.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2675_51x1537_2006.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... . 607 patterns found. (out of a total of 1537 sites) . 978 sites without polymorphism (63.63%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -34072.8971] [GTR parameters ] . ( 1 sec) [ -33181.7077] [Alpha ][ 0.500960] . ( 1 sec) [ -32621.5326] [ 4755] [depth= 9] . ( 1 sec) [ -32215.9875] [ 4694] [depth= 6] . ( 2 sec) [ -31773.1694] [ 4669] [depth= 1] . ( 2 sec) [ -31116.5613] [ 4657] [depth= 9] . ( 2 sec) [ -30915.4529] [ 4625] [depth= 1] . ( 2 sec) [ -30178.3476] [ 4519] [depth= 5] . ( 2 sec) [ -29817.8748] [ 4524] [depth= 1] . ( 2 sec) [ -29348.5441] [ 4482] [depth= 7] . ( 2 sec) [ -29066.8693] [ 4448] [depth= 1] . ( 2 sec) [ -28839.9266] [ 4440] [depth= 8] . ( 2 sec) [ -28690.6152] [ 4383] [depth= 4] . ( 2 sec) [ -28267.7564] [ 4293] [depth= 9] . ( 3 sec) [ -27945.0453] [ 4240] [depth= 4] . ( 3 sec) [ -27513.7764] [ 4164] [depth= 10] . ( 3 sec) [ -27402.2802] [ 4148] [depth= 3] . ( 3 sec) [ -26915.9734] [ 4141] [depth= 3] . ( 3 sec) [ -26278.3216] [ 4080] [depth= 6] . ( 3 sec) [ -25894.4311] [ 4007] [depth= 10] . ( 3 sec) [ -25365.3185] [ 3985] [depth= 1] . ( 3 sec) [ -24868.9886] [ 3880] [depth= 3] . ( 3 sec) [ -24770.3085] [ 3863] [depth= 1] . ( 3 sec) [ -24122.9037] [ 3853] [depth= 3] . ( 3 sec) [ -23854.5091] [ 3755] [depth= 6] . ( 4 sec) [ -22994.1797] [ 3721] [depth= 8] . ( 4 sec) [ -22897.6731] [ 3724] [depth= 5] . ( 4 sec) [ -22549.0677] [ 3722] [depth= 12] . ( 4 sec) [ -22196.8534] [ 3601] [depth= 3] . ( 4 sec) [ -21996.4020] [ 3544] [depth= 2] . ( 4 sec) [ -21405.0175] [ 3466] [depth= 3] . ( 4 sec) [ -20608.7042] [ 3464] [depth= 6] . ( 4 sec) [ -20568.6969] [ 3453] [depth= 10] . ( 4 sec) [ -20276.2889] [ 3347] [depth= 11] . ( 4 sec) [ -20272.7208] [ 3348] [depth= 3] . ( 4 sec) [ -19970.0286] [ 3313] [depth= 1] . ( 4 sec) [ -19961.6655] [ 3313] [depth= 2] . ( 5 sec) [ -19798.6294] [ 3313] [depth= 12] . ( 5 sec) [ -18408.8133] [ 3244] [depth= 6] . ( 5 sec) [ -18235.6604] [ 3221] [depth= 2] . ( 5 sec) [ -18113.9919] [ 3220] [depth= 4] . ( 5 sec) [ -18103.3659] [ 3220] [depth= 1] . ( 5 sec) [ -17788.1295] [ 3165] [depth= 13] . ( 5 sec) [ -17407.1435] [ 3165] [depth= 13] . ( 5 sec) [ -17398.1092] [ 3164] [depth= 1] . ( 6 sec) [ -17054.3263] [ 3027] [depth= 3] . ( 6 sec) [ -17053.9264] [ 3028] [depth= 12] . ( 6 sec) [ -17044.2154] [ 3028] [depth= 12] . ( 6 sec) [ -16576.8197] [ 2902] [depth= 7] . ( 6 sec) [ -15993.9679] [ 2913] [depth= 1] . ( 6 sec) [ -15492.9312] [ 2874] [depth= 10] . ( 6 sec) [ -15330.1102] [ 2866] [depth= 8] . ( 6 sec) [ -15135.6565] [ 2865] [depth= 1] . ( 6 sec) [ -14706.8773] [ 2638] [depth= 10] . ( 7 sec) [ -14637.7644] [ 2637] [depth= 1] . ( 7 sec) [ -14245.8375] [ 2631] [depth= 6] . ( 7 sec) [ -14241.0131] [ 2636] [depth= 8] . ( 8 sec) [ -14214.7352] [ 2636] [depth= 1] . ( 8 sec) [ -13845.0427] [ 2486] [depth= 12] . ( 8 sec) [ -13786.2657] [ 2474] [depth= 1] . ( 8 sec) [ -13757.8021] [ 2463] [depth= 1] . ( 8 sec) [ -13442.1600] [ 2408] [depth= 4] . ( 8 sec) [ -13250.9472] [ 2419] [depth= 1] . ( 8 sec) [ -13072.4182] [ 2389] [depth= 1] . ( 9 sec) [ -13030.3829] [ 2361] [depth= 4] . ( 9 sec) [ -12684.7403] [ 2360] [depth= 2] . ( 9 sec) [ -12401.8504] [ 2240] [depth= 9] . ( 9 sec) [ -12282.5965] [ 2266] [depth= 1] . ( 9 sec) [ -12023.0113] [ 2212] [depth= 10] . ( 9 sec) [ -11975.6669] [ 2212] [depth= 3] . ( 9 sec) [ -11975.2175] [ 2212] [depth= 1] . ( 9 sec) [ -11849.3642] [ 2172] [depth= 1] . ( 9 sec) [ -11610.7858] [ 2117] [depth= 3] . ( 9 sec) [ -11483.7487] [ 2049] [depth= 4] . ( 9 sec) [ -11160.4274] [ 2002] [depth= 5] . ( 10 sec) [ -11157.1878] [ 2002] [depth= 1] . ( 10 sec) [ -10996.5704] [ 1991] [depth= 2] . ( 10 sec) [ -10968.4271] [ 1991] [depth= 1] . ( 10 sec) [ -10822.7161] [ 1961] [depth= 5] . ( 10 sec) [ -10652.1813] [ 1925] [depth= 4] . ( 10 sec) [ -10594.1201] [ 1911] [depth= 3] . ( 10 sec) [ -10414.9817] [ 1881] [depth= 4] . ( 10 sec) [ -10408.5752] [ 1885] [depth= 13] . ( 10 sec) [ -10221.4583] [ 1841] [depth= 1] . ( 11 sec) [ -10191.6099] [ 1842] [depth= 1] . ( 11 sec) [ -10180.8095] [ 1841] [depth= 1] . ( 11 sec) [ -10046.9633] [ 1789] [depth= 1] . ( 11 sec) [ -10046.8854] [ 1789] [depth= 1] . ( 11 sec) [ -10027.4159] [ 1790] [depth= 1] . ( 11 sec) [ -10024.5138] [ 1782] [depth= 5] . ( 11 sec) [ -9952.2114] [ 1765] [depth= 3] . ( 12 sec) [ -9945.5318] [ 1765] [depth= 1] . ( 12 sec) [ -9876.7301] [ 1703] [depth= 6] . ( 12 sec) [ -9744.3725] [ 1631] [depth= 4] . ( 12 sec) [ -9666.3588] [ 1589] [depth= 1] . ( 12 sec) [ -9662.3637] [ 1591] [depth= 3] . ( 12 sec) [ -9654.2154] [ 1589] [depth= 2] . ( 12 sec) [ -9646.4960] [ 1594] [depth= 3] . ( 12 sec) [ -9646.4727] [ 1594] [depth= 2] . ( 13 sec) [ -9597.5020] [ 1566] [depth= 2] . ( 13 sec) [ -9577.1503] [ 1542] [depth= 4] . ( 13 sec) [ -9239.8974] [ 1540] [depth= 3] . ( 13 sec) [ -8817.3915] [ 1412] [depth= 2] . ( 13 sec) [ -8817.1466] [ 1412] [depth= 1] . ( 13 sec) [ -8810.7895] [ 1412] [depth= 1] . ( 13 sec) [ -8776.1536] [ 1412] [depth= 1] . ( 14 sec) [ -8764.7887] [ 1410] [depth= 2] . ( 14 sec) [ -8754.1806] [ 1408] [depth= 2] . ( 14 sec) [ -8743.5210] [ 1404] [depth= 1] . ( 14 sec) [ -8743.2385] [ 1404] [depth= 1] . ( 14 sec) [ -8741.5480] [ 1404] [depth= 1] . ( 14 sec) [ -8741.1786] [ 1404] [depth= 1] . ( 14 sec) [ -8690.3279] [ 1403] [depth= 1] . ( 15 sec) [ -8689.9167] [ 1403] [depth= 1] . ( 15 sec) [ -8661.4953] [ 1404] [depth= 2] . ( 15 sec) [ -8603.4151] [ 1373] [depth= 1] . ( 15 sec) [ -8536.3322] [ 1361] [depth= 1] . ( 15 sec) [ -8523.6730] [ 1361] [depth= 2] . ( 15 sec) [ -8242.6648] [Branch lengths ] . ( 19 sec) [ -8236.1404] [GTR parameters ] . ( 19 sec) [ -8163.6492] [Alpha ][ 0.250961] . ( 19 sec) [ -8142.2775] [ 1357] [depth= 4] . ( 19 sec) [ -8066.8499] [ 1329] [depth= 2] . ( 19 sec) [ -8053.6540] [ 1299] [depth= 5] . ( 20 sec) [ -8053.4332] [ 1299] [depth= 1] . ( 20 sec) [ -8052.8717] [ 1300] [depth= 1] . ( 20 sec) [ -8052.8413] [ 1300] [depth= 2] . ( 20 sec) [ -8035.0009] [ 1292] [depth= 4] . ( 21 sec) [ -8033.9368] [ 1292] [depth= 1] . ( 21 sec) [ -8017.8317] [ 1285] [depth= 1] . ( 21 sec) [ -8012.7872] [ 1286] [depth= 2] . ( 21 sec) [ -8011.8885] [ 1285] [depth= 1] . ( 22 sec) [ -8010.8389] [ 1284] [depth= 2] . ( 22 sec) [ -8004.1426] [ 1283] [depth= 1] . ( 22 sec) [ -7999.9318] [ 1283] [depth= 2] . ( 22 sec) [ -7998.9371] [ 1283] [depth= 1] . ( 22 sec) [ -7990.1377] [ 1280] [depth= 1] . ( 22 sec) [ -7977.1973] [ 1274] [depth= 1] . ( 23 sec) [ -7976.2164] [ 1275] [depth= 2] . ( 23 sec) [ -7975.9661] [ 1275] [depth= 1] . ( 23 sec) [ -7975.9518] [ 1275] [depth= 1] . ( 23 sec) [ -7913.3980] [ 1242] [depth= 2] . ( 23 sec) [ -7907.9840] [ 1240] [depth= 4] . ( 24 sec) [ -7907.8830] [ 1240] [depth= 3] . ( 24 sec) [ -7907.8469] [ 1240] [depth= 2] . ( 25 sec) [ -7907.0505] [ 1240] [depth= 1] . ( 26 sec) [ -7906.9009] [ 1240] [depth= 1] . ( 26 sec) [ -7881.3328] [ 1191] [depth= 6] . ( 26 sec) [ -7881.2081] [ 1193] [depth= 1] . ( 26 sec) [ -7881.1772] [ 1193] [depth= 1] . ( 27 sec) [ -7879.7525] [ 1195] [depth= 1] . ( 27 sec) [ -7879.5090] [ 1195] [depth= 1] . ( 27 sec) [ -7879.4803] [ 1195] [depth= 1] . ( 28 sec) [ -7877.7120] [ 1194] [depth= 1] . ( 29 sec) [ -7877.5587] [ 1194] [depth= 2] . ( 31 sec) [ -7877.5118] [ 1194] [depth= 1] . ( 31 sec) [ -7877.4211] [ 1194] [depth= 2] . ( 32 sec) [ -7877.3598] [ 1194] [depth= 1] . ( 32 sec) [ -7877.3160] [ 1194] [depth= 1] . ( 33 sec) [ -7877.2818] [ 1194] [depth= 1] . ( 34 sec) [ -7862.0689] [Branch lengths ] . ( 37 sec) [ -7861.0273] [GTR parameters ] . ( 37 sec) [ -7861.0211] [Alpha ][ 0.252772] . ( 39 sec) [ -7860.7669] [ 1194] [depth= 1] . ( 39 sec) [ -7860.1103] [ 1193] [depth= 1] . ( 40 sec) [ -7860.0809] [ 1193] [depth= 2] . ( 43 sec) [ -7860.0705] [ 1193] [depth= 2] . ( 55 sec) [ -7855.9657] [Branch lengths ] . ( 57 sec) [ -7855.9344] [GTR parameters ] . ( 57 sec) [ -7855.9340] [Alpha ][ 0.253245] . ( 74 sec) [ -7855.7220] [Branch lengths ] . ( 120 sec) [ -7855.7023] [Branch lengths ] . ( 120 sec) [ -7855.7023] [Topology ] . ( 121 sec) [ -7855.7006] [Topology ] . ( 123 sec) [ -7855.6998] [Topology ] . ( 123 sec) [ -7855.6997] [GTR parameters ] . ( 123 sec) [ -7855.6997] [Alpha ][ 0.252992] . ( 123 sec) [ -7855.6997] [Topology ] . ( 124 sec) [ -7855.6975] [Topology ] . ( 126 sec) [ -7855.6880] [Topology ] . ( 127 sec) [ -7855.6827] [Topology ] . ( 128 sec) [ -7855.6796] [Topology ] . ( 130 sec) [ -7855.6779] [Topology ] . ( 131 sec) [ -7855.6770] [Topology ] . ( 132 sec) [ -7855.6742] [GTR parameters ] . ( 132 sec) [ -7855.6741] [Alpha ][ 0.253245] . ( 132 sec) [ -7855.6741] [Topology ] . ( 133 sec) [ -7855.6734] [Topology ] . ( 133 sec) [ -7855.6734] [GTR parameters ] . ( 134 sec) [ -7855.6734] [Alpha ][ 0.253245] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.673425. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -36525.0652] [GTR parameters ] . ( 1 sec) [ -35614.2465] [Alpha ][ 0.500960] . ( 2 sec) [ -34840.0124] [ 4494] [depth= 11] . ( 2 sec) [ -34307.7958] [ 4441] [depth= 10] . ( 2 sec) [ -33817.5663] [ 4399] [depth= 1] . ( 2 sec) [ -33224.5901] [ 4339] [depth= 10] . ( 2 sec) [ -32640.9866] [ 4251] [depth= 1] . ( 2 sec) [ -32330.7201] [ 4243] [depth= 12] . ( 2 sec) [ -31509.1866] [ 4235] [depth= 1] . ( 2 sec) [ -30839.6396] [ 4222] [depth= 3] . ( 2 sec) [ -30546.7640] [ 4161] [depth= 1] . ( 2 sec) [ -29869.1858] [ 4147] [depth= 2] . ( 2 sec) [ -29790.4807] [ 4148] [depth= 1] . ( 2 sec) [ -28186.5924] [ 4140] [depth= 3] . ( 2 sec) [ -27535.7274] [ 4077] [depth= 7] . ( 2 sec) [ -27465.0690] [ 4063] [depth= 5] . ( 3 sec) [ -26974.1875] [ 4036] [depth= 2] . ( 3 sec) [ -26674.9976] [ 4029] [depth= 4] . ( 3 sec) [ -25969.1637] [ 3962] [depth= 7] . ( 3 sec) [ -25839.5107] [ 3960] [depth= 8] . ( 3 sec) [ -25604.2680] [ 3905] [depth= 1] . ( 3 sec) [ -25414.1934] [ 3855] [depth= 10] . ( 3 sec) [ -23810.9366] [ 3668] [depth= 14] . ( 3 sec) [ -23744.5456] [ 3663] [depth= 11] . ( 3 sec) [ -23410.9803] [ 3590] [depth= 10] . ( 3 sec) [ -23345.7677] [ 3586] [depth= 2] . ( 3 sec) [ -22057.8139] [ 3432] [depth= 9] . ( 3 sec) [ -21233.3082] [ 3331] [depth= 16] . ( 3 sec) [ -21229.6016] [ 3333] [depth= 1] . ( 4 sec) [ -20726.0963] [ 3162] [depth= 11] . ( 4 sec) [ -20039.8083] [ 3112] [depth= 18] . ( 4 sec) [ -19931.9375] [ 3090] [depth= 1] . ( 4 sec) [ -19921.6455] [ 3138] [depth= 1] . ( 4 sec) [ -19115.0928] [ 3047] [depth= 20] . ( 4 sec) [ -18780.6305] [ 2989] [depth= 1] . ( 4 sec) [ -18264.7098] [ 2987] [depth= 20] . ( 4 sec) [ -18186.4691] [ 2956] [depth= 1] . ( 4 sec) [ -17816.5496] [ 2912] [depth= 16] . ( 4 sec) [ -17793.5488] [ 2920] [depth= 1] . ( 4 sec) [ -16677.1579] [ 2857] [depth= 2] . ( 5 sec) [ -16063.8291] [ 2762] [depth= 18] . ( 5 sec) [ -14840.7633] [ 2605] [depth= 2] . ( 5 sec) [ -14760.7715] [ 2605] [depth= 1] . ( 5 sec) [ -14527.5470] [ 2529] [depth= 9] . ( 5 sec) [ -14237.5560] [ 2496] [depth= 4] . ( 5 sec) [ -13917.6833] [ 2388] [depth= 7] . ( 5 sec) [ -13912.9783] [ 2388] [depth= 1] . ( 5 sec) [ -13715.5719] [ 2386] [depth= 15] . ( 5 sec) [ -13254.2590] [ 2303] [depth= 4] . ( 5 sec) [ -13169.7126] [ 2301] [depth= 3] . ( 5 sec) [ -12638.1375] [ 2219] [depth= 8] . ( 5 sec) [ -12636.1454] [ 2221] [depth= 2] . ( 6 sec) [ -12613.7302] [ 2203] [depth= 10] . ( 6 sec) [ -12255.0108] [ 2131] [depth= 9] . ( 6 sec) [ -12188.0303] [ 2132] [depth= 1] . ( 6 sec) [ -11830.4282] [ 2014] [depth= 7] . ( 6 sec) [ -11825.9814] [ 2013] [depth= 2] . ( 6 sec) [ -11803.9021] [ 2009] [depth= 2] . ( 6 sec) [ -11802.7214] [ 2009] [depth= 1] . ( 6 sec) [ -11794.8157] [ 2009] [depth= 1] . ( 6 sec) [ -11783.6144] [ 1977] [depth= 2] . ( 6 sec) [ -11777.2484] [ 1977] [depth= 1] . ( 6 sec) [ -11708.0185] [ 1965] [depth= 7] . ( 7 sec) [ -11676.0049] [ 1965] [depth= 12] . ( 7 sec) [ -11365.1838] [ 1963] [depth= 4] . ( 7 sec) [ -11365.0770] [ 1963] [depth= 1] . ( 7 sec) [ -11356.2483] [ 1962] [depth= 2] . ( 7 sec) [ -11212.2455] [ 1947] [depth= 2] . ( 7 sec) [ -11185.0233] [ 1945] [depth= 1] . ( 7 sec) [ -10907.1647] [ 1925] [depth= 3] . ( 8 sec) [ -10900.7776] [ 1891] [depth= 1] . ( 8 sec) [ -10820.4075] [ 1875] [depth= 3] . ( 8 sec) [ -10690.4270] [ 1881] [depth= 5] . ( 8 sec) [ -10203.2898] [ 1731] [depth= 10] . ( 8 sec) [ -10189.0271] [ 1688] [depth= 1] . ( 8 sec) [ -10166.7789] [ 1652] [depth= 9] . ( 8 sec) [ -9986.4458] [ 1571] [depth= 7] . ( 8 sec) [ -9982.9418] [ 1571] [depth= 1] . ( 8 sec) [ -9914.3188] [ 1577] [depth= 4] . ( 9 sec) [ -9731.7592] [ 1518] [depth= 3] . ( 9 sec) [ -9719.2674] [ 1517] [depth= 2] . ( 9 sec) [ -9708.0971] [ 1512] [depth= 2] . ( 9 sec) [ -9618.6049] [ 1500] [depth= 1] . ( 9 sec) [ -9609.7685] [ 1488] [depth= 1] . ( 9 sec) [ -9597.5679] [ 1485] [depth= 1] . ( 9 sec) [ -9593.2433] [ 1476] [depth= 4] . ( 9 sec) [ -9566.3256] [ 1459] [depth= 2] . ( 9 sec) [ -9524.0559] [ 1453] [depth= 2] . ( 10 sec) [ -9478.3192] [ 1454] [depth= 1] . ( 10 sec) [ -9432.4924] [ 1460] [depth= 4] . ( 10 sec) [ -9414.9446] [ 1444] [depth= 2] . ( 10 sec) [ -9200.2421] [ 1386] [depth= 4] . ( 10 sec) [ -9053.4013] [ 1336] [depth= 5] . ( 10 sec) [ -9034.4571] [ 1335] [depth= 1] . ( 10 sec) [ -9028.0778] [ 1335] [depth= 4] . ( 10 sec) [ -9028.0121] [ 1335] [depth= 6] . ( 10 sec) [ -8840.6800] [ 1340] [depth= 1] . ( 10 sec) [ -8803.9324] [ 1340] [depth= 1] . ( 11 sec) [ -8800.9459] [ 1340] [depth= 5] . ( 11 sec) [ -8794.7490] [ 1340] [depth= 3] . ( 11 sec) [ -8794.5383] [ 1340] [depth= 1] . ( 11 sec) [ -8793.3271] [ 1340] [depth= 4] . ( 11 sec) [ -8783.3819] [ 1338] [depth= 1] . ( 11 sec) [ -8772.1370] [ 1338] [depth= 2] . ( 11 sec) [ -8771.9609] [ 1338] [depth= 1] . ( 12 sec) [ -8757.6610] [ 1314] [depth= 7] . ( 12 sec) [ -8672.2888] [ 1279] [depth= 1] . ( 12 sec) [ -8620.0749] [ 1277] [depth= 2] . ( 12 sec) [ -8618.7266] [ 1277] [depth= 1] . ( 12 sec) [ -8443.4242] [ 1233] [depth= 4] . ( 13 sec) [ -8100.2927] [Branch lengths ] . ( 17 sec) [ -7962.0418] [GTR parameters ] . ( 17 sec) [ -7913.5374] [Alpha ][ 0.263107] . ( 18 sec) [ -7906.8043] [ 1230] [depth= 1] . ( 18 sec) [ -7906.7017] [ 1230] [depth= 1] . ( 19 sec) [ -7901.7689] [ 1212] [depth= 1] . ( 20 sec) [ -7896.7754] [ 1205] [depth= 1] . ( 20 sec) [ -7896.1459] [ 1206] [depth= 1] . ( 20 sec) [ -7888.5915] [ 1199] [depth= 1] . ( 20 sec) [ -7888.5584] [ 1199] [depth= 1] . ( 20 sec) [ -7883.0593] [ 1196] [depth= 1] . ( 21 sec) [ -7882.4014] [ 1196] [depth= 1] . ( 21 sec) [ -7878.3064] [ 1193] [depth= 3] . ( 21 sec) [ -7878.2262] [ 1193] [depth= 2] . ( 22 sec) [ -7877.7434] [ 1193] [depth= 1] . ( 22 sec) [ -7877.7316] [ 1193] [depth= 1] . ( 23 sec) [ -7874.0866] [ 1202] [depth= 2] . ( 24 sec) [ -7874.0291] [ 1202] [depth= 1] . ( 24 sec) [ -7873.6229] [ 1199] [depth= 1] . ( 24 sec) [ -7873.6088] [ 1199] [depth= 1] . ( 24 sec) [ -7873.5958] [ 1199] [depth= 2] . ( 28 sec) [ -7873.5570] [ 1199] [depth= 2] . ( 29 sec) [ -7872.3890] [ 1203] [depth= 1] . ( 31 sec) [ -7872.3697] [ 1203] [depth= 3] . ( 32 sec) [ -7872.1948] [ 1203] [depth= 2] . ( 32 sec) [ -7872.1846] [ 1203] [depth= 1] . ( 35 sec) [ -7864.3271] [Branch lengths ] . ( 36 sec) [ -7864.3250] [GTR parameters ] . ( 36 sec) [ -7864.1131] [Alpha ][ 0.252276] . ( 38 sec) [ -7861.4385] [ 1202] [depth= 4] . ( 39 sec) [ -7857.7848] [ 1191] [depth= 2] . ( 41 sec) [ -7857.7318] [ 1190] [depth= 1] . ( 44 sec) [ -7857.7209] [ 1190] [depth= 2] . ( 53 sec) [ -7856.8169] [Branch lengths ] . ( 57 sec) [ -7855.9809] [GTR parameters ] . ( 57 sec) [ -7855.9727] [Alpha ][ 0.254442] . ( 72 sec) [ -7855.8536] [Branch lengths ] . ( 116 sec) [ -7855.8378] [Branch lengths ] . ( 116 sec) [ -7855.8378] [Topology ] . ( 118 sec) [ -7855.8359] [Topology ] . ( 119 sec) [ -7855.8349] [Topology ] . ( 120 sec) [ -7855.8341] [GTR parameters ] . ( 120 sec) [ -7855.8340] [Alpha ][ 0.254170] . ( 120 sec) [ -7855.8340] [Topology ] . ( 121 sec) [ -7855.8330] [Topology ] . ( 122 sec) [ -7855.8287] [Topology ] . ( 124 sec) [ -7855.8179] [Topology ] . ( 125 sec) [ -7855.8122] [Topology ] . ( 126 sec) [ -7855.8093] [Topology ] . ( 128 sec) [ -7855.8077] [Topology ] . ( 128 sec) [ -7855.8077] [GTR parameters ] . ( 128 sec) [ -7855.8077] [Alpha ][ 0.254170] . ( 128 sec) [ -7855.8077] [Topology ] . ( 130 sec) [ -7855.8068] [Topology ] . ( 130 sec) [ -7855.8068] [GTR parameters ] . ( 130 sec) [ -7855.8068] [Alpha ][ 0.254170] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.806787. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -36511.5724] [GTR parameters ] . ( 2 sec) [ -35661.7298] [Alpha ][ 0.500960] . ( 2 sec) [ -34809.5020] [ 4471] [depth= 11] . ( 2 sec) [ -34160.4323] [ 4395] [depth= 11] . ( 2 sec) [ -33911.5182] [ 4372] [depth= 1] . ( 2 sec) [ -33318.5461] [ 4369] [depth= 8] . ( 2 sec) [ -32710.9947] [ 4240] [depth= 2] . ( 2 sec) [ -32363.9135] [ 4239] [depth= 9] . ( 2 sec) [ -32281.2993] [ 4218] [depth= 2] . ( 2 sec) [ -31986.9171] [ 4198] [depth= 3] . ( 2 sec) [ -29277.3917] [ 4129] [depth= 4] . ( 2 sec) [ -29075.6693] [ 4109] [depth= 9] . ( 3 sec) [ -28996.9558] [ 4094] [depth= 7] . ( 3 sec) [ -28973.3318] [ 4094] [depth= 1] . ( 3 sec) [ -28603.6426] [ 4047] [depth= 11] . ( 3 sec) [ -28553.3958] [ 4050] [depth= 1] . ( 3 sec) [ -28258.3096] [ 3974] [depth= 14] . ( 3 sec) [ -28235.2499] [ 3957] [depth= 11] . ( 3 sec) [ -27170.0034] [ 3957] [depth= 1] . ( 3 sec) [ -26124.7080] [ 3872] [depth= 9] . ( 3 sec) [ -25767.5690] [ 3773] [depth= 2] . ( 3 sec) [ -25593.7807] [ 3761] [depth= 5] . ( 3 sec) [ -25552.4388] [ 3758] [depth= 13] . ( 3 sec) [ -25534.0979] [ 3754] [depth= 1] . ( 3 sec) [ -25126.4505] [ 3748] [depth= 12] . ( 4 sec) [ -25097.4225] [ 3747] [depth= 4] . ( 4 sec) [ -25059.2696] [ 3747] [depth= 7] . ( 4 sec) [ -24143.5714] [ 3655] [depth= 1] . ( 4 sec) [ -24015.5259] [ 3613] [depth= 13] . ( 4 sec) [ -23683.1686] [ 3612] [depth= 2] . ( 4 sec) [ -23339.0689] [ 3547] [depth= 5] . ( 4 sec) [ -22371.4569] [ 3536] [depth= 3] . ( 4 sec) [ -22217.8491] [ 3459] [depth= 11] . ( 4 sec) [ -21873.6818] [ 3407] [depth= 8] . ( 4 sec) [ -21497.5462] [ 3404] [depth= 1] . ( 5 sec) [ -21208.1165] [ 3336] [depth= 6] . ( 5 sec) [ -19931.2359] [ 3131] [depth= 5] . ( 5 sec) [ -19356.3854] [ 3127] [depth= 7] . ( 5 sec) [ -18656.8355] [ 3064] [depth= 8] . ( 5 sec) [ -18513.1422] [ 3031] [depth= 7] . ( 5 sec) [ -18000.1749] [ 2975] [depth= 9] . ( 5 sec) [ -17331.3743] [ 2949] [depth= 7] . ( 5 sec) [ -16752.6528] [ 2893] [depth= 1] . ( 5 sec) [ -16217.7314] [ 2797] [depth= 9] . ( 5 sec) [ -16192.1889] [ 2798] [depth= 1] . ( 6 sec) [ -16171.0184] [ 2796] [depth= 5] . ( 6 sec) [ -15560.9821] [ 2778] [depth= 2] . ( 6 sec) [ -15153.1169] [ 2784] [depth= 5] . ( 6 sec) [ -14872.5999] [ 2717] [depth= 5] . ( 6 sec) [ -14869.1438] [ 2717] [depth= 1] . ( 6 sec) [ -14839.1862] [ 2717] [depth= 11] . ( 6 sec) [ -14392.4681] [ 2582] [depth= 11] . ( 6 sec) [ -14390.9551] [ 2582] [depth= 1] . ( 7 sec) [ -14072.1330] [ 2570] [depth= 5] . ( 7 sec) [ -13865.5994] [ 2516] [depth= 9] . ( 7 sec) [ -13849.5543] [ 2518] [depth= 1] . ( 7 sec) [ -13356.7740] [ 2518] [depth= 9] . ( 7 sec) [ -13353.3749] [ 2522] [depth= 1] . ( 7 sec) [ -13125.9925] [ 2478] [depth= 2] . ( 7 sec) [ -12982.4952] [ 2463] [depth= 1] . ( 7 sec) [ -12945.3349] [ 2463] [depth= 10] . ( 8 sec) [ -12937.2635] [ 2464] [depth= 1] . ( 8 sec) [ -12514.3006] [ 2411] [depth= 9] . ( 8 sec) [ -12203.5724] [ 2322] [depth= 4] . ( 8 sec) [ -12044.3945] [ 2308] [depth= 2] . ( 8 sec) [ -11961.5778] [ 2299] [depth= 1] . ( 8 sec) [ -11799.1340] [ 2248] [depth= 1] . ( 8 sec) [ -11434.3752] [ 2239] [depth= 1] . ( 8 sec) [ -11346.8212] [ 2214] [depth= 1] . ( 8 sec) [ -11307.9165] [ 2183] [depth= 1] . ( 8 sec) [ -11232.2281] [ 2142] [depth= 6] . ( 8 sec) [ -11012.3423] [ 2141] [depth= 2] . ( 8 sec) [ -10702.9358] [ 2058] [depth= 9] . ( 9 sec) [ -10693.4360] [ 2058] [depth= 2] . ( 9 sec) [ -10627.4287] [ 2042] [depth= 3] . ( 9 sec) [ -10604.3863] [ 2044] [depth= 1] . ( 9 sec) [ -10559.1104] [ 2044] [depth= 1] . ( 9 sec) [ -10359.5847] [ 1949] [depth= 6] . ( 9 sec) [ -10325.7815] [ 1908] [depth= 1] . ( 9 sec) [ -10219.5412] [ 1833] [depth= 1] . ( 9 sec) [ -9975.4418] [ 1795] [depth= 1] . ( 10 sec) [ -9958.6090] [ 1794] [depth= 1] . ( 10 sec) [ -9598.3927] [ 1647] [depth= 4] . ( 10 sec) [ -9579.2449] [ 1647] [depth= 2] . ( 10 sec) [ -9579.1721] [ 1647] [depth= 4] . ( 10 sec) [ -9477.5361] [ 1628] [depth= 7] . ( 10 sec) [ -9427.5933] [ 1612] [depth= 1] . ( 10 sec) [ -9370.6642] [ 1600] [depth= 7] . ( 10 sec) [ -9319.0773] [ 1561] [depth= 2] . ( 11 sec) [ -9286.5048] [ 1563] [depth= 3] . ( 11 sec) [ -9278.8318] [ 1563] [depth= 2] . ( 11 sec) [ -9276.9335] [ 1563] [depth= 1] . ( 11 sec) [ -9266.5740] [ 1561] [depth= 5] . ( 11 sec) [ -9257.4872] [ 1561] [depth= 1] . ( 11 sec) [ -9224.8297] [ 1556] [depth= 2] . ( 11 sec) [ -9183.0824] [ 1476] [depth= 1] . ( 12 sec) [ -9182.6377] [ 1476] [depth= 1] . ( 12 sec) [ -9125.2585] [ 1476] [depth= 1] . ( 12 sec) [ -9121.0990] [ 1475] [depth= 1] . ( 12 sec) [ -9106.3131] [ 1477] [depth= 1] . ( 12 sec) [ -9087.5000] [ 1475] [depth= 2] . ( 12 sec) [ -9034.0768] [ 1470] [depth= 1] . ( 12 sec) [ -9033.7192] [ 1470] [depth= 2] . ( 12 sec) [ -8934.0481] [ 1470] [depth= 2] . ( 12 sec) [ -8932.3422] [ 1471] [depth= 1] . ( 12 sec) [ -8881.4714] [ 1472] [depth= 1] . ( 12 sec) [ -8864.6805] [ 1472] [depth= 2] . ( 13 sec) [ -8777.7469] [ 1456] [depth= 6] . ( 13 sec) [ -8773.2041] [ 1458] [depth= 1] . ( 13 sec) [ -8772.7616] [ 1458] [depth= 2] . ( 13 sec) [ -8768.8691] [ 1456] [depth= 1] . ( 13 sec) [ -8758.7119] [ 1457] [depth= 6] . ( 13 sec) [ -8749.2168] [ 1456] [depth= 6] . ( 13 sec) [ -8741.8317] [ 1455] [depth= 6] . ( 14 sec) [ -8495.1913] [Branch lengths ] . ( 16 sec) [ -8426.5166] [GTR parameters ] . ( 16 sec) [ -8324.0360] [Alpha ][ 0.250961] . ( 16 sec) [ -8317.4215] [ 1437] [depth= 1] . ( 16 sec) [ -8254.6762] [ 1425] [depth= 9] . ( 16 sec) [ -8254.2775] [ 1425] [depth= 1] . ( 17 sec) [ -8251.6286] [ 1422] [depth= 2] . ( 17 sec) [ -8251.6176] [ 1422] [depth= 2] . ( 17 sec) [ -8170.5730] [ 1342] [depth= 1] . ( 17 sec) [ -8133.0556] [ 1303] [depth= 3] . ( 17 sec) [ -8132.4475] [ 1303] [depth= 1] . ( 18 sec) [ -8132.1648] [ 1303] [depth= 1] . ( 18 sec) [ -8129.3004] [ 1302] [depth= 2] . ( 19 sec) [ -8127.1178] [ 1303] [depth= 1] . ( 19 sec) [ -8104.7392] [ 1270] [depth= 1] . ( 20 sec) [ -8048.6473] [ 1244] [depth= 3] . ( 20 sec) [ -8048.1957] [ 1244] [depth= 1] . ( 20 sec) [ -8045.1217] [ 1243] [depth= 1] . ( 20 sec) [ -8044.9455] [ 1243] [depth= 2] . ( 21 sec) [ -8044.8026] [ 1242] [depth= 1] . ( 21 sec) [ -8036.8581] [ 1238] [depth= 1] . ( 21 sec) [ -8036.7654] [ 1238] [depth= 2] . ( 21 sec) [ -8036.6980] [ 1238] [depth= 1] . ( 21 sec) [ -8036.6111] [ 1238] [depth= 1] . ( 22 sec) [ -8032.4224] [ 1241] [depth= 3] . ( 22 sec) [ -8031.7379] [ 1240] [depth= 2] . ( 23 sec) [ -8031.6934] [ 1240] [depth= 2] . ( 23 sec) [ -8029.4874] [ 1240] [depth= 1] . ( 23 sec) [ -8014.8046] [ 1235] [depth= 2] . ( 23 sec) [ -8013.4466] [ 1235] [depth= 3] . ( 23 sec) [ -8011.7405] [ 1235] [depth= 1] . ( 24 sec) [ -7913.3361] [ 1203] [depth= 1] . ( 24 sec) [ -7913.1779] [ 1203] [depth= 1] . ( 24 sec) [ -7900.8973] [ 1203] [depth= 1] . ( 25 sec) [ -7900.8652] [ 1203] [depth= 3] . ( 25 sec) [ -7899.6839] [ 1206] [depth= 1] . ( 25 sec) [ -7897.2041] [ 1203] [depth= 1] . ( 26 sec) [ -7897.1005] [ 1204] [depth= 1] . ( 26 sec) [ -7894.9027] [ 1203] [depth= 1] . ( 27 sec) [ -7892.8183] [ 1203] [depth= 1] . ( 28 sec) [ -7892.7812] [ 1203] [depth= 2] . ( 29 sec) [ -7892.7462] [ 1203] [depth= 1] . ( 29 sec) [ -7892.2698] [ 1205] [depth= 1] . ( 30 sec) [ -7892.0885] [ 1203] [depth= 1] . ( 31 sec) [ -7870.6871] [Branch lengths ] . ( 32 sec) [ -7868.9970] [GTR parameters ] . ( 32 sec) [ -7868.9896] [Alpha ][ 0.252956] . ( 33 sec) [ -7863.7834] [ 1191] [depth= 2] . ( 34 sec) [ -7862.8070] [ 1191] [depth= 1] . ( 40 sec) [ -7862.7723] [ 1191] [depth= 1] . ( 44 sec) [ -7861.1653] [ 1190] [depth= 1] . ( 49 sec) [ -7859.8090] [Branch lengths ] . ( 50 sec) [ -7859.7619] [GTR parameters ] . ( 50 sec) [ -7859.7598] [Alpha ][ 0.254037] . ( 69 sec) [ -7859.6188] [Branch lengths ] . ( 118 sec) [ -7859.5272] [Branch lengths ] . ( 118 sec) [ -7859.5272] [Topology ] . ( 120 sec) [ -7859.0796] [Topology ] . ( 121 sec) [ -7857.4531] [Topology ] . ( 122 sec) [ -7855.9550] [Topology ] . ( 124 sec) [ -7855.8393] [Topology ] . ( 125 sec) [ -7855.8154] [Topology ] . ( 126 sec) [ -7855.8097] [Topology ] . ( 127 sec) [ -7855.8078] [GTR parameters ] . ( 127 sec) [ -7855.8077] [Alpha ][ 0.254291] . ( 127 sec) [ -7855.8077] [Topology ] . ( 128 sec) [ -7855.8063] [Topology ] . ( 130 sec) [ -7855.8059] [Topology ] . ( 130 sec) [ -7855.8059] [GTR parameters ] . ( 130 sec) [ -7855.8059] [Alpha ][ 0.254291] . ( 130 sec) [ -7855.8059] [Topology ] . ( 131 sec) [ -7855.8058] [Topology ] . ( 131 sec) [ -7855.8058] [GTR parameters ] . ( 132 sec) [ -7855.8058] [Alpha ][ 0.254291] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.805770. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -35758.9924] [GTR parameters ] . ( 1 sec) [ -34837.8210] [Alpha ][ 0.500960] . ( 1 sec) [ -34266.7041] [ 4766] [depth= 7] . ( 1 sec) [ -32960.3245] [ 4717] [depth= 6] . ( 1 sec) [ -32751.5233] [ 4699] [depth= 5] . ( 1 sec) [ -32453.0203] [ 4693] [depth= 6] . ( 1 sec) [ -31994.8890] [ 4564] [depth= 3] . ( 1 sec) [ -31926.3088] [ 4561] [depth= 2] . ( 1 sec) [ -31104.5811] [ 4510] [depth= 8] . ( 1 sec) [ -29620.0275] [ 4510] [depth= 1] . ( 2 sec) [ -28155.1021] [ 4487] [depth= 1] . ( 2 sec) [ -27552.5661] [ 4427] [depth= 17] . ( 2 sec) [ -26485.9877] [ 4292] [depth= 10] . ( 2 sec) [ -26321.4871] [ 4289] [depth= 21] . ( 2 sec) [ -25851.5170] [ 4145] [depth= 4] . ( 2 sec) [ -25541.0429] [ 4141] [depth= 5] . ( 2 sec) [ -25152.1084] [ 4042] [depth= 13] . ( 2 sec) [ -24829.8936] [ 3945] [depth= 9] . ( 2 sec) [ -24223.8593] [ 3894] [depth= 2] . ( 2 sec) [ -24206.8595] [ 3893] [depth= 1] . ( 2 sec) [ -23986.4123] [ 3838] [depth= 6] . ( 2 sec) [ -23719.9862] [ 3830] [depth= 7] . ( 3 sec) [ -23022.5670] [ 3706] [depth= 14] . ( 3 sec) [ -22656.4197] [ 3707] [depth= 11] . ( 3 sec) [ -22481.5353] [ 3674] [depth= 1] . ( 3 sec) [ -22389.5290] [ 3656] [depth= 10] . ( 3 sec) [ -22015.7663] [ 3600] [depth= 3] . ( 3 sec) [ -21778.8416] [ 3578] [depth= 4] . ( 3 sec) [ -21163.7982] [ 3575] [depth= 11] . ( 3 sec) [ -20869.9748] [ 3484] [depth= 10] . ( 3 sec) [ -20845.9381] [ 3484] [depth= 14] . ( 3 sec) [ -19979.2207] [ 3377] [depth= 4] . ( 3 sec) [ -19857.4247] [ 3373] [depth= 14] . ( 3 sec) [ -19810.2120] [ 3371] [depth= 14] . ( 4 sec) [ -19533.4284] [ 3353] [depth= 9] . ( 4 sec) [ -17910.8212] [ 3281] [depth= 6] . ( 4 sec) [ -17602.2629] [ 3229] [depth= 1] . ( 4 sec) [ -17563.6567] [ 3229] [depth= 13] . ( 4 sec) [ -17537.7419] [ 3227] [depth= 6] . ( 4 sec) [ -17534.9652] [ 3227] [depth= 2] . ( 4 sec) [ -17480.4721] [ 3170] [depth= 12] . ( 4 sec) [ -17423.3197] [ 3170] [depth= 1] . ( 4 sec) [ -17293.4964] [ 3159] [depth= 5] . ( 4 sec) [ -17286.5934] [ 3158] [depth= 2] . ( 4 sec) [ -16467.9333] [ 2943] [depth= 4] . ( 5 sec) [ -16454.5913] [ 2943] [depth= 1] . ( 5 sec) [ -16047.2853] [ 2799] [depth= 10] . ( 5 sec) [ -15620.8442] [ 2752] [depth= 13] . ( 5 sec) [ -15380.7225] [ 2742] [depth= 1] . ( 5 sec) [ -15373.5517] [ 2754] [depth= 1] . ( 5 sec) [ -14971.6505] [ 2640] [depth= 9] . ( 5 sec) [ -14901.6820] [ 2617] [depth= 1] . ( 5 sec) [ -14824.5981] [ 2617] [depth= 2] . ( 5 sec) [ -14384.9314] [ 2567] [depth= 6] . ( 5 sec) [ -14044.8636] [ 2428] [depth= 6] . ( 5 sec) [ -13990.2367] [ 2429] [depth= 1] . ( 5 sec) [ -13989.9976] [ 2429] [depth= 2] . ( 6 sec) [ -13970.4149] [ 2409] [depth= 2] . ( 6 sec) [ -13924.6661] [ 2391] [depth= 3] . ( 6 sec) [ -13818.2949] [ 2376] [depth= 1] . ( 6 sec) [ -13211.8696] [ 2337] [depth= 6] . ( 6 sec) [ -12580.2089] [ 2270] [depth= 5] . ( 6 sec) [ -12203.3004] [ 2232] [depth= 12] . ( 6 sec) [ -12185.7592] [ 2233] [depth= 1] . ( 6 sec) [ -12171.9513] [ 2233] [depth= 7] . ( 6 sec) [ -12048.5295] [ 2148] [depth= 2] . ( 6 sec) [ -12042.7783] [ 2148] [depth= 1] . ( 6 sec) [ -11719.4133] [ 2011] [depth= 6] . ( 6 sec) [ -11709.7214] [ 2009] [depth= 11] . ( 7 sec) [ -11701.7849] [ 2008] [depth= 8] . ( 7 sec) [ -11561.5397] [ 1961] [depth= 1] . ( 7 sec) [ -11076.6466] [ 1864] [depth= 6] . ( 7 sec) [ -11065.4274] [ 1865] [depth= 2] . ( 7 sec) [ -10701.1020] [ 1828] [depth= 9] . ( 7 sec) [ -10663.7309] [ 1786] [depth= 3] . ( 7 sec) [ -10662.9648] [ 1788] [depth= 6] . ( 7 sec) [ -10657.2787] [ 1787] [depth= 1] . ( 8 sec) [ -10615.8557] [ 1763] [depth= 4] . ( 8 sec) [ -10604.4004] [ 1761] [depth= 4] . ( 8 sec) [ -10332.6095] [ 1755] [depth= 1] . ( 8 sec) [ -10218.4324] [ 1721] [depth= 5] . ( 8 sec) [ -10216.9783] [ 1721] [depth= 1] . ( 8 sec) [ -10196.1959] [ 1755] [depth= 1] . ( 8 sec) [ -9873.9704] [ 1673] [depth= 10] . ( 8 sec) [ -9673.0927] [ 1673] [depth= 3] . ( 8 sec) [ -9654.6186] [ 1667] [depth= 1] . ( 8 sec) [ -9550.9838] [ 1667] [depth= 2] . ( 8 sec) [ -9518.2441] [ 1645] [depth= 4] . ( 9 sec) [ -9441.7476] [ 1631] [depth= 1] . ( 9 sec) [ -9438.7052] [ 1630] [depth= 1] . ( 9 sec) [ -9438.1339] [ 1630] [depth= 1] . ( 9 sec) [ -9200.4909] [ 1534] [depth= 3] . ( 9 sec) [ -9193.0486] [ 1532] [depth= 1] . ( 9 sec) [ -9146.7741] [ 1533] [depth= 3] . ( 9 sec) [ -9143.9388] [ 1534] [depth= 2] . ( 9 sec) [ -9140.4285] [ 1534] [depth= 1] . ( 9 sec) [ -9122.4228] [ 1534] [depth= 1] . ( 9 sec) [ -9121.1662] [ 1534] [depth= 1] . ( 9 sec) [ -9070.2179] [ 1500] [depth= 3] . ( 10 sec) [ -9067.0416] [ 1500] [depth= 1] . ( 10 sec) [ -8853.3604] [ 1445] [depth= 11] . ( 10 sec) [ -8836.1242] [ 1445] [depth= 2] . ( 10 sec) [ -8791.1856] [ 1424] [depth= 1] . ( 10 sec) [ -8791.1568] [ 1425] [depth= 1] . ( 10 sec) [ -8789.5316] [ 1425] [depth= 2] . ( 10 sec) [ -8761.9318] [ 1425] [depth= 1] . ( 10 sec) [ -8759.1047] [ 1425] [depth= 3] . ( 10 sec) [ -8750.8792] [ 1425] [depth= 2] . ( 10 sec) [ -8750.4533] [ 1425] [depth= 2] . ( 11 sec) [ -8727.8959] [ 1424] [depth= 2] . ( 11 sec) [ -8706.4427] [ 1412] [depth= 5] . ( 12 sec) [ -8385.8382] [Branch lengths ] . ( 13 sec) [ -8307.4185] [GTR parameters ] . ( 13 sec) [ -8220.9298] [Alpha ][ 0.250961] . ( 14 sec) [ -8220.8429] [ 1412] [depth= 2] . ( 15 sec) [ -8220.5690] [ 1412] [depth= 1] . ( 15 sec) [ -8220.5283] [ 1412] [depth= 1] . ( 15 sec) [ -8147.6260] [ 1374] [depth= 4] . ( 15 sec) [ -8142.7741] [ 1372] [depth= 1] . ( 15 sec) [ -8142.2995] [ 1372] [depth= 2] . ( 15 sec) [ -8128.7563] [ 1361] [depth= 1] . ( 16 sec) [ -8128.7381] [ 1361] [depth= 1] . ( 16 sec) [ -8128.2884] [ 1357] [depth= 2] . ( 16 sec) [ -8128.2628] [ 1357] [depth= 2] . ( 16 sec) [ -8128.1690] [ 1357] [depth= 1] . ( 16 sec) [ -8117.6555] [ 1354] [depth= 2] . ( 17 sec) [ -8117.6153] [ 1354] [depth= 2] . ( 17 sec) [ -8106.0899] [ 1350] [depth= 3] . ( 17 sec) [ -8095.4228] [ 1321] [depth= 12] . ( 17 sec) [ -8095.3599] [ 1321] [depth= 2] . ( 17 sec) [ -8095.2163] [ 1321] [depth= 4] . ( 17 sec) [ -8094.8170] [ 1321] [depth= 1] . ( 18 sec) [ -8094.7943] [ 1321] [depth= 2] . ( 18 sec) [ -8094.7813] [ 1321] [depth= 3] . ( 19 sec) [ -8094.7678] [ 1321] [depth= 2] . ( 19 sec) [ -8092.4509] [ 1322] [depth= 1] . ( 20 sec) [ -8085.6408] [ 1318] [depth= 2] . ( 21 sec) [ -8017.5684] [ 1283] [depth= 6] . ( 21 sec) [ -8014.5176] [ 1283] [depth= 1] . ( 21 sec) [ -8014.3961] [ 1283] [depth= 1] . ( 21 sec) [ -8014.3829] [ 1283] [depth= 1] . ( 22 sec) [ -8005.9179] [ 1275] [depth= 1] . ( 23 sec) [ -7958.9451] [ 1235] [depth= 4] . ( 23 sec) [ -7955.5686] [ 1235] [depth= 1] . ( 24 sec) [ -7953.9853] [ 1234] [depth= 3] . ( 24 sec) [ -7939.6394] [ 1232] [depth= 1] . ( 24 sec) [ -7935.8906] [ 1232] [depth= 1] . ( 25 sec) [ -7935.6138] [ 1232] [depth= 1] . ( 25 sec) [ -7935.5618] [ 1232] [depth= 1] . ( 25 sec) [ -7935.4227] [ 1232] [depth= 1] . ( 26 sec) [ -7902.2530] [ 1203] [depth= 6] . ( 26 sec) [ -7902.1900] [ 1203] [depth= 3] . ( 26 sec) [ -7891.3731] [ 1201] [depth= 1] . ( 27 sec) [ -7889.2985] [ 1205] [depth= 1] . ( 27 sec) [ -7889.1231] [ 1205] [depth= 4] . ( 27 sec) [ -7889.0850] [ 1205] [depth= 3] . ( 28 sec) [ -7885.8115] [ 1202] [depth= 5] . ( 28 sec) [ -7882.2131] [ 1190] [depth= 2] . ( 28 sec) [ -7882.1905] [ 1190] [depth= 2] . ( 28 sec) [ -7881.4468] [ 1189] [depth= 2] . ( 29 sec) [ -7880.0718] [ 1193] [depth= 1] . ( 29 sec) [ -7864.2863] [Branch lengths ] . ( 31 sec) [ -7863.6198] [GTR parameters ] . ( 31 sec) [ -7863.6191] [Alpha ][ 0.251573] . ( 33 sec) [ -7863.5876] [ 1193] [depth= 1] . ( 37 sec) [ -7861.5950] [ 1189] [depth= 1] . ( 38 sec) [ -7860.5325] [ 1190] [depth= 1] . ( 38 sec) [ -7860.4160] [ 1190] [depth= 1] . ( 40 sec) [ -7860.3896] [ 1190] [depth= 1] . ( 46 sec) [ -7856.3150] [Branch lengths ] . ( 47 sec) [ -7856.2859] [GTR parameters ] . ( 47 sec) [ -7856.2792] [Alpha ][ 0.253506] . ( 62 sec) [ -7855.8672] [Branch lengths ] . ( 104 sec) [ -7855.8188] [Branch lengths ] . ( 105 sec) [ -7855.8188] [Topology ] . ( 106 sec) [ -7855.8135] [Topology ] . ( 107 sec) [ -7855.8115] [Topology ] . ( 109 sec) [ -7855.8104] [Topology ] . ( 110 sec) [ -7855.8099] [Topology ] . ( 110 sec) [ -7855.8077] [GTR parameters ] . ( 110 sec) [ -7855.8070] [Alpha ][ 0.254108] . ( 110 sec) [ -7855.8070] [Topology ] . ( 112 sec) [ -7855.8065] [Topology ] . ( 112 sec) [ -7855.8064] [GTR parameters ] . ( 112 sec) [ -7855.8064] [Alpha ][ 0.254108] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.806417. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -34907.5800] [GTR parameters ] . ( 2 sec) [ -34003.8645] [Alpha ][ 0.500960] . ( 2 sec) [ -33138.6186] [ 4592] [depth= 10] . ( 2 sec) [ -32305.0859] [ 4527] [depth= 9] . ( 2 sec) [ -31881.2785] [ 4512] [depth= 11] . ( 2 sec) [ -31748.2874] [ 4426] [depth= 1] . ( 2 sec) [ -31348.1858] [ 4349] [depth= 11] . ( 2 sec) [ -31011.1009] [ 4311] [depth= 3] . ( 2 sec) [ -30734.6422] [ 4250] [depth= 8] . ( 2 sec) [ -30110.6550] [ 4163] [depth= 5] . ( 2 sec) [ -28668.7200] [ 4161] [depth= 1] . ( 2 sec) [ -28158.7656] [ 4135] [depth= 1] . ( 3 sec) [ -28032.9878] [ 4072] [depth= 4] . ( 3 sec) [ -27064.3834] [ 4019] [depth= 1] . ( 3 sec) [ -26472.6661] [ 3962] [depth= 7] . ( 3 sec) [ -25461.8546] [ 3896] [depth= 5] . ( 3 sec) [ -25032.6970] [ 3855] [depth= 1] . ( 3 sec) [ -24645.3309] [ 3798] [depth= 16] . ( 3 sec) [ -23767.9087] [ 3737] [depth= 6] . ( 3 sec) [ -23564.6025] [ 3711] [depth= 3] . ( 3 sec) [ -23350.8701] [ 3707] [depth= 1] . ( 3 sec) [ -22611.0883] [ 3628] [depth= 7] . ( 3 sec) [ -22596.9700] [ 3625] [depth= 1] . ( 3 sec) [ -22389.3737] [ 3660] [depth= 1] . ( 3 sec) [ -22022.3128] [ 3592] [depth= 12] . ( 4 sec) [ -21448.7387] [ 3456] [depth= 2] . ( 4 sec) [ -20945.1065] [ 3448] [depth= 8] . ( 4 sec) [ -20657.8737] [ 3349] [depth= 2] . ( 4 sec) [ -19964.5612] [ 3139] [depth= 9] . ( 4 sec) [ -19769.7675] [ 3134] [depth= 2] . ( 4 sec) [ -19513.8562] [ 3110] [depth= 2] . ( 4 sec) [ -19031.2756] [ 3060] [depth= 8] . ( 4 sec) [ -18994.4455] [ 3060] [depth= 1] . ( 4 sec) [ -18619.8130] [ 2961] [depth= 11] . ( 4 sec) [ -18384.4478] [ 2906] [depth= 11] . ( 4 sec) [ -18163.1544] [ 2812] [depth= 5] . ( 4 sec) [ -18079.4168] [ 2816] [depth= 1] . ( 5 sec) [ -17780.8595] [ 2757] [depth= 2] . ( 5 sec) [ -17699.2310] [ 2723] [depth= 2] . ( 5 sec) [ -17399.8897] [ 2671] [depth= 7] . ( 5 sec) [ -17250.7899] [ 2652] [depth= 2] . ( 5 sec) [ -17213.0733] [ 2633] [depth= 1] . ( 5 sec) [ -17169.2979] [ 2631] [depth= 1] . ( 5 sec) [ -17154.4554] [ 2632] [depth= 10] . ( 5 sec) [ -16769.8147] [ 2512] [depth= 12] . ( 5 sec) [ -16680.1088] [ 2532] [depth= 1] . ( 5 sec) [ -16092.3251] [ 2520] [depth= 8] . ( 6 sec) [ -15692.4009] [ 2516] [depth= 5] . ( 6 sec) [ -15030.3326] [ 2450] [depth= 8] . ( 6 sec) [ -14659.4918] [ 2397] [depth= 7] . ( 6 sec) [ -14434.4652] [ 2391] [depth= 4] . ( 6 sec) [ -14408.7574] [ 2391] [depth= 1] . ( 6 sec) [ -14107.3225] [ 2359] [depth= 8] . ( 6 sec) [ -13868.2600] [ 2309] [depth= 1] . ( 6 sec) [ -13771.0634] [ 2279] [depth= 1] . ( 6 sec) [ -13418.9487] [ 2279] [depth= 1] . ( 6 sec) [ -13406.8852] [ 2279] [depth= 1] . ( 6 sec) [ -13037.9792] [ 2136] [depth= 14] . ( 6 sec) [ -13013.5769] [ 2135] [depth= 10] . ( 6 sec) [ -12937.0624] [ 2135] [depth= 7] . ( 7 sec) [ -12492.6195] [ 2118] [depth= 2] . ( 7 sec) [ -12462.4235] [ 2104] [depth= 3] . ( 7 sec) [ -12417.5131] [ 2092] [depth= 2] . ( 7 sec) [ -12321.5023] [ 2028] [depth= 6] . ( 7 sec) [ -12031.0773] [ 2032] [depth= 2] . ( 7 sec) [ -11976.3741] [ 2014] [depth= 1] . ( 7 sec) [ -11954.9562] [ 1992] [depth= 1] . ( 7 sec) [ -11912.4439] [ 1993] [depth= 1] . ( 7 sec) [ -11903.2569] [ 1993] [depth= 2] . ( 7 sec) [ -11497.9543] [ 1895] [depth= 8] . ( 7 sec) [ -11322.0428] [ 1848] [depth= 1] . ( 8 sec) [ -11257.7306] [ 1840] [depth= 1] . ( 8 sec) [ -11090.0420] [ 1835] [depth= 1] . ( 8 sec) [ -11044.3530] [ 1829] [depth= 5] . ( 8 sec) [ -11021.0942] [ 1826] [depth= 1] . ( 8 sec) [ -10699.0163] [ 1716] [depth= 5] . ( 8 sec) [ -10523.6829] [ 1714] [depth= 11] . ( 8 sec) [ -10487.3346] [ 1730] [depth= 1] . ( 8 sec) [ -10262.3538] [ 1665] [depth= 5] . ( 8 sec) [ -10080.2024] [ 1652] [depth= 2] . ( 8 sec) [ -9788.8875] [ 1601] [depth= 2] . ( 8 sec) [ -9585.6737] [ 1560] [depth= 2] . ( 8 sec) [ -9539.0986] [ 1559] [depth= 2] . ( 9 sec) [ -9484.5761] [ 1556] [depth= 2] . ( 9 sec) [ -9477.6809] [ 1559] [depth= 2] . ( 9 sec) [ -9460.3580] [ 1553] [depth= 1] . ( 9 sec) [ -9326.6324] [ 1527] [depth= 1] . ( 9 sec) [ -9294.3026] [ 1527] [depth= 4] . ( 9 sec) [ -9286.9310] [ 1527] [depth= 1] . ( 9 sec) [ -9285.9093] [ 1523] [depth= 1] . ( 9 sec) [ -9196.4754] [ 1482] [depth= 2] . ( 9 sec) [ -9143.0355] [ 1481] [depth= 1] . ( 10 sec) [ -9131.9821] [ 1475] [depth= 1] . ( 10 sec) [ -8761.2841] [ 1379] [depth= 6] . ( 10 sec) [ -8752.5406] [ 1378] [depth= 2] . ( 10 sec) [ -8750.4495] [ 1378] [depth= 1] . ( 10 sec) [ -8742.6816] [ 1378] [depth= 1] . ( 11 sec) [ -8735.5580] [ 1364] [depth= 3] . ( 11 sec) [ -8720.7328] [ 1344] [depth= 1] . ( 11 sec) [ -8720.3109] [ 1345] [depth= 1] . ( 11 sec) [ -8688.7423] [ 1349] [depth= 1] . ( 11 sec) [ -8664.3854] [ 1345] [depth= 1] . ( 11 sec) [ -8664.3090] [ 1350] [depth= 1] . ( 12 sec) [ -8664.1933] [ 1350] [depth= 1] . ( 12 sec) [ -8652.0978] [ 1351] [depth= 1] . ( 12 sec) [ -8629.6887] [ 1346] [depth= 1] . ( 12 sec) [ -8625.5887] [ 1346] [depth= 1] . ( 12 sec) [ -8621.4129] [ 1345] [depth= 1] . ( 12 sec) [ -8609.2286] [ 1346] [depth= 1] . ( 12 sec) [ -8605.8649] [ 1345] [depth= 1] . ( 13 sec) [ -8605.4488] [ 1345] [depth= 1] . ( 13 sec) [ -8261.0766] [Branch lengths ] . ( 17 sec) [ -8234.8893] [GTR parameters ] . ( 17 sec) [ -8155.1219] [Alpha ][ 0.250961] . ( 18 sec) [ -8136.8227] [ 1346] [depth= 2] . ( 18 sec) [ -8110.1345] [ 1322] [depth= 1] . ( 18 sec) [ -8109.3554] [ 1311] [depth= 3] . ( 18 sec) [ -8102.6193] [ 1318] [depth= 3] . ( 18 sec) [ -8102.2402] [ 1317] [depth= 2] . ( 18 sec) [ -8102.2213] [ 1317] [depth= 1] . ( 19 sec) [ -8100.6223] [ 1317] [depth= 1] . ( 19 sec) [ -8082.8295] [ 1291] [depth= 1] . ( 19 sec) [ -8043.9432] [ 1261] [depth= 1] . ( 20 sec) [ -8043.9099] [ 1261] [depth= 1] . ( 20 sec) [ -8040.9755] [ 1225] [depth= 2] . ( 20 sec) [ -8010.4514] [ 1216] [depth= 3] . ( 20 sec) [ -8010.3948] [ 1216] [depth= 1] . ( 20 sec) [ -8010.3725] [ 1216] [depth= 1] . ( 21 sec) [ -8004.4640] [ 1217] [depth= 1] . ( 21 sec) [ -7993.1982] [ 1216] [depth= 1] . ( 21 sec) [ -7989.4631] [ 1216] [depth= 1] . ( 21 sec) [ -7989.3983] [ 1216] [depth= 2] . ( 21 sec) [ -7988.5752] [ 1216] [depth= 1] . ( 21 sec) [ -7986.7672] [ 1218] [depth= 1] . ( 22 sec) [ -7981.6253] [ 1218] [depth= 2] . ( 22 sec) [ -7979.8426] [ 1218] [depth= 2] . ( 23 sec) [ -7977.7204] [ 1217] [depth= 1] . ( 23 sec) [ -7966.5268] [ 1208] [depth= 1] . ( 23 sec) [ -7962.9597] [ 1207] [depth= 1] . ( 23 sec) [ -7948.0856] [ 1207] [depth= 1] . ( 23 sec) [ -7940.9363] [ 1206] [depth= 3] . ( 23 sec) [ -7940.7831] [ 1206] [depth= 1] . ( 24 sec) [ -7940.6404] [ 1206] [depth= 1] . ( 24 sec) [ -7940.6239] [ 1206] [depth= 2] . ( 24 sec) [ -7939.0045] [ 1206] [depth= 1] . ( 24 sec) [ -7938.9112] [ 1206] [depth= 1] . ( 24 sec) [ -7924.9135] [ 1201] [depth= 1] . ( 25 sec) [ -7901.4585] [ 1190] [depth= 2] . ( 25 sec) [ -7899.7453] [ 1192] [depth= 1] . ( 28 sec) [ -7899.4387] [ 1192] [depth= 1] . ( 28 sec) [ -7899.3779] [ 1192] [depth= 1] . ( 32 sec) [ -7899.2888] [ 1192] [depth= 1] . ( 32 sec) [ -7898.6066] [ 1192] [depth= 1] . ( 32 sec) [ -7896.7318] [ 1192] [depth= 1] . ( 32 sec) [ -7896.7006] [ 1192] [depth= 1] . ( 33 sec) [ -7862.8917] [Branch lengths ] . ( 36 sec) [ -7860.7816] [GTR parameters ] . ( 36 sec) [ -7860.7391] [Alpha ][ 0.255814] . ( 39 sec) [ -7860.7241] [ 1192] [depth= 1] . ( 51 sec) [ -7857.7314] [Branch lengths ] . ( 52 sec) [ -7857.7308] [GTR parameters ] . ( 52 sec) [ -7857.7239] [Alpha ][ 0.253776] . ( 67 sec) [ -7857.3995] [Branch lengths ] . ( 111 sec) [ -7856.4225] [Branch lengths ] . ( 111 sec) [ -7856.4225] [Topology ] . ( 112 sec) [ -7856.2035] [Topology ] . ( 113 sec) [ -7856.0608] [Topology ] . ( 115 sec) [ -7855.9673] [Topology ] . ( 116 sec) [ -7855.8957] [Topology ] . ( 117 sec) [ -7855.8633] [Topology ] . ( 118 sec) [ -7855.8555] [Topology ] . ( 120 sec) [ -7855.8189] [GTR parameters ] . ( 120 sec) [ -7855.8189] [Alpha ][ 0.253522] . ( 120 sec) [ -7855.8189] [Topology ] . ( 121 sec) [ -7855.8163] [Topology ] . ( 122 sec) [ -7855.8157] [Topology ] . ( 123 sec) [ -7855.8157] [GTR parameters ] . ( 123 sec) [ -7855.8157] [Alpha ][ 0.253522] . ( 123 sec) [ -7855.8157] [Topology ] . ( 124 sec) [ -7855.8155] [Topology ] . ( 125 sec) [ -7855.8155] [GTR parameters ] . ( 125 sec) [ -7855.8155] [Alpha ][ 0.253522] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.815465. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -8178.2748] [GTR parameters ] . ( 4 sec) [ -8087.4232] [Alpha ][ 0.500960] . ( 4 sec) [ -8087.4232] [Topology ] . ( 5 sec) [ -7959.9720] [Topology ] . ( 7 sec) [ -7936.8427] [Topology ] . ( 8 sec) [ -7933.2782] [Topology ] . ( 9 sec) [ -7932.4736] [Topology ] . ( 11 sec) [ -7932.2115] [Topology ] . ( 12 sec) [ -7931.9493] [Topology ] . ( 13 sec) [ -7930.8733] [Topology ] . ( 15 sec) [ -7927.9431] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -7926.6478] [GTR parameters ] . ( 27 sec) [ -7886.3932] [Alpha ][ 0.264515] . ( 27 sec) [ -7886.3932] [Topology ] . ( 28 sec) [ -7882.1933] [Topology ] . ( 30 sec) [ -7881.8491] [Topology ] . ( 31 sec) [ -7881.6938] [Topology ] . ( 32 sec) [ -7881.6300] [Topology ] . ( 33 sec) [ -7881.6105] [Topology ] . ( 35 sec) [ -7881.6038] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -7880.9586] [GTR parameters ] . ( 47 sec) [ -7880.7604] [Alpha ][ 0.253715] . ( 47 sec) [ -7880.7604] [Topology ] . ( 48 sec) [ -7880.7346] [Topology ] . ( 49 sec) [ -7880.7314] [Topology ] . ( 51 sec) [ -7880.7299] [Topology ] . ( 52 sec) [ -7880.7292] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -7880.7245] [GTR parameters ] . ( 63 sec) [ -7880.7226] [Alpha ][ 0.252603] . ( 63 sec) [ -7880.7226] [Topology ] . ( 65 sec) [ -7880.7218] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -7880.7218] [GTR parameters ] . ( 75 sec) [ -7880.7218] [Alpha ][ 0.252603] . ( 75 sec) [ -7880.7218] [Topology ] . ( 76 sec) [ -7880.7215] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 99 sec) [ -8178.2748] [GTR parameters ] . ( 99 sec) [ -8087.4232] [Alpha ][ 0.500960] . ( 100 sec) [ -8087.0972] [ 1200] [depth= 1] . ( 101 sec) [ -8084.7754] [ 1202] [depth= 1] . ( 101 sec) [ -8082.7059] [ 1201] [depth= 1] . ( 101 sec) [ -8082.5110] [ 1201] [depth= 1] . ( 101 sec) [ -8082.2716] [ 1201] [depth= 1] . ( 101 sec) [ -8081.9018] [ 1200] [depth= 2] . ( 101 sec) [ -8079.7678] [ 1200] [depth= 1] . ( 102 sec) [ -8078.9041] [ 1200] [depth= 1] . ( 102 sec) [ -8078.5930] [ 1200] [depth= 1] . ( 102 sec) [ -8078.4987] [ 1200] [depth= 1] . ( 102 sec) [ -8078.4207] [ 1200] [depth= 2] . ( 103 sec) [ -8069.1232] [ 1200] [depth= 1] . ( 103 sec) [ -8055.0493] [ 1198] [depth= 1] . ( 103 sec) [ -8053.5396] [ 1198] [depth= 2] . ( 103 sec) [ -8053.5137] [ 1198] [depth= 2] . ( 103 sec) [ -8049.2586] [ 1197] [depth= 1] . ( 103 sec) [ -8047.0850] [ 1197] [depth= 1] . ( 104 sec) [ -8046.9941] [ 1197] [depth= 2] . ( 104 sec) [ -8046.6394] [ 1197] [depth= 2] . ( 104 sec) [ -8046.5629] [ 1197] [depth= 1] . ( 105 sec) [ -8043.9070] [ 1197] [depth= 5] . ( 105 sec) [ -8034.1401] [ 1195] [depth= 2] . ( 105 sec) [ -8029.8403] [ 1195] [depth= 1] . ( 105 sec) [ -7981.5911] [ 1193] [depth= 1] . ( 105 sec) [ -7981.2213] [ 1193] [depth= 1] . ( 106 sec) [ -7979.5751] [ 1194] [depth= 1] . ( 107 sec) [ -7973.7832] [ 1193] [depth= 1] . ( 107 sec) [ -7973.5404] [ 1193] [depth= 1] . ( 107 sec) [ -7973.5261] [ 1193] [depth= 1] . ( 107 sec) [ -7954.2323] [ 1201] [depth= 1] . ( 107 sec) [ -7953.2675] [ 1202] [depth= 2] . ( 107 sec) [ -7951.8497] [ 1204] [depth= 1] . ( 107 sec) [ -7949.4161] [ 1202] [depth= 1] . ( 108 sec) [ -7942.7037] [ 1201] [depth= 1] . ( 109 sec) [ -7941.8535] [ 1201] [depth= 2] . ( 109 sec) [ -7936.2058] [ 1193] [depth= 1] . ( 110 sec) [ -7929.6872] [ 1192] [depth= 2] . ( 111 sec) [ -7929.6752] [ 1192] [depth= 1] . ( 111 sec) [ -7929.6434] [ 1192] [depth= 2] . ( 113 sec) [ -7929.0723] [ 1192] [depth= 1] . ( 114 sec) [ -7902.7152] [Branch lengths ] . ( 116 sec) [ -7901.2669] [GTR parameters ] . ( 116 sec) [ -7861.2592] [Alpha ][ 0.264044] . ( 117 sec) [ -7861.2490] [ 1192] [depth= 1] . ( 117 sec) [ -7861.1443] [ 1190] [depth= 1] . ( 118 sec) [ -7861.0911] [ 1190] [depth= 2] . ( 120 sec) [ -7860.9953] [ 1190] [depth= 1] . ( 127 sec) [ -7859.7277] [ 1190] [depth= 1] . ( 130 sec) [ -7856.7396] [Branch lengths ] . ( 132 sec) [ -7856.2157] [GTR parameters ] . ( 132 sec) [ -7856.0277] [Alpha ][ 0.253416] . ( 141 sec) [ -7856.0165] [ 1190] [depth= 1] . ( 149 sec) [ -7855.8353] [Branch lengths ] . ( 151 sec) [ -7855.8266] [GTR parameters ] . ( 151 sec) [ -7855.8264] [Alpha ][ 0.253774] . ( 199 sec) [ -7855.8081] [Branch lengths ] . ( 199 sec) [ -7855.8081] [Topology ] . ( 201 sec) [ -7855.8066] [Topology ] . ( 202 sec) [ -7855.8062] [Topology ] . ( 202 sec) [ -7855.8060] [GTR parameters ] . ( 202 sec) [ -7855.8058] [Alpha ][ 0.254136] . ( 202 sec) [ -7855.8058] [Topology ] . ( 204 sec) [ -7855.8055] [Topology ] . ( 204 sec) [ -7855.8055] [GTR parameters ] . ( 204 sec) [ -7855.8055] [Alpha ][ 0.254136] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7880.721493 . Log likelihood obtained after SPR moves : -7855.805506 . Log likelihood of the current tree: -7855.805506. . Printing the most likely tree in file 'nucleic_M2675_51x1537_2006.phy_phyml_tree.txt'... . Best log likelihood : -7855.673425 . Time used 0h3m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 894.40user 0.00system 15:04.21elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps