.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data26.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... . 317 patterns found. (out of a total of 500 sites) . 165 sites without polymorphism (33.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13063.9296] [GTR parameters ] . ( 1 sec) [ -12814.6466] [Alpha ][ 0.500960] . ( 1 sec) [ -12739.3851] [ 2148] [depth= 4] . ( 1 sec) [ -12525.8266] [ 2103] [depth= 11] . ( 1 sec) [ -11958.0597] [ 2078] [depth= 5] . ( 1 sec) [ -11623.1935] [ 2075] [depth= 6] . ( 1 sec) [ -11514.2669] [ 2045] [depth= 6] . ( 1 sec) [ -11494.8334] [ 2038] [depth= 6] . ( 1 sec) [ -11395.6723] [ 2024] [depth= 5] . ( 1 sec) [ -11312.3480] [ 2013] [depth= 2] . ( 1 sec) [ -11051.4876] [ 1956] [depth= 16] . ( 1 sec) [ -10637.7548] [ 1872] [depth= 14] . ( 1 sec) [ -10602.9131] [ 1873] [depth= 2] . ( 1 sec) [ -10387.8347] [ 1872] [depth= 1] . ( 1 sec) [ -10380.4202] [ 1871] [depth= 1] . ( 1 sec) [ -10346.9693] [ 1870] [depth= 4] . ( 1 sec) [ -10296.0214] [ 1855] [depth= 6] . ( 1 sec) [ -10119.9591] [ 1853] [depth= 2] . ( 1 sec) [ -10059.0339] [ 1835] [depth= 3] . ( 1 sec) [ -9897.7751] [ 1835] [depth= 2] . ( 1 sec) [ -9703.1889] [ 1772] [depth= 4] . ( 1 sec) [ -9552.1003] [ 1751] [depth= 5] . ( 1 sec) [ -9487.8692] [ 1750] [depth= 6] . ( 1 sec) [ -9305.1803] [ 1684] [depth= 14] . ( 1 sec) [ -9108.8378] [ 1644] [depth= 9] . ( 2 sec) [ -8949.3241] [ 1605] [depth= 7] . ( 2 sec) [ -8853.2015] [ 1608] [depth= 4] . ( 2 sec) [ -8750.2221] [ 1586] [depth= 6] . ( 2 sec) [ -8688.8884] [ 1568] [depth= 8] . ( 2 sec) [ -8561.7039] [ 1517] [depth= 11] . ( 2 sec) [ -8421.7587] [ 1515] [depth= 3] . ( 2 sec) [ -8391.5222] [ 1518] [depth= 1] . ( 2 sec) [ -8371.6542] [ 1515] [depth= 1] . ( 2 sec) [ -8240.6186] [ 1491] [depth= 17] . ( 2 sec) [ -8223.9371] [ 1491] [depth= 14] . ( 2 sec) [ -8209.1470] [ 1480] [depth= 1] . ( 2 sec) [ -8116.9876] [ 1461] [depth= 2] . ( 2 sec) [ -7984.3695] [ 1461] [depth= 8] . ( 2 sec) [ -7949.3598] [ 1456] [depth= 1] . ( 2 sec) [ -7937.1591] [ 1453] [depth= 2] . ( 2 sec) [ -7857.6582] [ 1405] [depth= 13] . ( 2 sec) [ -7847.4502] [ 1403] [depth= 1] . ( 2 sec) [ -7498.9532] [ 1402] [depth= 16] . ( 2 sec) [ -7175.6715] [ 1327] [depth= 11] . ( 2 sec) [ -7156.7266] [ 1327] [depth= 1] . ( 2 sec) [ -7046.5656] [ 1328] [depth= 1] . ( 2 sec) [ -6995.6021] [ 1267] [depth= 1] . ( 2 sec) [ -6953.7298] [ 1247] [depth= 3] . ( 2 sec) [ -6720.4504] [ 1194] [depth= 16] . ( 2 sec) [ -6594.9876] [ 1185] [depth= 1] . ( 2 sec) [ -6541.1776] [ 1177] [depth= 18] . ( 2 sec) [ -6539.8925] [ 1176] [depth= 2] . ( 2 sec) [ -6415.3248] [ 1133] [depth= 13] . ( 3 sec) [ -6404.3663] [ 1132] [depth= 3] . ( 3 sec) [ -6386.2698] [ 1127] [depth= 1] . ( 3 sec) [ -6380.9778] [ 1128] [depth= 1] . ( 3 sec) [ -6350.9395] [ 1125] [depth= 1] . ( 3 sec) [ -6323.8394] [ 1102] [depth= 11] . ( 3 sec) [ -6231.2317] [ 1090] [depth= 8] . ( 3 sec) [ -6204.1825] [ 1110] [depth= 1] . ( 3 sec) [ -6049.2727] [ 1066] [depth= 11] . ( 3 sec) [ -6048.0805] [ 1064] [depth= 1] . ( 3 sec) [ -6045.0900] [ 1064] [depth= 1] . ( 3 sec) [ -5971.3595] [ 1040] [depth= 2] . ( 3 sec) [ -5958.1851] [ 1034] [depth= 3] . ( 3 sec) [ -5947.8476] [ 1031] [depth= 1] . ( 3 sec) [ -5603.5183] [ 1030] [depth= 3] . ( 3 sec) [ -5524.1363] [ 1006] [depth= 2] . ( 3 sec) [ -5477.6823] [ 991] [depth= 3] . ( 3 sec) [ -5408.4233] [ 992] [depth= 1] . ( 3 sec) [ -5278.9691] [ 936] [depth= 14] . ( 3 sec) [ -5264.2283] [ 923] [depth= 2] . ( 3 sec) [ -5261.0929] [ 922] [depth= 1] . ( 3 sec) [ -5193.4989] [ 880] [depth= 2] . ( 3 sec) [ -5156.5409] [ 866] [depth= 1] . ( 3 sec) [ -5152.3733] [ 865] [depth= 1] . ( 3 sec) [ -5148.3239] [ 868] [depth= 1] . ( 4 sec) [ -5134.2902] [ 861] [depth= 1] . ( 4 sec) [ -5132.1452] [ 861] [depth= 1] . ( 4 sec) [ -5010.0958] [Branch lengths ] . ( 4 sec) [ -5006.1711] [GTR parameters ] . ( 4 sec) [ -4986.9992] [Alpha ][ 0.947072] . ( 4 sec) [ -4974.5351] [ 848] [depth= 2] . ( 5 sec) [ -4971.4055] [ 845] [depth= 1] . ( 5 sec) [ -4971.3816] [ 845] [depth= 1] . ( 5 sec) [ -4859.5946] [ 802] [depth= 6] . ( 5 sec) [ -4858.8908] [ 801] [depth= 1] . ( 5 sec) [ -4853.6143] [ 798] [depth= 2] . ( 6 sec) [ -4853.5794] [ 798] [depth= 1] . ( 6 sec) [ -4853.5004] [ 798] [depth= 1] . ( 7 sec) [ -4845.8705] [Branch lengths ] . ( 8 sec) [ -4845.7095] [GTR parameters ] . ( 8 sec) [ -4844.5044] [Alpha ][ 1.141584] . ( 11 sec) [ -4844.3562] [Branch lengths ] . ( 30 sec) [ -4844.3473] [Branch lengths ] . ( 30 sec) [ -4844.3473] [Topology ] . ( 30 sec) [ -4844.3470] [Topology ] . ( 30 sec) [ -4844.3448] [GTR parameters ] . ( 31 sec) [ -4844.3438] [Alpha ][ 1.147927] . ( 31 sec) [ -4844.3438] [Topology ] . ( 31 sec) [ -4844.3438] [Topology ] . ( 31 sec) [ -4844.3438] [GTR parameters ] . ( 31 sec) [ -4844.3438] [Alpha ][ 1.147927] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4844.343750. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13040.7939] [GTR parameters ] . ( 1 sec) [ -12798.0150] [Alpha ][ 0.500960] . ( 1 sec) [ -12576.7062] [ 2196] [depth= 9] . ( 1 sec) [ -12230.9526] [ 2160] [depth= 9] . ( 1 sec) [ -11945.3420] [ 2130] [depth= 4] . ( 1 sec) [ -11713.6943] [ 2126] [depth= 6] . ( 1 sec) [ -11632.5091] [ 2092] [depth= 1] . ( 1 sec) [ -11610.0315] [ 2091] [depth= 1] . ( 1 sec) [ -11573.3048] [ 2094] [depth= 1] . ( 1 sec) [ -11549.5461] [ 2089] [depth= 2] . ( 1 sec) [ -11485.1505] [ 2048] [depth= 2] . ( 1 sec) [ -11417.0932] [ 2045] [depth= 3] . ( 1 sec) [ -10955.3890] [ 1974] [depth= 10] . ( 1 sec) [ -10899.0997] [ 1972] [depth= 2] . ( 1 sec) [ -10882.1379] [ 1970] [depth= 1] . ( 1 sec) [ -10849.8553] [ 1967] [depth= 3] . ( 1 sec) [ -10311.1196] [ 1870] [depth= 20] . ( 1 sec) [ -10234.8870] [ 1863] [depth= 9] . ( 1 sec) [ -9764.7047] [ 1796] [depth= 19] . ( 2 sec) [ -9748.6569] [ 1792] [depth= 6] . ( 2 sec) [ -9545.5653] [ 1791] [depth= 2] . ( 2 sec) [ -9503.9173] [ 1777] [depth= 1] . ( 2 sec) [ -9383.6603] [ 1737] [depth= 11] . ( 2 sec) [ -9374.1924] [ 1741] [depth= 5] . ( 2 sec) [ -9360.6249] [ 1745] [depth= 1] . ( 2 sec) [ -9216.6493] [ 1705] [depth= 1] . ( 2 sec) [ -9113.2631] [ 1667] [depth= 4] . ( 2 sec) [ -8982.0739] [ 1652] [depth= 5] . ( 2 sec) [ -8929.6759] [ 1649] [depth= 2] . ( 2 sec) [ -8863.8524] [ 1645] [depth= 6] . ( 2 sec) [ -8780.8527] [ 1646] [depth= 1] . ( 2 sec) [ -8419.3243] [ 1568] [depth= 14] . ( 2 sec) [ -8371.6434] [ 1564] [depth= 1] . ( 2 sec) [ -8287.8418] [ 1542] [depth= 5] . ( 2 sec) [ -8280.4294] [ 1542] [depth= 1] . ( 2 sec) [ -7894.0800] [ 1445] [depth= 5] . ( 2 sec) [ -7891.8678] [ 1446] [depth= 1] . ( 2 sec) [ -7884.4070] [ 1445] [depth= 1] . ( 2 sec) [ -7866.9509] [ 1442] [depth= 2] . ( 2 sec) [ -7851.8554] [ 1447] [depth= 1] . ( 2 sec) [ -7821.9027] [ 1436] [depth= 2] . ( 2 sec) [ -7788.7404] [ 1430] [depth= 2] . ( 2 sec) [ -7781.0033] [ 1429] [depth= 3] . ( 2 sec) [ -7634.6795] [ 1419] [depth= 7] . ( 2 sec) [ -7597.8785] [ 1424] [depth= 7] . ( 2 sec) [ -7514.5569] [ 1373] [depth= 7] . ( 2 sec) [ -7389.8685] [ 1369] [depth= 6] . ( 2 sec) [ -7199.6397] [ 1313] [depth= 8] . ( 3 sec) [ -7180.2740] [ 1308] [depth= 4] . ( 3 sec) [ -7148.9328] [ 1310] [depth= 1] . ( 3 sec) [ -6921.1558] [ 1295] [depth= 4] . ( 3 sec) [ -6879.5935] [ 1282] [depth= 4] . ( 3 sec) [ -6776.3938] [ 1282] [depth= 3] . ( 3 sec) [ -6710.1454] [ 1253] [depth= 4] . ( 3 sec) [ -6655.7573] [ 1243] [depth= 1] . ( 3 sec) [ -6653.5183] [ 1245] [depth= 2] . ( 3 sec) [ -6474.2376] [ 1241] [depth= 1] . ( 3 sec) [ -6321.2333] [ 1195] [depth= 1] . ( 3 sec) [ -6098.9854] [ 1186] [depth= 5] . ( 3 sec) [ -6038.9937] [ 1153] [depth= 4] . ( 3 sec) [ -5965.9404] [ 1127] [depth= 6] . ( 3 sec) [ -5762.7794] [ 1042] [depth= 6] . ( 3 sec) [ -5736.6733] [ 1042] [depth= 1] . ( 3 sec) [ -5705.2362] [ 1043] [depth= 1] . ( 3 sec) [ -5619.3729] [ 1028] [depth= 4] . ( 3 sec) [ -5577.3896] [ 1027] [depth= 5] . ( 3 sec) [ -5556.9765] [ 1016] [depth= 1] . ( 3 sec) [ -5506.6423] [ 972] [depth= 3] . ( 3 sec) [ -5484.4423] [ 958] [depth= 1] . ( 3 sec) [ -5391.8503] [ 913] [depth= 5] . ( 4 sec) [ -5259.3581] [ 874] [depth= 5] . ( 4 sec) [ -5249.1293] [ 868] [depth= 1] . ( 4 sec) [ -5094.4494] [ 827] [depth= 3] . ( 4 sec) [ -5056.6116] [ 816] [depth= 1] . ( 4 sec) [ -5055.0499] [ 815] [depth= 1] . ( 4 sec) [ -4996.2659] [ 816] [depth= 1] . ( 4 sec) [ -4995.0509] [ 816] [depth= 2] . ( 4 sec) [ -4968.6167] [ 814] [depth= 2] . ( 4 sec) [ -4942.4435] [ 806] [depth= 2] . ( 4 sec) [ -4934.1486] [ 802] [depth= 1] . ( 4 sec) [ -4901.2139] [Branch lengths ] . ( 5 sec) [ -4893.7780] [GTR parameters ] . ( 5 sec) [ -4870.0923] [Alpha ][ 1.000132] . ( 5 sec) [ -4860.7845] [ 799] [depth= 1] . ( 6 sec) [ -4860.7653] [ 799] [depth= 1] . ( 6 sec) [ -4859.5214] [ 798] [depth= 1] . ( 8 sec) [ -4857.0539] [Branch lengths ] . ( 8 sec) [ -4857.0064] [GTR parameters ] . ( 8 sec) [ -4856.5478] [Alpha ][ 1.123036] . ( 11 sec) [ -4852.8325] [Branch lengths ] . ( 30 sec) [ -4845.1775] [Branch lengths ] . ( 30 sec) [ -4845.1775] [Topology ] . ( 31 sec) [ -4844.4231] [Topology ] . ( 31 sec) [ -4844.3677] [Topology ] . ( 32 sec) [ -4844.3635] [Topology ] . ( 33 sec) [ -4844.3631] [Topology ] . ( 33 sec) [ -4844.3594] [GTR parameters ] . ( 33 sec) [ -4844.3437] [Alpha ][ 1.147492] . ( 33 sec) [ -4844.3437] [Topology ] . ( 34 sec) [ -4844.3436] [Topology ] . ( 34 sec) [ -4844.3436] [GTR parameters ] . ( 34 sec) [ -4844.3436] [Alpha ][ 1.147492] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4844.343606. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13689.7669] [GTR parameters ] . ( 1 sec) [ -13433.2984] [Alpha ][ 0.500960] . ( 1 sec) [ -13225.1925] [ 2210] [depth= 8] . ( 1 sec) [ -12974.5977] [ 2179] [depth= 13] . ( 1 sec) [ -12931.3826] [ 2177] [depth= 3] . ( 1 sec) [ -12867.3281] [ 2177] [depth= 1] . ( 1 sec) [ -12853.0403] [ 2175] [depth= 8] . ( 1 sec) [ -12838.7019] [ 2175] [depth= 1] . ( 1 sec) [ -12746.8040] [ 2149] [depth= 3] . ( 1 sec) [ -12631.8056] [ 2138] [depth= 10] . ( 1 sec) [ -12396.8341] [ 2086] [depth= 1] . ( 1 sec) [ -12199.0638] [ 2054] [depth= 8] . ( 1 sec) [ -11855.6262] [ 1968] [depth= 6] . ( 1 sec) [ -11780.4787] [ 1947] [depth= 12] . ( 1 sec) [ -11759.9096] [ 1939] [depth= 7] . ( 1 sec) [ -11432.5940] [ 1937] [depth= 4] . ( 1 sec) [ -11028.8684] [ 1921] [depth= 2] . ( 1 sec) [ -10639.2704] [ 1920] [depth= 2] . ( 1 sec) [ -10230.6416] [ 1890] [depth= 1] . ( 1 sec) [ -10201.6885] [ 1887] [depth= 1] . ( 1 sec) [ -10127.8702] [ 1870] [depth= 9] . ( 1 sec) [ -9660.7291] [ 1791] [depth= 7] . ( 1 sec) [ -9608.6848] [ 1808] [depth= 9] . ( 1 sec) [ -9407.4688] [ 1719] [depth= 2] . ( 1 sec) [ -9281.6361] [ 1719] [depth= 9] . ( 1 sec) [ -8933.8523] [ 1718] [depth= 10] . ( 1 sec) [ -8848.6987] [ 1671] [depth= 2] . ( 1 sec) [ -8715.1212] [ 1660] [depth= 6] . ( 1 sec) [ -8548.9678] [ 1656] [depth= 13] . ( 1 sec) [ -8507.3935] [ 1629] [depth= 7] . ( 2 sec) [ -8432.3554] [ 1594] [depth= 1] . ( 2 sec) [ -8339.4191] [ 1583] [depth= 7] . ( 2 sec) [ -8074.1229] [ 1577] [depth= 8] . ( 2 sec) [ -7990.7771] [ 1578] [depth= 1] . ( 2 sec) [ -7922.9996] [ 1549] [depth= 3] . ( 2 sec) [ -7664.8968] [ 1485] [depth= 7] . ( 2 sec) [ -7266.2812] [ 1446] [depth= 6] . ( 2 sec) [ -7231.1282] [ 1446] [depth= 3] . ( 2 sec) [ -7112.7498] [ 1411] [depth= 1] . ( 2 sec) [ -7007.2931] [ 1374] [depth= 1] . ( 2 sec) [ -6976.4010] [ 1375] [depth= 2] . ( 2 sec) [ -6898.9521] [ 1358] [depth= 4] . ( 2 sec) [ -6847.9005] [ 1348] [depth= 1] . ( 2 sec) [ -6655.3226] [ 1309] [depth= 2] . ( 2 sec) [ -6501.7891] [ 1305] [depth= 6] . ( 2 sec) [ -6389.0433] [ 1273] [depth= 1] . ( 2 sec) [ -6381.3150] [ 1268] [depth= 1] . ( 2 sec) [ -6212.4446] [ 1200] [depth= 6] . ( 2 sec) [ -6077.4023] [ 1162] [depth= 2] . ( 2 sec) [ -6070.3146] [ 1158] [depth= 4] . ( 2 sec) [ -6030.9029] [ 1145] [depth= 6] . ( 2 sec) [ -6007.5993] [ 1145] [depth= 2] . ( 2 sec) [ -5975.3690] [ 1123] [depth= 3] . ( 2 sec) [ -5914.9840] [ 1119] [depth= 11] . ( 2 sec) [ -5904.1446] [ 1119] [depth= 1] . ( 2 sec) [ -5899.8759] [ 1118] [depth= 2] . ( 2 sec) [ -5871.6951] [ 1092] [depth= 2] . ( 3 sec) [ -5848.4505] [ 1074] [depth= 3] . ( 3 sec) [ -5788.1461] [ 1066] [depth= 4] . ( 3 sec) [ -5699.2935] [ 1043] [depth= 9] . ( 3 sec) [ -5645.0447] [ 1030] [depth= 1] . ( 3 sec) [ -5638.9015] [ 1029] [depth= 1] . ( 3 sec) [ -5619.9178] [ 1042] [depth= 1] . ( 3 sec) [ -5515.7000] [ 1000] [depth= 7] . ( 3 sec) [ -5506.0688] [ 998] [depth= 1] . ( 3 sec) [ -5496.2654] [ 1004] [depth= 1] . ( 3 sec) [ -5481.1762] [ 999] [depth= 1] . ( 3 sec) [ -5459.9276] [ 979] [depth= 1] . ( 3 sec) [ -5390.3025] [ 954] [depth= 4] . ( 3 sec) [ -5382.3631] [ 959] [depth= 4] . ( 3 sec) [ -5370.5917] [ 958] [depth= 2] . ( 3 sec) [ -5353.4711] [ 952] [depth= 1] . ( 3 sec) [ -5353.1887] [ 952] [depth= 1] . ( 3 sec) [ -5253.0689] [ 901] [depth= 5] . ( 3 sec) [ -5234.4342] [ 898] [depth= 3] . ( 3 sec) [ -5220.4527] [ 890] [depth= 2] . ( 4 sec) [ -5204.6854] [ 891] [depth= 1] . ( 4 sec) [ -5176.7341] [ 877] [depth= 1] . ( 4 sec) [ -5163.5087] [ 869] [depth= 2] . ( 4 sec) [ -5156.7658] [ 868] [depth= 1] . ( 4 sec) [ -5090.6694] [Branch lengths ] . ( 4 sec) [ -5084.7288] [GTR parameters ] . ( 4 sec) [ -5059.7922] [Alpha ][ 0.999923] . ( 5 sec) [ -5043.5903] [ 862] [depth= 2] . ( 5 sec) [ -5040.8282] [ 859] [depth= 1] . ( 5 sec) [ -5027.7238] [ 854] [depth= 1] . ( 5 sec) [ -4992.3386] [ 842] [depth= 1] . ( 6 sec) [ -4989.9033] [ 845] [depth= 1] . ( 6 sec) [ -4983.9720] [ 842] [depth= 1] . ( 6 sec) [ -4983.9587] [ 842] [depth= 1] . ( 6 sec) [ -4964.1352] [ 829] [depth= 1] . ( 6 sec) [ -4865.6017] [ 802] [depth= 2] . ( 6 sec) [ -4862.5863] [ 802] [depth= 1] . ( 7 sec) [ -4849.1462] [ 798] [depth= 2] . ( 7 sec) [ -4848.4746] [ 798] [depth= 1] . ( 8 sec) [ -4845.4988] [Branch lengths ] . ( 8 sec) [ -4845.0422] [GTR parameters ] . ( 8 sec) [ -4844.3806] [Alpha ][ 1.148148] . ( 11 sec) [ -4844.3474] [Branch lengths ] . ( 30 sec) [ -4844.3463] [Branch lengths ] . ( 30 sec) [ -4844.3463] [Topology ] . ( 31 sec) [ -4844.3462] [Topology ] . ( 31 sec) [ -4844.3437] [GTR parameters ] . ( 31 sec) [ -4844.3437] [Alpha ][ 1.148148] . ( 31 sec) [ -4844.3437] [Topology ] . ( 32 sec) [ -4844.3437] [Topology ] . ( 32 sec) [ -4844.3437] [GTR parameters ] . ( 32 sec) [ -4844.3437] [Alpha ][ 1.148148] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4844.343704. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13321.5570] [GTR parameters ] . ( 1 sec) [ -13071.2040] [Alpha ][ 0.500960] . ( 1 sec) [ -13045.4829] [ 2139] [depth= 8] . ( 1 sec) [ -12801.6189] [ 2108] [depth= 9] . ( 1 sec) [ -12477.7518] [ 2069] [depth= 2] . ( 1 sec) [ -12412.9030] [ 2038] [depth= 1] . ( 1 sec) [ -12223.3517] [ 1997] [depth= 4] . ( 1 sec) [ -12009.4259] [ 1984] [depth= 2] . ( 1 sec) [ -12007.6615] [ 1984] [depth= 1] . ( 1 sec) [ -11888.2124] [ 1951] [depth= 1] . ( 1 sec) [ -11718.5430] [ 1912] [depth= 7] . ( 1 sec) [ -11498.1708] [ 1897] [depth= 2] . ( 1 sec) [ -11452.3210] [ 1894] [depth= 1] . ( 1 sec) [ -11390.2956] [ 1872] [depth= 1] . ( 1 sec) [ -11103.5033] [ 1847] [depth= 2] . ( 1 sec) [ -11021.2232] [ 1846] [depth= 4] . ( 1 sec) [ -10831.3322] [ 1815] [depth= 1] . ( 1 sec) [ -10807.0186] [ 1811] [depth= 1] . ( 1 sec) [ -10595.8261] [ 1806] [depth= 11] . ( 1 sec) [ -10252.2242] [ 1811] [depth= 1] . ( 1 sec) [ -10027.7467] [ 1762] [depth= 17] . ( 2 sec) [ -9982.6555] [ 1749] [depth= 1] . ( 2 sec) [ -9800.1048] [ 1696] [depth= 6] . ( 2 sec) [ -9658.3132] [ 1656] [depth= 8] . ( 2 sec) [ -9591.2004] [ 1632] [depth= 10] . ( 2 sec) [ -9469.0182] [ 1632] [depth= 1] . ( 2 sec) [ -9468.1722] [ 1630] [depth= 9] . ( 2 sec) [ -9393.1250] [ 1596] [depth= 11] . ( 2 sec) [ -9368.1129] [ 1587] [depth= 1] . ( 2 sec) [ -9060.0967] [ 1546] [depth= 9] . ( 2 sec) [ -8940.4548] [ 1533] [depth= 1] . ( 2 sec) [ -8719.5534] [ 1511] [depth= 6] . ( 2 sec) [ -8346.8262] [ 1506] [depth= 8] . ( 2 sec) [ -8142.9931] [ 1469] [depth= 9] . ( 2 sec) [ -7978.8420] [ 1417] [depth= 1] . ( 2 sec) [ -7582.4210] [ 1413] [depth= 3] . ( 2 sec) [ -7549.3118] [ 1404] [depth= 1] . ( 2 sec) [ -7504.5501] [ 1400] [depth= 13] . ( 2 sec) [ -7446.9415] [ 1395] [depth= 4] . ( 2 sec) [ -7349.0326] [ 1316] [depth= 5] . ( 2 sec) [ -7325.7289] [ 1315] [depth= 8] . ( 2 sec) [ -7315.7972] [ 1313] [depth= 8] . ( 2 sec) [ -7264.7089] [ 1314] [depth= 2] . ( 2 sec) [ -7107.2837] [ 1265] [depth= 10] . ( 2 sec) [ -7077.0056] [ 1264] [depth= 1] . ( 2 sec) [ -6998.5012] [ 1219] [depth= 2] . ( 2 sec) [ -6876.1728] [ 1201] [depth= 8] . ( 3 sec) [ -6800.1169] [ 1206] [depth= 3] . ( 3 sec) [ -6679.7484] [ 1192] [depth= 1] . ( 3 sec) [ -6477.5179] [ 1171] [depth= 8] . ( 3 sec) [ -6374.8359] [ 1171] [depth= 1] . ( 3 sec) [ -6373.1482] [ 1171] [depth= 2] . ( 3 sec) [ -6346.8417] [ 1133] [depth= 3] . ( 3 sec) [ -6344.4807] [ 1136] [depth= 3] . ( 3 sec) [ -6151.7687] [ 1135] [depth= 1] . ( 3 sec) [ -5973.6172] [ 1070] [depth= 5] . ( 3 sec) [ -5949.9757] [ 1069] [depth= 4] . ( 3 sec) [ -5946.8264] [ 1070] [depth= 1] . ( 3 sec) [ -5738.4039] [ 1000] [depth= 4] . ( 3 sec) [ -5650.0567] [ 985] [depth= 4] . ( 3 sec) [ -5607.2686] [ 983] [depth= 1] . ( 3 sec) [ -5446.2106] [ 940] [depth= 5] . ( 3 sec) [ -5247.6412] [ 897] [depth= 3] . ( 3 sec) [ -5239.3148] [ 897] [depth= 2] . ( 3 sec) [ -5230.0012] [ 895] [depth= 3] . ( 3 sec) [ -5229.4891] [ 895] [depth= 1] . ( 3 sec) [ -5224.9676] [ 868] [depth= 2] . ( 3 sec) [ -5224.2839] [ 869] [depth= 1] . ( 3 sec) [ -5222.3169] [ 869] [depth= 1] . ( 4 sec) [ -5221.8668] [ 872] [depth= 1] . ( 4 sec) [ -5182.4564] [ 879] [depth= 2] . ( 4 sec) [ -5153.7362] [ 860] [depth= 2] . ( 4 sec) [ -5147.6861] [ 859] [depth= 1] . ( 4 sec) [ -5146.0832] [ 857] [depth= 1] . ( 4 sec) [ -5134.7585] [ 859] [depth= 2] . ( 4 sec) [ -5124.3075] [ 857] [depth= 1] . ( 4 sec) [ -5119.0286] [ 859] [depth= 1] . ( 4 sec) [ -5060.9508] [ 852] [depth= 2] . ( 4 sec) [ -5056.9747] [ 851] [depth= 1] . ( 4 sec) [ -4969.0039] [Branch lengths ] . ( 5 sec) [ -4965.0956] [GTR parameters ] . ( 5 sec) [ -4945.7676] [Alpha ][ 0.953951] . ( 5 sec) [ -4917.5276] [ 832] [depth= 6] . ( 5 sec) [ -4915.8907] [ 830] [depth= 1] . ( 5 sec) [ -4914.3224] [ 828] [depth= 1] . ( 5 sec) [ -4910.2822] [ 824] [depth= 5] . ( 5 sec) [ -4909.1294] [ 822] [depth= 3] . ( 5 sec) [ -4908.9787] [ 822] [depth= 1] . ( 5 sec) [ -4908.9320] [ 821] [depth= 1] . ( 5 sec) [ -4902.0000] [ 819] [depth= 1] . ( 5 sec) [ -4898.7582] [ 819] [depth= 1] . ( 6 sec) [ -4898.7331] [ 820] [depth= 1] . ( 6 sec) [ -4894.9831] [ 817] [depth= 1] . ( 6 sec) [ -4873.1699] [ 806] [depth= 2] . ( 6 sec) [ -4869.4537] [ 804] [depth= 1] . ( 6 sec) [ -4856.1498] [ 800] [depth= 2] . ( 7 sec) [ -4851.4650] [ 798] [depth= 2] . ( 8 sec) [ -4846.0146] [Branch lengths ] . ( 8 sec) [ -4845.5708] [GTR parameters ] . ( 8 sec) [ -4844.4798] [Alpha ][ 1.139901] . ( 11 sec) [ -4844.3555] [Branch lengths ] . ( 30 sec) [ -4844.3475] [Branch lengths ] . ( 30 sec) [ -4844.3475] [Topology ] . ( 31 sec) [ -4844.3472] [Topology ] . ( 31 sec) [ -4844.3454] [GTR parameters ] . ( 31 sec) [ -4844.3438] [Alpha ][ 1.147924] . ( 31 sec) [ -4844.3438] [Topology ] . ( 32 sec) [ -4844.3437] [Topology ] . ( 32 sec) [ -4844.3437] [GTR parameters ] . ( 32 sec) [ -4844.3437] [Alpha ][ 1.147924] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4844.343683. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13670.7521] [GTR parameters ] . ( 1 sec) [ -13410.6633] [Alpha ][ 0.500960] . ( 1 sec) [ -13343.7653] [ 2222] [depth= 7] . ( 1 sec) [ -12898.7037] [ 2189] [depth= 7] . ( 1 sec) [ -12870.2216] [ 2185] [depth= 4] . ( 1 sec) [ -12767.0128] [ 2185] [depth= 1] . ( 1 sec) [ -12763.7362] [ 2179] [depth= 1] . ( 1 sec) [ -12737.4523] [ 2179] [depth= 4] . ( 1 sec) [ -12575.7624] [ 2167] [depth= 6] . ( 1 sec) [ -12489.5905] [ 2211] [depth= 1] . ( 1 sec) [ -12124.5587] [ 2111] [depth= 2] . ( 1 sec) [ -11630.1791] [ 2019] [depth= 3] . ( 1 sec) [ -11378.1084] [ 2011] [depth= 6] . ( 1 sec) [ -11340.8466] [ 1996] [depth= 2] . ( 1 sec) [ -10901.7902] [ 1950] [depth= 9] . ( 1 sec) [ -10871.5427] [ 1926] [depth= 1] . ( 2 sec) [ -10822.1437] [ 1925] [depth= 2] . ( 2 sec) [ -10766.7656] [ 1923] [depth= 6] . ( 2 sec) [ -10708.4328] [ 1923] [depth= 1] . ( 2 sec) [ -10527.6397] [ 1902] [depth= 8] . ( 2 sec) [ -10523.6438] [ 1902] [depth= 1] . ( 2 sec) [ -10428.3590] [ 1899] [depth= 15] . ( 2 sec) [ -10030.3332] [ 1853] [depth= 10] . ( 2 sec) [ -9762.0058] [ 1812] [depth= 13] . ( 2 sec) [ -9604.8018] [ 1757] [depth= 12] . ( 2 sec) [ -9539.8653] [ 1757] [depth= 1] . ( 2 sec) [ -9369.7914] [ 1707] [depth= 3] . ( 2 sec) [ -9261.7846] [ 1707] [depth= 1] . ( 2 sec) [ -9098.2169] [ 1690] [depth= 9] . ( 2 sec) [ -9079.2987] [ 1690] [depth= 1] . ( 2 sec) [ -8920.1225] [ 1638] [depth= 4] . ( 2 sec) [ -8879.8459] [ 1630] [depth= 1] . ( 2 sec) [ -8876.6999] [ 1630] [depth= 1] . ( 2 sec) [ -8681.4646] [ 1591] [depth= 7] . ( 2 sec) [ -8637.8243] [ 1581] [depth= 2] . ( 2 sec) [ -8633.7810] [ 1585] [depth= 1] . ( 2 sec) [ -8476.9835] [ 1539] [depth= 7] . ( 2 sec) [ -8308.5853] [ 1528] [depth= 8] . ( 2 sec) [ -8283.8143] [ 1521] [depth= 1] . ( 2 sec) [ -8104.9530] [ 1509] [depth= 10] . ( 2 sec) [ -8090.7223] [ 1508] [depth= 8] . ( 2 sec) [ -8053.9535] [ 1503] [depth= 1] . ( 2 sec) [ -7886.8657] [ 1467] [depth= 9] . ( 2 sec) [ -7708.6347] [ 1460] [depth= 4] . ( 2 sec) [ -7678.5419] [ 1471] [depth= 1] . ( 2 sec) [ -7665.0739] [ 1460] [depth= 1] . ( 3 sec) [ -7490.1394] [ 1413] [depth= 5] . ( 3 sec) [ -7455.3015] [ 1404] [depth= 1] . ( 3 sec) [ -7350.3967] [ 1382] [depth= 8] . ( 3 sec) [ -7182.1612] [ 1326] [depth= 8] . ( 3 sec) [ -7012.1871] [ 1283] [depth= 7] . ( 3 sec) [ -6969.2971] [ 1278] [depth= 10] . ( 3 sec) [ -6807.4278] [ 1225] [depth= 7] . ( 3 sec) [ -6723.4744] [ 1220] [depth= 6] . ( 3 sec) [ -6722.3356] [ 1204] [depth= 3] . ( 3 sec) [ -6661.2795] [ 1197] [depth= 4] . ( 3 sec) [ -6645.7786] [ 1198] [depth= 2] . ( 3 sec) [ -6379.7438] [ 1174] [depth= 2] . ( 3 sec) [ -6277.2188] [ 1167] [depth= 6] . ( 3 sec) [ -6220.8465] [ 1147] [depth= 3] . ( 3 sec) [ -6207.2244] [ 1146] [depth= 1] . ( 3 sec) [ -6191.2210] [ 1142] [depth= 1] . ( 3 sec) [ -6181.1141] [ 1144] [depth= 1] . ( 3 sec) [ -6140.7172] [ 1134] [depth= 3] . ( 3 sec) [ -6099.0771] [ 1144] [depth= 1] . ( 3 sec) [ -5916.8484] [ 1077] [depth= 8] . ( 3 sec) [ -5843.4292] [ 1076] [depth= 1] . ( 3 sec) [ -5838.4233] [ 1072] [depth= 2] . ( 3 sec) [ -5723.0319] [ 1049] [depth= 1] . ( 4 sec) [ -5696.2252] [ 1039] [depth= 1] . ( 4 sec) [ -5537.6260] [ 988] [depth= 5] . ( 4 sec) [ -5519.0202] [ 985] [depth= 1] . ( 4 sec) [ -5518.0409] [ 986] [depth= 2] . ( 4 sec) [ -5472.7852] [ 972] [depth= 2] . ( 4 sec) [ -5395.6294] [ 939] [depth= 1] . ( 4 sec) [ -5229.0868] [ 899] [depth= 1] . ( 4 sec) [ -5107.4519] [ 889] [depth= 3] . ( 4 sec) [ -5088.9607] [ 891] [depth= 1] . ( 4 sec) [ -5086.8780] [ 891] [depth= 1] . ( 4 sec) [ -5085.9722] [ 893] [depth= 1] . ( 4 sec) [ -5060.3192] [ 883] [depth= 1] . ( 4 sec) [ -5037.9556] [ 870] [depth= 1] . ( 4 sec) [ -5036.8366] [ 868] [depth= 1] . ( 4 sec) [ -5023.6533] [ 865] [depth= 3] . ( 4 sec) [ -5018.9561] [ 864] [depth= 2] . ( 4 sec) [ -4996.8665] [Branch lengths ] . ( 5 sec) [ -4992.6494] [GTR parameters ] . ( 5 sec) [ -4974.4428] [Alpha ][ 0.933029] . ( 5 sec) [ -4883.7751] [ 812] [depth= 5] . ( 5 sec) [ -4876.6280] [ 809] [depth= 1] . ( 5 sec) [ -4874.4826] [ 807] [depth= 1] . ( 5 sec) [ -4867.0149] [ 804] [depth= 1] . ( 5 sec) [ -4860.6408] [ 800] [depth= 1] . ( 6 sec) [ -4858.9437] [ 798] [depth= 1] . ( 8 sec) [ -4855.1771] [Branch lengths ] . ( 8 sec) [ -4854.9337] [GTR parameters ] . ( 8 sec) [ -4853.7461] [Alpha ][ 1.122002] . ( 11 sec) [ -4848.3049] [Branch lengths ] . ( 30 sec) [ -4844.3955] [Branch lengths ] . ( 30 sec) [ -4844.3955] [Topology ] . ( 31 sec) [ -4844.3707] [Topology ] . ( 32 sec) [ -4844.3691] [Topology ] . ( 32 sec) [ -4844.3689] [Topology ] . ( 33 sec) [ -4844.3606] [GTR parameters ] . ( 33 sec) [ -4844.3438] [Alpha ][ 1.147387] . ( 33 sec) [ -4844.3438] [Topology ] . ( 33 sec) [ -4844.3436] [Topology ] . ( 33 sec) [ -4844.3435] [GTR parameters ] . ( 33 sec) [ -4844.3435] [Alpha ][ 1.148535] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4844.343542. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4865.141674 . ( 0 sec) [ -4860.9842] [GTR parameters ] . ( 1 sec) [ -4860.5234] [Alpha ][ 1.125341] . ( 1 sec) [ -4860.5234] [Topology ] . ( 1 sec) [ -4845.9236] [Topology ] . ( 2 sec) [ -4844.6195] [Topology ] . ( 3 sec) [ -4844.4342] [Topology ] . ( 3 sec) [ -4844.3950] [Topology ] . ( 4 sec) [ -4844.3845] [Topology ] . ( 4 sec) [ -4844.3813] [Topology ] . ( 5 sec) [ -4844.3803] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4844.380302 . ( 9 sec) [ -4844.3571] [GTR parameters ] . ( 9 sec) [ -4844.3447] [Alpha ][ 1.146930] . ( 9 sec) [ -4844.3447] [Topology ] . ( 10 sec) [ -4844.3440] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4844.343980 . ( 14 sec) [ -4844.3440] [GTR parameters ] . ( 14 sec) [ -4844.3439] [Alpha ][ 1.148077] . ( 14 sec) [ -4844.3439] [Topology ] . ( 14 sec) [ -4844.3437] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -4860.9842] [GTR parameters ] . ( 23 sec) [ -4860.5234] [Alpha ][ 1.125341] . ( 23 sec) [ -4856.9701] [ 798] [depth= 1] . ( 24 sec) [ -4853.6229] [ 798] [depth= 1] . ( 25 sec) [ -4853.2771] [ 798] [depth= 1] . ( 26 sec) [ -4844.4682] [Branch lengths ] . ( 26 sec) [ -4844.4460] [GTR parameters ] . ( 26 sec) [ -4844.4375] [Alpha ][ 1.144208] . ( 29 sec) [ -4844.3483] [Branch lengths ] . ( 48 sec) [ -4844.3440] [Branch lengths ] . ( 48 sec) [ -4844.3440] [Topology ] . ( 48 sec) [ -4844.3439] [Topology ] . ( 49 sec) [ -4844.3438] [GTR parameters ] . ( 49 sec) [ -4844.3435] [Alpha ][ 1.147835] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4844.343707 . Log likelihood obtained after SPR moves : -4844.343476 . Log likelihood of the current tree: -4844.343476. . Printing the most likely tree in file 'data26.phy_phyml_tree.txt'... . Best log likelihood : -4844.343476 . Time used 0h0m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo