec) [ -4750.9751] [ 744] [depth= 1] . ( 5 sec) [ -4738.8596] [ 737] [depth= 1] . ( 5 sec) [ -4691.8277] [ 725] [depth= 1] . ( 5 sec) [ -4691.3576] [ 724] [depth= 1] . ( 5 sec) [ -4689.0590] [ 722] [depth= 1] . ( 5 sec) [ -4686.9064] [ 720] [depth= 2] . ( 5 sec) [ -4686.4204] [ 720] [depth= 1] . ( 5 sec) [ -4685.0880] [ 720] [depth= 1] . ( 6 sec) [ -4684.9595] [ 720] [depth= 1] . ( 6 sec) [ -4684.9157] [ 720] [depth= 1] . ( 6 sec) [ -4680.4192] [ 718] [depth= 1] . ( 8 sec) [ -4676.9655] [Branch lengths ] . ( 8 sec) [ -4676.8833] [GTR parameters ] . ( 8 sec) [ -4676.5000] [Alpha ][ 0.893764] . ( 11 sec) [ -4676.3291] [Branch lengths ] . ( 29 sec) [ -4676.3131] [Branch lengths ] . ( 29 sec) [ -4676.3131] [Topology ] . ( 29 sec) [ -4676.3123] [Topology ] . ( 29 sec) [ -4676.3121] [GTR parameters ] . ( 29 sec) [ -4676.3073] [Alpha ][ 0.904623] . ( 29 sec) [ -4676.3073] [Topology ] . ( 30 sec) [ -4676.3067] [Topology ] . ( 30 sec) [ -4676.3067] [GTR parameters ] . ( 30 sec) [ -4676.3067] [Alpha ][ 0.904623] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4676.306686. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9276.3032] [GTR parameters ] . ( 1 sec) [ -9120.4146] [Alpha ][ 0.500960] . ( 1 sec) [ -8745.9060] [ 1507] [depth= 6] . ( 1 sec) [ -8661.9459] [ 1478] [depth= 11] . ( 1 sec) [ -8640.6884] [ 1474] [depth= 4] . ( 1 sec) [ -8565.8959] [ 1474] [depth= 1] . ( 1 sec) [ -8528.1984] [ 1473] [depth= 6] . ( 1 sec) [ -8497.6041] [ 1472] [depth= 3] . ( 1 sec) [ -8472.2101] [ 1470] [depth= 8] . ( 1 sec) [ -8340.9152] [ 1445] [depth= 14] . ( 1 sec) [ -8150.1440] [ 1430] [depth= 12] . ( 1 sec) [ -8065.3484] [ 1405] [depth= 1] . ( 1 sec) [ -7990.9331] [ 1389] [depth= 15] . ( 1 sec) [ -7815.6980] [ 1359] [depth= 12] . ( 1 sec) [ -7805.7843] [ 1357] [depth= 6] . ( 1 sec) [ -7794.4144] [ 1357] [depth= 2] . ( 1 sec) [ -7713.6372] [ 1351] [depth= 11] . ( 1 sec) [ -7646.5248] [ 1340] [depth= 1] . ( 1 sec) [ -7587.7329] [ 1338] [depth= 5] . ( 1 sec) [ -7525.0491] [ 1336] [depth= 6] . ( 1 sec) [ -7362.9102] [ 1299] [depth= 14] . ( 1 sec) [ -7295.1635] [ 1296] [depth= 6] . ( 1 sec) [ -7242.6133] [ 1287] [depth= 7] . ( 1 sec) [ -7119.8018] [ 1281] [depth= 9] . ( 1 sec) [ -6980.1041] [ 1239] [depth= 1] . ( 1 sec) [ -6882.7025] [ 1234] [depth= 4] . ( 1 sec) [ -6760.0785] [ 1207] [depth= 7] . ( 1 sec) [ -6711.2284] [ 1191] [depth= 3] . ( 2 sec) [ -6686.5505] [ 1181] [depth= 5] . ( 2 sec) [ -6635.7927] [ 1171] [depth= 5] . ( 2 sec) [ -6630.2435] [ 1181] [depth= 1] . ( 2 sec) [ -6505.1180] [ 1155] [depth= 12] . ( 2 sec) [ -6401.1289] [ 1137] [depth= 4] . ( 2 sec) [ -6372.4858] [ 1124] [depth= 1] . ( 2 sec) [ -6290.0541] [ 1105] [depth= 9] . ( 2 sec) [ -6156.4883] [ 1074] [depth= 10] . ( 2 sec) [ -6139.4487] [ 1067] [depth= 1] . ( 2 sec) [ -6057.0750] [ 1060] [depth= 1] . ( 2 sec) [ -6024.3273] [ 1063] [depth= 1] . ( 2 sec) [ -6016.2926] [ 1060] [depth= 1] . ( 2 sec) [ -5862.5498] [ 1013] [depth= 13] . ( 2 sec) [ -5846.9603] [ 1013] [depth= 2] . ( 2 sec) [ -5843.6626] [ 1011] [depth= 1] . ( 2 sec) [ -5740.9039] [ 983] [depth= 5] . ( 2 sec) [ -5691.9727] [ 971] [depth= 6] . ( 2 sec) [ -5621.3223] [ 957] [depth= 4] . ( 2 sec) [ -5508.2284] [ 921] [depth= 7] . ( 2 sec) [ -5505.3175] [ 919] [depth= 1] . ( 2 sec) [ -5413.1986] [ 895] [depth= 5] . ( 2 sec) [ -5378.4094] [ 881] [depth= 4] . ( 2 sec) [ -5376.7928] [ 882] [depth= 1] . ( 2 sec) [ -5310.9631] [ 870] [depth= 2] . ( 2 sec) [ -5302.2446] [ 870] [depth= 2] . ( 2 sec) [ -5281.8106] [ 858] [depth= 2] . ( 2 sec) [ -5274.3021] [ 855] [depth= 1] . ( 3 sec) [ -5267.2172] [ 853] [depth= 1] . ( 3 sec) [ -5244.6928] [ 848] [depth= 1] . ( 3 sec) [ -5169.5888] [ 840] [depth= 1] . ( 3 sec) [ -5092.0825] [ 812] [depth= 2] . ( 3 sec) [ -5084.7426] [ 812] [depth= 1] . ( 3 sec) [ -5084.3688] [ 812] [depth= 1] . ( 3 sec) [ -5076.0912] [ 811] [depth= 4] . ( 3 sec) [ -5058.5705] [ 810] [depth= 1] . ( 3 sec) [ -5048.9526] [ 810] [depth= 1] . ( 3 sec) [ -5015.8214] [ 795] [depth= 3] . ( 3 sec) [ -4953.4241] [ 783] [depth= 5] . ( 3 sec) [ -4866.5775] [ 768] [depth= 1] . ( 3 sec) [ -4842.1678] [ 760] [depth= 1] . ( 3 sec) [ -4842.1537] [ 760] [depth= 1] . ( 3 sec) [ -4834.6068] [ 761] [depth= 5] . ( 3 sec) [ -4798.6020] [ 750] [depth= 5] . ( 3 sec) [ -4795.5045] [ 750] [depth= 1] . ( 3 sec) [ -4795.4538] [ 750] [depth= 1] . ( 3 sec) [ -4790.6768] [ 745] [depth= 3] . ( 4 sec) [ -4767.5393] [Branch lengths ] . ( 4 sec) [ -4766.7299] [GTR parameters ] . ( 4 sec) [ -4755.8977] [Alpha ][ 0.824231] . ( 4 sec) [ -4730.7152] [ 737] [depth= 2] . ( 4 sec) [ -4699.1259] [ 726] [depth= 1] . ( 4 sec) [ -4686.4336] [ 720] [depth= 2] . ( 5 sec) [ -4686.3769] [ 720] [depth= 1] . ( 5 sec) [ -4682.0652] [ 718] [depth= 1] . ( 5 sec) [ -4680.7184] [ 718] [depth= 1] . ( 7 sec) [ -4676.7012] [Branch lengths ] . ( 8 sec) [ -4676.6389] [GTR parameters ] . ( 8 sec) [ -4676.3584] [Alpha ][ 0.900359] . ( 11 sec) [ -4676.3108] [Branch lengths ] . ( 28 sec) [ -4676.3078] [Branch lengths ] . ( 28 sec) [ -4676.3078] [Topology ] . ( 29 sec) [ -4676.3076] [Topology ] . ( 29 sec) [ -4676.3074] [GTR parameters ] . ( 29 sec) [ -4676.3065] [Alpha ][ 0.904791] . ( 29 sec) [ -4676.3065] [Topology ] . ( 29 sec) [ -4676.3064] [Topology ] . ( 30 sec) [ -4676.3064] [GTR parameters ] . ( 30 sec) [ -4676.3064] [Alpha ][ 0.904791] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4676.306434. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4690.275845 . ( 1 sec) [ -4685.6353] [GTR parameters ] . ( 1 sec) [ -4685.0967] [Alpha ][ 0.878928] . ( 1 sec) [ -4685.0967] [Topology ] . ( 2 sec) [ -4677.5186] [Topology ] . ( 2 sec) [ -4676.6086] [Topology ] . ( 3 sec) [ -4676.4124] [Topology ] . ( 3 sec) [ -4676.3612] [Topology ] . ( 4 sec) [ -4676.3466] [Topology ] . ( 5 sec) [ -4676.3421] [Topology ] . ( 5 sec) [ -4676.3407] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4676.340732 . ( 9 sec) [ -4676.3369] [GTR parameters ] . ( 9 sec) [ -4676.3096] [Alpha ][ 0.903671] . ( 9 sec) [ -4676.3096] [Topology ] . ( 9 sec) [ -4676.3076] [Topology ] . ( 10 sec) [ -4676.3070] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4676.306977 . ( 14 sec) [ -4676.3070] [GTR parameters ] . ( 14 sec) [ -4676.3069] [Alpha ][ 0.904574] . ( 14 sec) [ -4676.3069] [Topology ] . ( 14 sec) [ -4676.3067] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 22 sec) [ -4685.6353] [GTR parameters ] . ( 22 sec) [ -4685.0967] [Alpha ][ 0.878928] . ( 22 sec) [ -4684.1047] [ 718] [depth= 1] . ( 22 sec) [ -4684.0629] [ 718] [depth= 1] . ( 23 sec) [ -4683.4607] [ 718] [depth= 1] . ( 23 sec) [ -4682.6754] [ 718] [depth= 1] . ( 23 sec) [ -4682.4650] [ 718] [depth= 1] . ( 23 sec) [ -4681.9375] [ 718] [depth= 1] . ( 23 sec) [ -4681.7946] [ 719] [depth= 1] . ( 23 sec) [ -4681.3218] [ 718] [depth= 1] . ( 25 sec) [ -4680.6303] [ 718] [depth= 1] . ( 25 sec) [ -4680.4831] [ 718] [depth= 1] . ( 25 sec) [ -4680.4423] [ 718] [depth= 1] . ( 25 sec) [ -4680.3144] [ 718] [depth= 1] . ( 25 sec) [ -4676.4045] [Branch lengths ] . ( 25 sec) [ -4676.4016] [GTR parameters ] . ( 25 sec) [ -4676.3830] [Alpha ][ 0.899229] . ( 29 sec) [ -4676.3125] [Branch lengths ] . ( 46 sec) [ -4676.3083] [Branch lengths ] . ( 46 sec) [ -4676.3083] [Topology ] . ( 47 sec) [ -4676.3081] [Topology ] . ( 47 sec) [ -4676.3080] [GTR parameters ] . ( 47 sec) [ -4676.3067] [Alpha ][ 0.904772] . ( 47 sec) [ -4676.3067] [Topology ] . ( 47 sec) [ -4676.3066] [Topology ] . ( 47 sec) [ -4676.3066] [GTR parameters ] . ( 47 sec) [ -4676.3066] [Alpha ][ 0.904772] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4676.306664 . Log likelihood obtained after SPR moves : -4676.306579 . Log likelihood of the current tree: -4676.306579. . Printing the most likely tree in file 'data44.phy_phyml_tree.txt'... . Best log likelihood : -4676.306434 . Time used 0h0m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo