.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data97.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... . 269 patterns found. (out of a total of 500 sites) . 214 sites without polymorphism (42.80%). . [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) [ -11933.0468] [GTR parameters ] . ( 1 sec) [ -11706.7360] [Alpha ][ 0.500960] . ( 1 sec) [ -11554.4373] [ 1624] [depth= 8] . ( 1 sec) [ -11488.8206] [ 1619] [depth= 6] . ( 1 sec) [ -11235.6273] [ 1610] [depth= 4] . ( 1 sec) [ -11200.4973] [ 1609] [depth= 5] . ( 1 sec) [ -11162.4571] [ 1590] [depth= 1] . ( 1 sec) [ -11132.6334] [ 1588] [depth= 6] . ( 1 sec) [ -9838.7764] [ 1573] [depth= 5] . ( 1 sec) [ -9622.9772] [ 1574] [depth= 1] . ( 1 sec) [ -9622.9317] [ 1577] [depth= 1] . ( 1 sec) [ -9495.4082] [ 1556] [depth= 9] . ( 1 sec) [ -9369.5784] [ 1561] [depth= 1] . ( 1 sec) [ -9039.5040] [ 1567] [depth= 11] . ( 1 sec) [ -8974.3471] [ 1532] [depth= 10] . ( 1 sec) [ -8758.7135] [ 1462] [depth= 10] . ( 1 sec) [ -8716.3227] [ 1462] [depth= 3] . ( 1 sec) [ -8667.4734] [ 1461] [depth= 4] . ( 1 sec) [ -8571.4308] [ 1439] [depth= 5] . ( 1 sec) [ -8481.4018] [ 1439] [depth= 3] . ( 1 sec) [ -8374.8110] [ 1406] [depth= 7] . ( 1 sec) [ -8217.7255] [ 1406] [depth= 10] . ( 1 sec) [ -8176.3772] [ 1389] [depth= 8] . ( 1 sec) [ -8170.2196] [ 1386] [depth= 6] . ( 1 sec) [ -8133.6597] [ 1387] [depth= 1] . ( 1 sec) [ -8128.2040] [ 1380] [depth= 10] . ( 1 sec) [ -8058.1854] [ 1340] [depth= 9] . ( 1 sec) [ -7987.7494] [ 1338] [depth= 1] . ( 1 sec) [ -7537.2618] [ 1293] [depth= 1] . ( 1 sec) [ -7432.8800] [ 1291] [depth= 10] . ( 1 sec) [ -7207.5538] [ 1212] [depth= 7] . ( 1 sec) [ -7183.7713] [ 1210] [depth= 1] . ( 1 sec) [ -7144.7040] [ 1206] [depth= 3] . ( 1 sec) [ -6993.5779] [ 1208] [depth= 3] . ( 2 sec) [ -6891.8525] [ 1201] [depth= 7] . ( 2 sec) [ -6881.9058] [ 1198] [depth= 1] . ( 2 sec) [ -6778.6338] [ 1173] [depth= 2] . ( 2 sec) [ -6665.2699] [ 1166] [depth= 9] . ( 2 sec) [ -6478.4488] [ 1123] [depth= 9] . ( 2 sec) [ -6349.3838] [ 1099] [depth= 12] . ( 2 sec) [ -6307.3702] [ 1093] [depth= 1] . ( 2 sec) [ -6194.4938] [ 1085] [depth= 7] . ( 2 sec) [ -6122.0341] [ 1066] [depth= 4] . ( 2 sec) [ -6110.3499] [ 1065] [depth= 10] . ( 2 sec) [ -6095.5799] [ 1066] [depth= 1] . ( 2 sec) [ -5969.1545] [ 1057] [depth= 2] . ( 2 sec) [ -5747.8243] [ 1037] [depth= 3] . ( 2 sec) [ -5568.4870] [ 991] [depth= 7] . ( 2 sec) [ -5534.8649] [ 977] [depth= 1] . ( 2 sec) [ -5519.0833] [ 976] [depth= 6] . ( 2 sec) [ -5517.2449] [ 978] [depth= 1] . ( 2 sec) [ -5350.6722] [ 948] [depth= 10] . ( 2 sec) [ -5260.3842] [ 930] [depth= 6] . ( 2 sec) [ -5213.6318] [ 917] [depth= 2] . ( 2 sec) [ -5169.0325] [ 907] [depth= 1] . ( 2 sec) [ -5118.5559] [ 890] [depth= 2] . ( 2 sec) [ -5112.5742] [ 891] [depth= 3] . ( 2 sec) [ -5096.6476] [ 884] [depth= 1] . ( 2 sec) [ -5090.8309] [ 882] [depth= 2] . ( 2 sec) [ -4995.6186] [ 862] [depth= 8] . ( 2 sec) [ -4939.7218] [ 839] [depth= 1] . ( 2 sec) [ -4937.7364] [ 856] [depth= 3] . ( 2 sec) [ -4802.7136] [ 815] [depth= 2] . ( 2 sec) [ -4796.7240] [ 813] [depth= 1] . ( 3 sec) [ -4786.4786] [ 793] [depth= 4] . ( 3 sec) [ -4777.1806] [ 793] [depth= 2] . ( 3 sec) [ -4722.5372] [ 778] [depth= 3] . ( 3 sec) [ -4719.2425] [ 779] [depth= 1] . ( 3 sec) [ -4718.0851] [ 778] [depth= 1] . ( 3 sec) [ -4718.0680] [ 776] [depth= 1] . ( 3 sec) [ -4710.9978] [ 773] [depth= 1] . ( 3 sec) [ -4710.3120] [ 774] [depth= 1] . ( 3 sec) [ -4577.5035] [ 752] [depth= 3] . ( 3 sec) [ -4561.2792] [ 738] [depth= 2] . ( 3 sec) [ -4439.7622] [ 722] [depth= 3] . ( 3 sec) [ -4401.0101] [ 701] [depth= 1] . ( 3 sec) [ -4385.2954] [ 677] [depth= 2] . ( 3 sec) [ -4385.0873] [ 678] [depth= 1] . ( 3 sec) [ -4383.6141] [ 682] [depth= 1] . ( 3 sec) [ -4364.4408] [ 682] [depth= 4] . ( 3 sec) [ -4360.9484] [ 681] [depth= 1] . ( 3 sec) [ -4360.9071] [ 680] [depth= 1] . ( 3 sec) [ -4229.2088] [ 641] [depth= 9] . ( 4 sec) [ -4201.3502] [Branch lengths ] . ( 4 sec) [ -4186.3475] [GTR parameters ] . ( 4 sec) [ -4175.8924] [Alpha ][ 0.857307] . ( 4 sec) [ -4160.0875] [ 634] [depth= 1] . ( 4 sec) [ -4157.7206] [ 631] [depth= 1] . ( 4 sec) [ -4151.0195] [ 627] [depth= 1] . ( 4 sec) [ -4148.9024] [ 626] [depth= 1] . ( 5 sec) [ -4148.7714] [ 625] [depth= 1] . ( 5 sec) [ -4141.7232] [ 625] [depth= 2] . ( 5 sec) [ -4115.5352] [ 613] [depth= 1] . ( 5 sec) [ -4112.9588] [ 611] [depth= 1] . ( 6 sec) [ -4112.5668] [ 612] [depth= 1] . ( 6 sec) [ -4112.5002] [ 612] [depth= 1] . ( 7 sec) [ -4108.9954] [Branch lengths ] . ( 7 sec) [ -4108.9203] [GTR parameters ] . ( 7 sec) [ -4108.6033] [Alpha ][ 0.953490] . ( 8 sec) [ -4108.5452] [ 611] [depth= 1] . ( 10 sec) [ -4105.4419] [Branch lengths ] . ( 10 sec) [ -4105.4400] [GTR parameters ] . ( 10 sec) [ -4105.4372] [Alpha ][ 0.963485] . ( 13 sec) [ -4104.1595] [Branch lengths ] . ( 28 sec) [ -4104.1531] [Branch lengths ] . ( 28 sec) [ -4104.1531] [Topology ] . ( 28 sec) [ -4104.1531] [Topology ] . ( 28 sec) [ -4104.1530] [GTR parameters ] . ( 28 sec) [ -4104.1530] [Alpha ][ 0.963485] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4104.153016. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10621.4627] [GTR parameters ] . ( 0 sec) [ -10395.6722] [Alpha ][ 0.500960] . ( 1 sec) [ -10214.6694] [ 1686] [depth= 3] . ( 1 sec) [ -10023.8227] [ 1659] [depth= 3] . ( 1 sec) [ -9889.8435] [ 1659] [depth= 1] . ( 1 sec) [ -9811.4219] [ 1656] [depth= 5] . ( 1 sec) [ -9783.3808] [ 1652] [depth= 5] . ( 1 sec) [ -9681.8448] [ 1650] [depth= 6] . ( 1 sec) [ -9611.3969] [ 1641] [depth= 1] . ( 1 sec) [ -9453.1761] [ 1639] [depth= 5] . ( 1 sec) [ -9333.0413] [ 1595] [depth= 1] . ( 1 sec) [ -9260.6863] [ 1579] [depth= 4] . ( 1 sec) [ -9182.1409] [ 1572] [depth= 1] . ( 1 sec) [ -9168.5558] [ 1570] [depth= 2] . ( 1 sec) [ -9078.9243] [ 1563] [depth= 5] . ( 1 sec) [ -8929.7871] [ 1561] [depth= 5] . ( 1 sec) [ -8761.1916] [ 1526] [depth= 14] . ( 1 sec) [ -8533.5042] [ 1478] [depth= 5] . ( 1 sec) [ -8470.5427] [ 1475] [depth= 3] . ( 1 sec) [ -8454.8251] [ 1474] [depth= 1] . ( 1 sec) [ -8299.4500] [ 1451] [depth= 3] . ( 1 sec) [ -8281.3720] [ 1451] [depth= 1] . ( 1 sec) [ -8264.7293] [ 1451] [depth= 1] . ( 1 sec) [ -8232.4851] [ 1451] [depth= 1] . ( 1 sec) [ -8230.6434] [ 1440] [depth= 2] . ( 1 sec) [ -8061.5762] [ 1389] [depth= 6] . ( 1 sec) [ -8013.2101] [ 1390] [depth= 16] . ( 1 sec) [ -8002.7365] [ 1379] [depth= 3] . ( 1 sec) [ -7941.2601] [ 1390] [depth= 2] . ( 1 sec) [ -7844.7473] [ 1378] [depth= 1] . ( 1 sec) [ -7799.0020] [ 1376] [depth= 1] . ( 1 sec) [ -7721.9305] [ 1372] [depth= 3] . ( 1 sec) [ -7613.0500] [ 1371] [depth= 13] . ( 1 sec) [ -7445.3296] [ 1308] [depth= 9] . ( 1 sec) [ -7332.2543] [ 1271] [depth= 1] . ( 1 sec) [ -7240.2139] [ 1266] [depth= 9] . ( 1 sec) [ -7056.3005] [ 1237] [depth= 8] . ( 1 sec) [ -7033.9127] [ 1235] [depth= 1] . ( 2 sec) [ -6812.0734] [ 1176] [depth= 6] . ( 2 sec) [ -6809.1403] [ 1176] [depth= 1] . ( 2 sec) [ -6772.3640] [ 1173] [depth= 4] . ( 2 sec) [ -6485.5342] [ 1173] [depth= 9] . ( 2 sec) [ -6233.7375] [ 1121] [depth= 11] . ( 2 sec) [ -6096.7506] [ 1062] [depth= 5] . ( 2 sec) [ -6094.5316] [ 1062] [depth= 1] . ( 2 sec) [ -5894.3117] [ 1037] [depth= 10] . ( 2 sec) [ -5879.5779] [ 1037] [depth= 4] . ( 2 sec) [ -5860.7121] [ 1024] [depth= 5] . ( 2 sec) [ -5712.0090] [ 974] [depth= 6] . ( 2 sec) [ -5696.1048] [ 971] [depth= 4] . ( 2 sec) [ -5549.6201] [ 925] [depth= 7] . ( 2 sec) [ -5362.0653] [ 900] [depth= 7] . ( 2 sec) [ -5298.0579] [ 900] [depth= 1] . ( 2 sec) [ -5285.8209] [ 898] [depth= 1] . ( 2 sec) [ -5187.0924] [ 867] [depth= 8] . ( 2 sec) [ -5151.2138] [ 866] [depth= 10] . ( 2 sec) [ -5113.3734] [ 867] [depth= 1] . ( 2 sec) [ -5091.4647] [ 869] [depth= 1] . ( 2 sec) [ -4991.8579] [ 852] [depth= 6] . ( 2 sec) [ -4890.7570] [ 848] [depth= 5] . ( 2 sec) [ -4876.2469] [ 819] [depth= 5] . ( 2 sec) [ -4873.3686] [ 818] [depth= 1] . ( 2 sec) [ -4868.5353] [ 817] [depth= 1] . ( 2 sec) [ -4840.5161] [ 789] [depth= 1] . ( 2 sec) [ -4818.1875] [ 786] [depth= 3] . ( 2 sec) [ -4796.3494] [ 778] [depth= 4] . ( 2 sec) [ -4749.9189] [ 762] [depth= 2] . ( 2 sec) [ -4744.3583] [ 762] [depth= 1] . ( 3 sec) [ -4717.3942] [ 748] [depth= 1] . ( 3 sec) [ -4685.7280] [ 741] [depth= 1] . ( 3 sec) [ -4659.8746] [ 741] [depth= 1] . ( 3 sec) [ -4623.3431] [ 740] [depth= 1] . ( 3 sec) [ -4588.3701] [ 730] [depth= 4] . ( 3 sec) [ -4534.8908] [ 719] [depth= 1] . ( 3 sec) [ -4492.1027] [ 706] [depth= 7] . ( 3 sec) [ -4477.2991] [ 691] [depth= 7] . ( 3 sec) [ -4464.8234] [ 685] [depth= 1] . ( 3 sec) [ -4452.2381] [ 683] [depth= 1] . ( 3 sec) [ -4356.2724] [ 667] [depth= 6] . ( 3 sec) [ -4320.9801] [ 654] [depth= 2] . ( 3 sec) [ -4316.5673] [ 652] [depth= 1] . ( 3 sec) [ -4283.1575] [ 653] [depth= 1] . ( 3 sec) [ -4280.3211] [ 650] [depth= 1] . ( 3 sec) [ -4275.2251] [ 648] [depth= 1] . ( 3 sec) [ -4274.8058] [ 646] [depth= 1] . ( 3 sec) [ -4250.5357] [ 641] [depth= 3] . ( 4 sec) [ -4195.5247] [Branch lengths ] . ( 4 sec) [ -4188.2455] [GTR parameters ] . ( 4 sec) [ -4177.0789] [Alpha ][ 0.877696] . ( 4 sec) [ -4158.0578] [ 626] [depth= 1] . ( 4 sec) [ -4152.8249] [ 627] [depth= 1] . ( 4 sec) [ -4151.2709] [ 627] [depth= 1] . ( 4 sec) [ -4115.1200] [ 616] [depth= 1] . ( 5 sec) [ -4112.1651] [ 617] [depth= 1] . ( 5 sec) [ -4111.4507] [ 616] [depth= 1] . ( 5 sec) [ -4109.3779] [ 615] [depth= 1] . ( 5 sec) [ -4106.8274] [ 612] [depth= 1] . ( 5 sec) [ -4106.6063] [ 611] [depth= 1] . ( 7 sec) [ -4104.5491] [Branch lengths ] . ( 7 sec) [ -4104.4035] [GTR parameters ] . ( 7 sec) [ -4104.1810] [Alpha ][ 0.960406] . ( 10 sec) [ -4104.1545] [Branch lengths ] . ( 25 sec) [ -4104.1534] [Branch lengths ] . ( 25 sec) [ -4104.1534] [Topology ] . ( 25 sec) [ -4104.1533] [Topology ] . ( 25 sec) [ -4104.1533] [GTR parameters ] . ( 25 sec) [ -4104.1530] [Alpha ][ 0.963513] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4104.152972. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12462.5852] [GTR parameters ] . ( 0 sec) [ -12235.1155] [Alpha ][ 0.500960] . ( 1 sec) [ -12114.3580] [ 1651] [depth= 8] . ( 1 sec) [ -11940.6968] [ 1632] [depth= 8] . ( 1 sec) [ -11854.5141] [ 1629] [depth= 4] . ( 1 sec) [ -11844.2459] [ 1629] [depth= 1] . ( 1 sec) [ -11843.8252] [ 1628] [depth= 1] . ( 1 sec) [ -11835.3717] [ 1628] [depth= 4] . ( 1 sec) [ -10443.1248] [ 1580] [depth= 10] . ( 1 sec) [ -10385.4787] [ 1576] [depth= 2] . ( 1 sec) [ -10222.5575] [ 1532] [depth= 10] . ( 1 sec) [ -10222.0887] [ 1525] [depth= 7] . ( 1 sec) [ -10072.0707] [ 1482] [depth= 4] . ( 1 sec) [ -10018.9197] [ 1482] [depth= 1] . ( 1 sec) [ -9117.0820] [ 1437] [depth= 7] . ( 1 sec) [ -9065.4744] [ 1435] [depth= 5] . ( 1 sec) [ -9063.2755] [ 1435] [depth= 1] . ( 1 sec) [ -9034.4202] [ 1395] [depth= 6] . ( 1 sec) [ -9024.8683] [ 1395] [depth= 1] . ( 1 sec) [ -9009.4722] [ 1394] [depth= 13] . ( 1 sec) [ -8961.5720] [ 1394] [depth= 1] . ( 1 sec) [ -8884.3835] [ 1374] [depth= 11] . ( 1 sec) [ -8761.2658] [ 1373] [depth= 1] . ( 1 sec) [ -8734.5091] [ 1365] [depth= 4] . ( 1 sec) [ -8096.2855] [ 1313] [depth= 10] . ( 1 sec) [ -7973.8193] [ 1311] [depth= 10] . ( 1 sec) [ -7829.9649] [ 1292] [depth= 8] . ( 1 sec) [ -7704.8112] [ 1254] [depth= 6] . ( 1 sec) [ -7561.5650] [ 1230] [depth= 11] . ( 1 sec) [ -7270.2205] [ 1200] [depth= 6] . ( 1 sec) [ -7175.2963] [ 1202] [depth= 10] . ( 1 sec) [ -7011.5919] [ 1183] [depth= 7] . ( 1 sec) [ -7004.2838] [ 1182] [depth= 2] . ( 1 sec) [ -6815.6485] [ 1166] [depth= 8] . ( 1 sec) [ -6811.5328] [ 1167] [depth= 1] . ( 1 sec) [ -6727.3811] [ 1166] [depth= 3] . ( 1 sec) [ -6606.8517] [ 1139] [depth= 4] . ( 1 sec) [ -6580.9385] [ 1144] [depth= 2] . ( 1 sec) [ -6487.3959] [ 1106] [depth= 2] . ( 2 sec) [ -6485.7475] [ 1106] [depth= 1] . ( 2 sec) [ -6480.4548] [ 1105] [depth= 2] . ( 2 sec) [ -6341.8371] [ 1084] [depth= 5] . ( 2 sec) [ -6213.5635] [ 1039] [depth= 11] . ( 2 sec) [ -6104.3806] [ 1006] [depth= 6] . ( 2 sec) [ -6080.3175] [ 1005] [depth= 7] . ( 2 sec) [ -5783.7604] [ 966] [depth= 9] . ( 2 sec) [ -5751.3378] [ 963] [depth= 1] . ( 2 sec) [ -5749.2655] [ 964] [depth= 2] . ( 2 sec) [ -5604.4126] [ 923] [depth= 4] . ( 2 sec) [ -5573.3760] [ 922] [depth= 1] . ( 2 sec) [ -5531.6963] [ 922] [depth= 1] . ( 2 sec) [ -5504.5258] [ 903] [depth= 4] . ( 2 sec) [ -5484.2166] [ 902] [depth= 3] . ( 2 sec) [ -5429.1866] [ 897] [depth= 2] . ( 2 sec) [ -5253.8725] [ 864] [depth= 1] . ( 2 sec) [ -5119.0644] [ 822] [depth= 12] . ( 2 sec) [ -5085.9656] [ 807] [depth= 1] . ( 2 sec) [ -5046.9378] [ 807] [depth= 8] . ( 2 sec) [ -5012.5336] [ 805] [depth= 7] . ( 2 sec) [ -4898.8429] [ 776] [depth= 8] . ( 2 sec) [ -4874.6904] [ 777] [depth= 1] . ( 2 sec) [ -4849.1669] [ 768] [depth= 2] . ( 2 sec) [ -4846.4966] [ 769] [depth= 1] . ( 2 sec) [ -4756.4771] [ 751] [depth= 5] . ( 2 sec) [ -4682.4078] [ 733] [depth= 2] . ( 2 sec) [ -4678.9901] [ 731] [depth= 1] . ( 2 sec) [ -4677.5335] [ 731] [depth= 4] . ( 2 sec) [ -4608.9625] [ 707] [depth= 2] . ( 2 sec) [ -4597.0718] [ 701] [depth= 3] . ( 3 sec) [ -4593.6892] [ 702] [depth= 1] . ( 3 sec) [ -4507.7862] [ 681] [depth= 1] . ( 3 sec) [ -4506.3562] [ 682] [depth= 1] . ( 3 sec) [ -4485.2456] [ 674] [depth= 1] . ( 3 sec) [ -4403.8903] [ 675] [depth= 1] . ( 3 sec) [ -4368.0349] [ 665] [depth= 1] . ( 3 sec) [ -4357.8358] [ 661] [depth= 1] . ( 3 sec) [ -4349.4224] [ 660] [depth= 1] . ( 3 sec) [ -4339.9372] [ 659] [depth= 1] . ( 3 sec) [ -4304.1528] [Branch lengths ] . ( 4 sec) [ -4290.0563] [GTR parameters ] . ( 4 sec) [ -4280.8534] [Alpha ][ 0.824009] . ( 4 sec) [ -4256.1225] [ 655] [depth= 2] . ( 4 sec) [ -4254.0030] [ 654] [depth= 1] . ( 4 sec) [ -4251.3958] [ 653] [depth= 1] . ( 4 sec) [ -4230.1331] [ 648] [depth= 1] . ( 4 sec) [ -4201.8250] [ 638] [depth= 3] . ( 5 sec) [ -4201.0645] [ 637] [depth= 1] . ( 5 sec) [ -4153.8152] [ 624] [depth= 1] . ( 5 sec) [ -4133.4364] [ 620] [depth= 1] . ( 5 sec) [ -4123.1864] [ 617] [depth= 1] . ( 5 sec) [ -4122.8111] [ 617] [depth= 2] . ( 6 sec) [ -4109.5270] [ 611] [depth= 1] . ( 6 sec) [ -4108.0901] [ 612] [depth= 1] . ( 6 sec) [ -4107.2672] [ 611] [depth= 1] . ( 7 sec) [ -4104.9656] [Branch lengths ] . ( 7 sec) [ -4104.8396] [GTR parameters ] . ( 7 sec) [ -4104.2023] [Alpha ][ 0.958528] . ( 10 sec) [ -4104.1566] [Branch lengths ] . ( 25 sec) [ -4104.1540] [Branch lengths ] . ( 25 sec) [ -4104.1540] [Topology ] . ( 25 sec) [ -4104.1539] [Topology ] . ( 26 sec) [ -4104.1537] [GTR parameters ] . ( 26 sec) [ -4104.1530] [Alpha ][ 0.963516] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4104.153019. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10452.8495] [GTR parameters ] . ( 1 sec) [ -10229.2823] [Alpha ][ 0.500960] . ( 1 sec) [ -10122.2912] [ 1642] [depth= 8] . ( 1 sec) [ -9884.9848] [ 1587] [depth= 9] . ( 1 sec) [ -9757.7829] [ 1576] [depth= 2] . ( 1 sec) [ -9680.8730] [ 1548] [depth= 1] . ( 1 sec) [ -9554.2413] [ 1535] [depth= 4] . ( 1 sec) [ -9517.9494] [ 1526] [depth= 2] . ( 1 sec) [ -9425.4516] [ 1523] [depth= 5] . ( 1 sec) [ -9327.3214] [ 1494] [depth= 1] . ( 1 sec) [ -9277.3654] [ 1480] [depth= 6] . ( 1 sec) [ -9148.0149] [ 1467] [depth= 5] . ( 1 sec) [ -8907.0370] [ 1465] [depth= 5] . ( 1 sec) [ -8708.6982] [ 1431] [depth= 3] . ( 1 sec) [ -8639.9674] [ 1423] [depth= 2] . ( 1 sec) [ -8605.1845] [ 1421] [depth= 3] . ( 1 sec) [ -8517.0170] [ 1409] [depth= 3] . ( 1 sec) [ -8439.3714] [ 1408] [depth= 1] . ( 1 sec) [ -8434.5216] [ 1408] [depth= 7] . ( 1 sec) [ -7946.3689] [ 1348] [depth= 5] . ( 1 sec) [ -7906.0581] [ 1344] [depth= 10] . ( 1 sec) [ -7864.1097] [ 1344] [depth= 4] . ( 1 sec) [ -7731.1229] [ 1324] [depth= 11] . ( 1 sec) [ -7701.4706] [ 1316] [depth= 9] . ( 2 sec) [ -7517.8932] [ 1295] [depth= 2] . ( 2 sec) [ -7501.4191] [ 1295] [depth= 2] . ( 2 sec) [ -7399.6104] [ 1273] [depth= 3] . ( 2 sec) [ -7290.2468] [ 1266] [depth= 17] . ( 2 sec) [ -6917.1341] [ 1234] [depth= 8] . ( 2 sec) [ -6879.3307] [ 1235] [depth= 8] . ( 2 sec) [ -6805.1584] [ 1203] [depth= 1] . ( 2 sec) [ -6780.5655] [ 1202] [depth= 3] . ( 2 sec) [ -6738.6901] [ 1189] [depth= 1] . ( 2 sec) [ -6568.8668] [ 1183] [depth= 9] . ( 2 sec) [ -6478.7613] [ 1168] [depth= 12] . ( 2 sec) [ -6372.3684] [ 1135] [depth= 8] . ( 2 sec) [ -6226.6763] [ 1114] [depth= 3] . ( 2 sec) [ -6218.9140] [ 1109] [depth= 1] . ( 2 sec) [ -6094.9123] [ 1067] [depth= 2] . ( 2 sec) [ -6077.7413] [ 1070] [depth= 1] . ( 2 sec) [ -6058.9465] [ 1066] [depth= 11] . ( 2 sec) [ -5948.1934] [ 1044] [depth= 14] . ( 2 sec) [ -5901.8759] [ 1034] [depth= 5] . ( 2 sec) [ -5851.1087] [ 1001] [depth= 5] . ( 2 sec) [ -5822.2778] [ 1001] [depth= 2] . ( 2 sec) [ -5787.5556] [ 999] [depth= 2] . ( 2 sec) [ -5690.3948] [ 997] [depth= 2] . ( 2 sec) [ -5661.0195] [ 996] [depth= 1] . ( 2 sec) [ -5591.5570] [ 979] [depth= 6] . ( 2 sec) [ -5586.3418] [ 978] [depth= 1] . ( 2 sec) [ -5575.0567] [ 980] [depth= 2] . ( 2 sec) [ -5573.0230] [ 979] [depth= 1] . ( 2 sec) [ -5498.2698] [ 967] [depth= 2] . ( 2 sec) [ -5328.3763] [ 970] [depth= 1] . ( 3 sec) [ -5274.7404] [ 956] [depth= 2] . ( 3 sec) [ -5259.3810] [ 950] [depth= 1] . ( 3 sec) [ -5246.3196] [ 940] [depth= 3] . ( 3 sec) [ -5215.3476] [ 904] [depth= 5] . ( 3 sec) [ -5178.7778] [ 894] [depth= 5] . ( 3 sec) [ -5147.1926] [ 877] [depth= 1] . ( 3 sec) [ -5146.9927] [ 878] [depth= 1] . ( 3 sec) [ -5086.1977] [ 859] [depth= 2] . ( 3 sec) [ -5064.6708] [ 849] [depth= 1] . ( 3 sec) [ -5055.1087] [ 848] [depth= 4] . ( 3 sec) [ -5028.7122] [ 840] [depth= 1] . ( 3 sec) [ -4964.4766] [ 811] [depth= 1] . ( 3 sec) [ -4944.6764] [ 800] [depth= 6] . ( 3 sec) [ -4898.3602] [ 791] [depth= 3] . ( 3 sec) [ -4842.1062] [ 784] [depth= 2] . ( 3 sec) [ -4819.8512] [ 783] [depth= 6] . ( 3 sec) [ -4795.3727] [ 778] [depth= 1] . ( 3 sec) [ -4770.0885] [ 779] [depth= 1] . ( 3 sec) [ -4769.0598] [ 779] [depth= 1] . ( 3 sec) [ -4758.3869] [ 799] [depth= 2] . ( 3 sec) [ -4725.8471] [ 788] [depth= 1] . ( 3 sec) [ -4670.8188] [ 767] [depth= 1] . ( 3 sec) [ -4668.6623] [ 771] [depth= 1] . ( 3 sec) [ -4553.3130] [ 716] [depth= 5] . ( 3 sec) [ -4507.5874] [ 697] [depth= 4] . ( 3 sec) [ -4463.7639] [ 695] [depth= 2] . ( 3 sec) [ -4459.3863] [ 698] [depth= 1] . ( 4 sec) [ -4437.4317] [ 694] [depth= 2] . ( 4 sec) [ -4424.5798] [ 691] [depth= 2] . ( 4 sec) [ -4356.2641] [Branch lengths ] . ( 4 sec) [ -4349.8871] [GTR parameters ] . ( 4 sec) [ -4342.6541] [Alpha ][ 0.763484] . ( 4 sec) [ -4153.0020] [ 633] [depth= 4] . ( 4 sec) [ -4146.6572] [ 620] [depth= 2] . ( 4 sec) [ -4143.5154] [ 619] [depth= 1] . ( 5 sec) [ -4137.4152] [ 615] [depth= 1] . ( 5 sec) [ -4137.1993] [ 615] [depth= 1] . ( 5 sec) [ -4130.4967] [ 611] [depth= 1] . ( 5 sec) [ -4117.2262] [ 612] [depth= 1] . ( 5 sec) [ -4116.6140] [ 611] [depth= 1] . ( 5 sec) [ -4112.6974] [ 612] [depth= 1] . ( 6 sec) [ -4112.0309] [ 611] [depth= 1] . ( 6 sec) [ -4109.5884] [ 612] [depth= 1] . ( 7 sec) [ -4106.5193] [Branch lengths ] . ( 7 sec) [ -4105.9681] [GTR parameters ] . ( 7 sec) [ -4104.4890] [Alpha ][ 0.957370] . ( 8 sec) [ -4104.3827] [ 611] [depth= 1] . ( 10 sec) [ -4104.1598] [Branch lengths ] . ( 10 sec) [ -4104.1584] [GTR parameters ] . ( 10 sec) [ -4104.1575] [Alpha ][ 0.963141] . ( 25 sec) [ -4104.1532] [Branch lengths ] . ( 25 sec) [ -4104.1532] [Topology ] . ( 26 sec) [ -4104.1531] [Topology ] . ( 26 sec) [ -4104.1531] [GTR parameters ] . ( 26 sec) [ -4104.1531] [Alpha ][ 0.964104] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4104.153087. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10725.3548] [GTR parameters ] . ( 1 sec) [ -10497.7447] [Alpha ][ 0.500960] . ( 1 sec) [ -10308.8890] [ 1688] [depth= 6] . ( 1 sec) [ -10137.4578] [ 1659] [depth= 11] . ( 1 sec) [ -10085.5508] [ 1655] [depth= 2] . ( 1 sec) [ -10034.9365] [ 1654] [depth= 3] . ( 1 sec) [ -9873.1220] [ 1645] [depth= 7] . ( 1 sec) [ -9861.0980] [ 1644] [depth= 4] . ( 1 sec) [ -9745.9453] [ 1640] [depth= 14] . ( 1 sec) [ -9597.4308] [ 1641] [depth= 1] . ( 1 sec) [ -9383.9283] [ 1592] [depth= 17] . ( 1 sec) [ -9282.8561] [ 1568] [depth= 6] . ( 1 sec) [ -9207.7524] [ 1526] [depth= 16] . ( 1 sec) [ -9036.5963] [ 1520] [depth= 9] . ( 1 sec) [ -8538.3772] [ 1480] [depth= 8] . ( 1 sec) [ -8503.5667] [ 1472] [depth= 1] . ( 1 sec) [ -8476.1418] [ 1469] [depth= 6] . ( 1 sec) [ -8459.1062] [ 1469] [depth= 1] . ( 1 sec) [ -8248.3174] [ 1467] [depth= 13] . ( 1 sec) [ -8243.2395] [ 1419] [depth= 2] . ( 1 sec) [ -7967.2352] [ 1415] [depth= 12] . ( 1 sec) [ -7885.2616] [ 1397] [depth= 12] . ( 1 sec) [ -7625.1620] [ 1336] [depth= 17] . ( 1 sec) [ -7491.4932] [ 1296] [depth= 10] . ( 1 sec) [ -7464.2786] [ 1281] [depth= 3] . ( 1 sec) [ -7388.0860] [ 1265] [depth= 3] . ( 1 sec) [ -7369.3366] [ 1267] [depth= 6] . ( 1 sec) [ -7224.4682] [ 1254] [depth= 14] . ( 1 sec) [ -7050.5143] [ 1230] [depth= 5] . ( 1 sec) [ -6993.2190] [ 1222] [depth= 5] . ( 1 sec) [ -6814.2438] [ 1183] [depth= 5] . ( 2 sec) [ -6804.0115] [ 1180] [depth= 2] . ( 2 sec) [ -6760.6533] [ 1185] [depth= 2] . ( 2 sec) [ -6592.4391] [ 1131] [depth= 3] . ( 2 sec) [ -6539.7117] [ 1121] [depth= 1] . ( 2 sec) [ -6477.6715] [ 1090] [depth= 1] . ( 2 sec) [ -6422.3271] [ 1084] [depth= 5] . ( 2 sec) [ -6279.2882] [ 1072] [depth= 10] . ( 2 sec) [ -6219.9608] [ 1066] [depth= 4] . ( 2 sec) [ -6216.0674] [ 1066] [depth= 2] . ( 2 sec) [ -6084.7011] [ 1041] [depth= 7] . ( 2 sec) [ -6079.3416] [ 1043] [depth= 1] . ( 2 sec) [ -5950.2043] [ 997] [depth= 8] . ( 2 sec) [ -5921.1990] [ 995] [depth= 2] . ( 2 sec) [ -5829.1448] [ 957] [depth= 4] . ( 2 sec) [ -5727.6692] [ 938] [depth= 3] . ( 2 sec) [ -5702.3649] [ 932] [depth= 8] . ( 2 sec) [ -5680.2500] [ 926] [depth= 3] . ( 2 sec) [ -5641.6433] [ 924] [depth= 1] . ( 2 sec) [ -5640.6784] [ 898] [depth= 4] . ( 2 sec) [ -5546.7423] [ 895] [depth= 2] . ( 2 sec) [ -5418.8275] [ 867] [depth= 1] . ( 2 sec) [ -5288.0129] [ 844] [depth= 1] . ( 2 sec) [ -5129.4990] [ 814] [depth= 4] . ( 2 sec) [ -5095.0414] [ 813] [depth= 1] . ( 3 sec) [ -5078.0399] [ 800] [depth= 1] . ( 3 sec) [ -5077.2474] [ 802] [depth= 1] . ( 3 sec) [ -4992.6353] [ 780] [depth= 7] . ( 3 sec) [ -4956.1927] [ 776] [depth= 2] . ( 3 sec) [ -4926.2178] [ 776] [depth= 1] . ( 3 sec) [ -4881.0534] [ 772] [depth= 1] . ( 3 sec) [ -4868.5839] [ 755] [depth= 3] . ( 3 sec) [ -4766.0043] [ 747] [depth= 3] . ( 3 sec) [ -4762.8981] [ 747] [depth= 3] . ( 3 sec) [ -4692.5066] [ 738] [depth= 2] . ( 3 sec) [ -4675.4522] [ 736] [depth= 4] . ( 3 sec) [ -4661.0176] [ 742] [depth= 1] . ( 3 sec) [ -4638.9482] [ 732] [depth= 1] . ( 3 sec) [ -4634.4849] [ 714] [depth= 1] . ( 3 sec) [ -4631.6858] [ 714] [depth= 1] . ( 3 sec) [ -4627.9383] [ 715] [depth= 1] . ( 3 sec) [ -4627.4866] [ 703] [depth= 1] . ( 3 sec) [ -4621.6910] [ 702] [depth= 1] . ( 3 sec) [ -4587.7500] [ 690] [depth= 9] . ( 3 sec) [ -4484.5899] [ 694] [depth= 1] . ( 3 sec) [ -4464.9485] [ 688] [depth= 1] . ( 3 sec) [ -4460.9380] [ 687] [depth= 2] . ( 3 sec) [ -4451.8597] [ 687] [depth= 2] . ( 3 sec) [ -4435.1252] [ 698] [depth= 4] . ( 3 sec) [ -4398.7723] [ 687] [depth= 3] . ( 3 sec) [ -4356.3609] [ 679] [depth= 1] . ( 4 sec) [ -4314.1911] [Branch lengths ] . ( 4 sec) [ -4300.2657] [GTR parameters ] . ( 4 sec) [ -4292.2588] [Alpha ][ 0.780225] . ( 4 sec) [ -4291.3202] [ 676] [depth= 1] . ( 4 sec) [ -4291.0062] [ 676] [depth= 2] . ( 4 sec) [ -4276.4606] [ 671] [depth= 1] . ( 5 sec) [ -4262.4346] [ 664] [depth= 1] . ( 5 sec) [ -4262.4029] [ 662] [depth= 1] . ( 5 sec) [ -4242.2274] [ 653] [depth= 3] . ( 5 sec) [ -4240.9808] [ 652] [depth= 2] . ( 5 sec) [ -4228.4051] [ 647] [depth= 1] . ( 5 sec) [ -4216.5613] [ 640] [depth= 1] . ( 5 sec) [ -4214.5074] [ 639] [depth= 1] . ( 5 sec) [ -4213.6732] [ 639] [depth= 1] . ( 5 sec) [ -4188.2852] [ 626] [depth= 1] . ( 5 sec) [ -4184.3292] [ 625] [depth= 1] . ( 5 sec) [ -4140.7988] [ 612] [depth= 1] . ( 5 sec) [ -4139.4630] [ 611] [depth= 1] . ( 6 sec) [ -4120.5487] [ 615] [depth= 1] . ( 6 sec) [ -4113.7397] [ 611] [depth= 1] . ( 7 sec) [ -4109.9781] [Branch lengths ] . ( 7 sec) [ -4109.6147] [GTR parameters ] . ( 7 sec) [ -4108.4791] [Alpha ][ 0.952269] . ( 10 sec) [ -4107.0411] [Branch lengths ] . ( 25 sec) [ -4104.3047] [Branch lengths ] . ( 25 sec) [ -4104.3047] [Topology ] . ( 25 sec) [ -4104.1706] [Topology ] . ( 26 sec) [ -4104.1608] [Topology ] . ( 27 sec) [ -4104.1601] [Topology ] . ( 27 sec) [ -4104.1567] [GTR parameters ] . ( 27 sec) [ -4104.1530] [Alpha ][ 0.963882] . ( 27 sec) [ -4104.1530] [Topology ] . ( 27 sec) [ -4104.1529] [Topology ] . ( 27 sec) [ -4104.1529] [GTR parameters ] . ( 27 sec) [ -4104.1529] [Alpha ][ 0.963882] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4104.152883. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4111.471889 . ( 1 sec) [ -4110.4914] [GTR parameters ] . ( 1 sec) [ -4110.4093] [Alpha ][ 0.944284] . ( 1 sec) [ -4110.4093] [Topology ] . ( 1 sec) [ -4104.9272] [Topology ] . ( 2 sec) [ -4104.3231] [Topology ] . ( 2 sec) [ -4104.2064] [Topology ] . ( 3 sec) [ -4104.1784] [Topology ] . ( 3 sec) [ -4104.1711] [Topology ] . ( 4 sec) [ -4104.1691] [Topology ] . ( 5 sec) [ -4104.1685] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4104.168519 . ( 8 sec) [ -4104.1638] [GTR parameters ] . ( 8 sec) [ -4104.1535] [Alpha ][ 0.962692] . ( 8 sec) [ -4104.1535] [Topology ] . ( 8 sec) [ -4104.1529] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4104.152929 . ( 12 sec) [ -4104.1529] [GTR parameters ] . ( 12 sec) [ -4104.1529] [Alpha ][ 0.963655] . ( 12 sec) [ -4104.1529] [Topology ] . ( 12 sec) [ -4104.1528] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 19 sec) [ -4110.4914] [GTR parameters ] . ( 19 sec) [ -4110.4093] [Alpha ][ 0.944284] . ( 21 sec) [ -4109.8399] [ 611] [depth= 1] . ( 21 sec) [ -4109.7768] [ 612] [depth= 1] . ( 21 sec) [ -4109.6872] [ 612] [depth= 1] . ( 21 sec) [ -4109.6429] [ 612] [depth= 1] . ( 22 sec) [ -4104.4713] [Branch lengths ] . ( 22 sec) [ -4104.4705] [GTR parameters ] . ( 22 sec) [ -4104.4652] [Alpha ][ 0.958101] . ( 24 sec) [ -4104.4060] [ 611] [depth= 1] . ( 25 sec) [ -4104.1627] [Branch lengths ] . ( 25 sec) [ -4104.1609] [GTR parameters ] . ( 25 sec) [ -4104.1603] [Alpha ][ 0.962574] . ( 42 sec) [ -4104.1529] [Branch lengths ] . ( 42 sec) [ -4104.1529] [Topology ] . ( 43 sec) [ -4104.1527] [Topology ] . ( 43 sec) [ -4104.1527] [GTR parameters ] . ( 43 sec) [ -4104.1527] [Alpha ][ 0.963537] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4104.152764 . Log likelihood obtained after SPR moves : -4104.152700 . Log likelihood of the current tree: -4104.152700. . Printing the most likely tree in file 'data97.phy_phyml_tree.txt'... . Best log likelihood : -4104.152700 . Time used 0h0m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo