.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2944_80x1495_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 494 patterns found. (out of a total of 1495 sites) . 1077 sites without polymorphism (72.04%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -18844.2730] [GTR parameters ] . ( 3 sec) [ -18443.1075] [Alpha ][ 0.500960] . ( 3 sec) [ -18209.6678] [ 2665] [depth= 16] . ( 3 sec) [ -17829.6889] [ 2626] [depth= 13] . ( 3 sec) [ -17780.8486] [ 2625] [depth= 3] . ( 3 sec) [ -17688.3381] [ 2611] [depth= 1] . ( 3 sec) [ -17570.2226] [ 2609] [depth= 15] . ( 3 sec) [ -17434.5408] [ 2592] [depth= 2] . ( 3 sec) [ -17419.7532] [ 2589] [depth= 9] . ( 3 sec) [ -17370.3213] [ 2577] [depth= 2] . ( 4 sec) [ -17305.4526] [ 2573] [depth= 1] . ( 4 sec) [ -17283.0248] [ 2570] [depth= 2] . ( 4 sec) [ -17229.0767] [ 2565] [depth= 9] . ( 4 sec) [ -17166.2127] [ 2544] [depth= 4] . ( 4 sec) [ -17121.6686] [ 2539] [depth= 15] . ( 4 sec) [ -17061.2655] [ 2530] [depth= 15] . ( 4 sec) [ -17017.8329] [ 2523] [depth= 18] . ( 4 sec) [ -16938.0744] [ 2514] [depth= 6] . ( 4 sec) [ -16923.9290] [ 2513] [depth= 2] . ( 4 sec) [ -16883.0419] [ 2508] [depth= 9] . ( 5 sec) [ -16849.5844] [ 2507] [depth= 6] . ( 5 sec) [ -16516.7266] [ 2466] [depth= 2] . ( 5 sec) [ -16490.0986] [ 2468] [depth= 1] . ( 5 sec) [ -16472.8032] [ 2463] [depth= 8] . ( 5 sec) [ -16432.0298] [ 2455] [depth= 1] . ( 5 sec) [ -16377.3963] [ 2454] [depth= 2] . ( 5 sec) [ -16335.3899] [ 2453] [depth= 2] . ( 5 sec) [ -16255.9044] [ 2450] [depth= 14] . ( 5 sec) [ -16061.6698] [ 2440] [depth= 12] . ( 5 sec) [ -15945.3858] [ 2417] [depth= 3] . ( 5 sec) [ -15848.0564] [ 2415] [depth= 14] . ( 6 sec) [ -15800.0448] [ 2398] [depth= 5] . ( 6 sec) [ -15729.1853] [ 2377] [depth= 9] . ( 6 sec) [ -15691.8801] [ 2374] [depth= 18] . ( 6 sec) [ -15559.2123] [ 2356] [depth= 1] . ( 6 sec) [ -15506.1929] [ 2355] [depth= 10] . ( 6 sec) [ -15480.1745] [ 2342] [depth= 4] . ( 6 sec) [ -15397.9581] [ 2335] [depth= 1] . ( 6 sec) [ -15343.6026] [ 2331] [depth= 7] . ( 6 sec) [ -15291.4564] [ 2315] [depth= 5] . ( 7 sec) [ -15246.3039] [ 2311] [depth= 14] . ( 7 sec) [ -15106.9226] [ 2278] [depth= 12] . ( 7 sec) [ -14974.7153] [ 2255] [depth= 15] . ( 7 sec) [ -14941.6113] [ 2250] [depth= 7] . ( 7 sec) [ -14856.0045] [ 2233] [depth= 20] . ( 7 sec) [ -14614.8465] [ 2196] [depth= 18] . ( 7 sec) [ -14611.8662] [ 2199] [depth= 7] . ( 7 sec) [ -14605.4719] [ 2200] [depth= 1] . ( 7 sec) [ -14531.2963] [ 2186] [depth= 9] . ( 8 sec) [ -14461.8054] [ 2174] [depth= 5] . ( 8 sec) [ -14459.1541] [ 2175] [depth= 1] . ( 8 sec) [ -14040.0501] [ 2168] [depth= 19] . ( 8 sec) [ -13983.5104] [ 2142] [depth= 14] . ( 8 sec) [ -13917.1667] [ 2125] [depth= 11] . ( 8 sec) [ -13875.0113] [ 2114] [depth= 12] . ( 8 sec) [ -13779.6747] [ 2099] [depth= 6] . ( 8 sec) [ -13766.3339] [ 2099] [depth= 1] . ( 9 sec) [ -13744.0433] [ 2093] [depth= 1] . ( 9 sec) [ -13706.5893] [ 2092] [depth= 10] . ( 9 sec) [ -13636.4225] [ 2066] [depth= 5] . ( 9 sec) [ -13489.0465] [ 2043] [depth= 3] . ( 9 sec) [ -13478.9629] [ 2041] [depth= 2] . ( 9 sec) [ -13467.3617] [ 2039] [depth= 2] . ( 9 sec) [ -13430.5910] [ 2034] [depth= 9] . ( 9 sec) [ -13404.9913] [ 2033] [depth= 1] . ( 9 sec) [ -13367.5240] [ 2022] [depth= 10] . ( 9 sec) [ -13350.9209] [ 2022] [depth= 1] . ( 9 sec) [ -13237.8989] [ 2015] [depth= 8] . ( 10 sec) [ -13190.1958] [ 1995] [depth= 12] . ( 10 sec) [ -13056.1600] [ 1993] [depth= 1] . ( 10 sec) [ -13032.2604] [ 1988] [depth= 1] . ( 10 sec) [ -12879.5015] [ 1958] [depth= 8] . ( 10 sec) [ -12746.3844] [ 1962] [depth= 1] . ( 10 sec) [ -12693.5178] [ 1969] [depth= 7] . ( 10 sec) [ -12692.6506] [ 1972] [depth= 1] . ( 10 sec) [ -12644.0354] [ 1954] [depth= 4] . ( 10 sec) [ -12594.6852] [ 1937] [depth= 9] . ( 10 sec) [ -12562.2468] [ 1934] [depth= 1] . ( 11 sec) [ -12407.4504] [ 1908] [depth= 10] . ( 11 sec) [ -12379.2950] [ 1903] [depth= 2] . ( 11 sec) [ -12362.0715] [ 1896] [depth= 2] . ( 11 sec) [ -12289.4899] [ 1892] [depth= 5] . ( 11 sec) [ -12124.0494] [ 1833] [depth= 9] . ( 11 sec) [ -12122.2977] [ 1833] [depth= 12] . ( 11 sec) [ -11954.0256] [ 1823] [depth= 8] . ( 12 sec) [ -11895.8257] [ 1814] [depth= 6] . ( 12 sec) [ -11888.3462] [ 1815] [depth= 1] . ( 12 sec) [ -11883.4413] [ 1814] [depth= 1] . ( 12 sec) [ -11856.9270] [ 1809] [depth= 8] . ( 12 sec) [ -11807.0694] [ 1808] [depth= 1] . ( 12 sec) [ -11720.7806] [ 1790] [depth= 11] . ( 12 sec) [ -11708.0497] [ 1790] [depth= 1] . ( 12 sec) [ -11696.6765] [ 1788] [depth= 6] . ( 13 sec) [ -11623.8156] [ 1762] [depth= 19] . ( 13 sec) [ -11532.8144] [ 1725] [depth= 2] . ( 13 sec) [ -11510.7014] [ 1729] [depth= 10] . ( 13 sec) [ -11490.9723] [ 1723] [depth= 1] . ( 13 sec) [ -11445.8378] [ 1720] [depth= 5] . ( 13 sec) [ -11408.0823] [ 1716] [depth= 1] . ( 13 sec) [ -11385.8806] [ 1715] [depth= 4] . ( 13 sec) [ -11307.6548] [ 1698] [depth= 1] . ( 13 sec) [ -11281.2228] [ 1694] [depth= 2] . ( 13 sec) [ -11143.7885] [ 1663] [depth= 3] . ( 14 sec) [ -11132.1589] [ 1655] [depth= 6] . ( 14 sec) [ -11125.7408] [ 1654] [depth= 1] . ( 14 sec) [ -11070.7728] [ 1652] [depth= 5] . ( 14 sec) [ -11033.9229] [ 1650] [depth= 9] . ( 14 sec) [ -10933.6397] [ 1630] [depth= 17] . ( 14 sec) [ -10838.0652] [ 1604] [depth= 6] . ( 14 sec) [ -10818.8276] [ 1602] [depth= 2] . ( 14 sec) [ -10773.8987] [ 1588] [depth= 20] . ( 14 sec) [ -10773.6852] [ 1588] [depth= 1] . ( 15 sec) [ -10773.0505] [ 1587] [depth= 1] . ( 15 sec) [ -10773.0333] [ 1590] [depth= 1] . ( 15 sec) [ -10715.0576] [ 1576] [depth= 5] . ( 16 sec) [ -10705.9831] [ 1575] [depth= 2] . ( 16 sec) [ -10705.9422] [ 1576] [depth= 2] . ( 16 sec) [ -10695.0635] [ 1574] [depth= 1] . ( 16 sec) [ -10690.4797] [ 1572] [depth= 1] . ( 16 sec) [ -10684.2330] [ 1574] [depth= 17] . ( 16 sec) [ -10655.5685] [ 1571] [depth= 1] . ( 16 sec) [ -10648.5480] [ 1568] [depth= 1] . ( 16 sec) [ -10561.8578] [ 1544] [depth= 21] . ( 16 sec) [ -10561.7893] [ 1546] [depth= 1] . ( 16 sec) [ -10494.9370] [ 1541] [depth= 12] . ( 17 sec) [ -10452.2454] [ 1537] [depth= 15] . ( 17 sec) [ -10444.8181] [ 1538] [depth= 14] . ( 17 sec) [ -10387.5165] [ 1519] [depth= 13] . ( 17 sec) [ -10381.4313] [ 1517] [depth= 1] . ( 17 sec) [ -10311.5286] [ 1500] [depth= 12] . ( 17 sec) [ -10248.3502] [ 1493] [depth= 11] . ( 18 sec) [ -10242.7787] [ 1492] [depth= 4] . ( 18 sec) [ -10216.3778] [ 1492] [depth= 24] . ( 18 sec) [ -10145.4144] [ 1452] [depth= 15] . ( 18 sec) [ -10127.0993] [ 1448] [depth= 1] . ( 18 sec) [ -10097.1506] [ 1440] [depth= 2] . ( 18 sec) [ -10095.6314] [ 1439] [depth= 1] . ( 18 sec) [ -10085.9761] [ 1437] [depth= 1] . ( 18 sec) [ -10084.5369] [ 1436] [depth= 6] . ( 19 sec) [ -10079.9466] [ 1435] [depth= 1] . ( 19 sec) [ -10035.3794] [ 1423] [depth= 2] . ( 20 sec) [ -9955.8469] [ 1414] [depth= 1] . ( 20 sec) [ -9934.3073] [ 1410] [depth= 6] . ( 20 sec) [ -9922.6087] [ 1408] [depth= 4] . ( 20 sec) [ -9921.5462] [ 1406] [depth= 1] . ( 20 sec) [ -9904.5303] [ 1401] [depth= 13] . ( 20 sec) [ -9902.5038] [ 1401] [depth= 1] . ( 21 sec) [ -9880.3347] [ 1392] [depth= 12] . ( 21 sec) [ -9866.3953] [ 1383] [depth= 7] . ( 21 sec) [ -9711.8732] [ 1384] [depth= 1] . ( 21 sec) [ -9710.8316] [ 1384] [depth= 1] . ( 21 sec) [ -9709.4155] [ 1382] [depth= 2] . ( 21 sec) [ -9708.1462] [ 1382] [depth= 1] . ( 21 sec) [ -9685.4302] [ 1377] [depth= 10] . ( 21 sec) [ -9613.9530] [ 1358] [depth= 5] . ( 21 sec) [ -9567.6726] [ 1344] [depth= 7] . ( 22 sec) [ -9564.8015] [ 1343] [depth= 1] . ( 22 sec) [ -9562.2387] [ 1342] [depth= 1] . ( 22 sec) [ -9501.6759] [ 1326] [depth= 13] . ( 22 sec) [ -9493.0847] [ 1325] [depth= 5] . ( 23 sec) [ -9491.2680] [ 1327] [depth= 1] . ( 23 sec) [ -9489.4860] [ 1327] [depth= 1] . ( 23 sec) [ -9489.1564] [ 1327] [depth= 2] . ( 23 sec) [ -9488.3894] [ 1327] [depth= 6] . ( 24 sec) [ -9472.9948] [ 1327] [depth= 3] . ( 25 sec) [ -9467.3818] [ 1327] [depth= 1] . ( 25 sec) [ -9463.6388] [ 1326] [depth= 2] . ( 25 sec) [ -9458.1163] [ 1325] [depth= 1] . ( 25 sec) [ -9450.6290] [ 1323] [depth= 1] . ( 25 sec) [ -9449.3291] [ 1323] [depth= 1] . ( 25 sec) [ -9443.3815] [ 1322] [depth= 10] . ( 26 sec) [ -9358.7563] [Branch lengths ] . ( 30 sec) [ -9346.5230] [GTR parameters ] . ( 30 sec) [ -9312.8335] [Alpha ][ 0.302087] . ( 31 sec) [ -9310.4703] [ 1322] [depth= 6] . ( 31 sec) [ -9308.7585] [ 1322] [depth= 1] . ( 31 sec) [ -9261.3171] [ 1309] [depth= 4] . ( 31 sec) [ -9255.1452] [ 1307] [depth= 1] . ( 32 sec) [ -9253.3926] [ 1306] [depth= 1] . ( 32 sec) [ -9251.9487] [ 1295] [depth= 3] . ( 32 sec) [ -9249.8220] [ 1295] [depth= 1] . ( 32 sec) [ -9249.7701] [ 1295] [depth= 2] . ( 32 sec) [ -9243.3582] [ 1295] [depth= 9] . ( 33 sec) [ -9242.2995] [ 1295] [depth= 1] . ( 33 sec) [ -9242.2409] [ 1295] [depth= 2] . ( 33 sec) [ -9241.6173] [ 1294] [depth= 3] . ( 33 sec) [ -9240.9370] [ 1294] [depth= 1] . ( 33 sec) [ -9240.8676] [ 1294] [depth= 1] . ( 34 sec) [ -9235.1540] [ 1298] [depth= 3] . ( 34 sec) [ -9233.5546] [ 1296] [depth= 2] . ( 34 sec) [ -9232.8000] [ 1294] [depth= 4] . ( 36 sec) [ -9231.7288] [ 1295] [depth= 1] . ( 37 sec) [ -9184.0302] [ 1281] [depth= 4] . ( 38 sec) [ -9182.8731] [ 1280] [depth= 1] . ( 38 sec) [ -9182.3196] [ 1280] [depth= 1] . ( 38 sec) [ -9181.8953] [ 1280] [depth= 1] . ( 39 sec) [ -9180.0016] [ 1281] [depth= 1] . ( 39 sec) [ -9174.4998] [ 1280] [depth= 1] . ( 39 sec) [ -9173.2674] [ 1277] [depth= 3] . ( 39 sec) [ -9144.6644] [ 1273] [depth= 2] . ( 39 sec) [ -9144.5468] [ 1272] [depth= 1] . ( 40 sec) [ -9139.3414] [ 1270] [depth= 1] . ( 40 sec) [ -9132.2346] [ 1268] [depth= 10] . ( 40 sec) [ -9128.8769] [ 1268] [depth= 1] . ( 40 sec) [ -9121.1796] [ 1267] [depth= 3] . ( 41 sec) [ -9121.0528] [ 1269] [depth= 1] . ( 41 sec) [ -9117.7161] [ 1267] [depth= 3] . ( 41 sec) [ -9113.3868] [ 1266] [depth= 1] . ( 42 sec) [ -9112.7346] [ 1264] [depth= 2] . ( 46 sec) [ -9106.5327] [ 1262] [depth= 1] . ( 48 sec) [ -9105.8689] [ 1265] [depth= 1] . ( 49 sec) [ -9105.8026] [ 1265] [depth= 1] . ( 49 sec) [ -9099.3614] [ 1263] [depth= 1] . ( 50 sec) [ -9098.7520] [ 1263] [depth= 1] . ( 51 sec) [ -9098.0367] [ 1263] [depth= 1] . ( 51 sec) [ -9095.3048] [ 1261] [depth= 1] . ( 52 sec) [ -9088.0621] [ 1257] [depth= 1] . ( 52 sec) [ -9066.3770] [ 1252] [depth= 2] . ( 53 sec) [ -9066.1707] [ 1252] [depth= 1] . ( 53 sec) [ -9066.0240] [ 1252] [depth= 1] . ( 53 sec) [ -9065.9694] [ 1251] [depth= 3] . ( 53 sec) [ -9065.8367] [ 1252] [depth= 1] . ( 53 sec) [ -9062.0390] [ 1250] [depth= 1] . ( 54 sec) [ -9062.0289] [ 1250] [depth= 1] . ( 55 sec) [ -9061.8876] [ 1250] [depth= 1] . ( 57 sec) [ -9059.7976] [ 1249] [depth= 2] . ( 58 sec) [ -9056.8900] [ 1248] [depth= 1] . ( 59 sec) [ -9038.1561] [ 1243] [depth= 6] . ( 59 sec) [ -9034.0622] [ 1243] [depth= 3] . ( 59 sec) [ -9027.2603] [ 1241] [depth= 1] . ( 59 sec) [ -9020.1917] [ 1239] [depth= 1] . ( 60 sec) [ -9008.1986] [Branch lengths ] . ( 64 sec) [ -9006.6414] [GTR parameters ] . ( 64 sec) [ -9006.4305] [Alpha ][ 0.313996] . ( 65 sec) [ -9006.3217] [ 1240] [depth= 5] . ( 67 sec) [ -9006.2375] [ 1241] [depth= 1] . ( 68 sec) [ -9001.9798] [ 1240] [depth= 3] . ( 76 sec) [ -9000.6660] [ 1243] [depth= 2] . ( 77 sec) [ -9000.3066] [ 1243] [depth= 1] . ( 77 sec) [ -9000.1192] [ 1243] [depth= 1] . ( 82 sec) [ -8998.3123] [ 1242] [depth= 1] . ( 88 sec) [ -8995.3726] [ 1241] [depth= 2] . ( 103 sec) [ -8992.4044] [Branch lengths ] . ( 106 sec) [ -8992.3531] [GTR parameters ] . ( 106 sec) [ -8992.3531] [Alpha ][ 0.314310] . ( 113 sec) [ -8992.2550] [ 1242] [depth= 3] . ( 117 sec) [ -8992.1203] [ 1241] [depth= 1] . ( 119 sec) [ -8991.9453] [ 1242] [depth= 1] . ( 130 sec) [ -8991.8773] [ 1242] [depth= 1] . ( 147 sec) [ -8991.4054] [Branch lengths ] . ( 148 sec) [ -8991.4052] [GTR parameters ] . ( 148 sec) [ -8991.4046] [Alpha ][ 0.313622] . ( 230 sec) [ -8991.3272] [Branch lengths ] . ( 230 sec) [ -8991.3272] [Topology ] . ( 232 sec) [ -8991.2279] [Topology ] . ( 234 sec) [ -8990.7838] [Topology ] . ( 236 sec) [ -8990.7604] [Topology ] . ( 238 sec) [ -8990.7553] [Topology ] . ( 239 sec) [ -8990.7528] [Topology ] . ( 241 sec) [ -8990.7513] [Topology ] . ( 243 sec) [ -8990.7503] [Topology ] . ( 244 sec) [ -8990.7498] [GTR parameters ] . ( 244 sec) [ -8990.7497] [Alpha ][ 0.313308] . ( 244 sec) [ -8990.7497] [Topology ] . ( 246 sec) [ -8990.7491] [Topology ] . ( 249 sec) [ -8990.7072] [GTR parameters ] . ( 249 sec) [ -8990.7069] [Alpha ][ 0.313683] . ( 249 sec) [ -8990.7069] [Topology ] . ( 251 sec) [ -8990.7064] [Topology ] . ( 251 sec) [ -8990.7064] [GTR parameters ] . ( 251 sec) [ -8990.7064] [Alpha ][ 0.313683] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8990.706392. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -18590.6793] [GTR parameters ] . ( 2 sec) [ -18206.4461] [Alpha ][ 0.500960] . ( 2 sec) [ -17939.7555] [ 2640] [depth= 2] . ( 2 sec) [ -17768.9036] [ 2605] [depth= 9] . ( 2 sec) [ -17764.4793] [ 2604] [depth= 1] . ( 3 sec) [ -17735.0977] [ 2601] [depth= 6] . ( 3 sec) [ -17602.6296] [ 2589] [depth= 6] . ( 3 sec) [ -17586.7929] [ 2587] [depth= 4] . ( 3 sec) [ -17585.1330] [ 2585] [depth= 4] . ( 3 sec) [ -17574.1076] [ 2587] [depth= 2] . ( 3 sec) [ -17536.9177] [ 2586] [depth= 13] . ( 3 sec) [ -17496.2498] [ 2586] [depth= 2] . ( 3 sec) [ -17487.9553] [ 2579] [depth= 13] . ( 3 sec) [ -17368.9073] [ 2578] [depth= 2] . ( 3 sec) [ -17145.5148] [ 2569] [depth= 5] . ( 3 sec) [ -17086.4871] [ 2573] [depth= 1] . ( 4 sec) [ -16965.2484] [ 2562] [depth= 15] . ( 4 sec) [ -16879.7884] [ 2522] [depth= 10] . ( 4 sec) [ -16730.6952] [ 2504] [depth= 10] . ( 4 sec) [ -16388.2792] [ 2480] [depth= 19] . ( 4 sec) [ -16350.1714] [ 2469] [depth= 11] . ( 4 sec) [ -16349.2781] [ 2470] [depth= 1] . ( 4 sec) [ -16149.2547] [ 2447] [depth= 14] . ( 4 sec) [ -15990.2977] [ 2419] [depth= 9] . ( 4 sec) [ -15980.3906] [ 2413] [depth= 12] . ( 4 sec) [ -15906.4186] [ 2395] [depth= 8] . ( 4 sec) [ -15849.7868] [ 2379] [depth= 12] . ( 5 sec) [ -15815.7386] [ 2376] [depth= 21] . ( 5 sec) [ -15792.7364] [ 2366] [depth= 16] . ( 5 sec) [ -15790.6396] [ 2366] [depth= 1] . ( 5 sec) [ -15669.8176] [ 2339] [depth= 18] . ( 5 sec) [ -15626.1464] [ 2322] [depth= 11] . ( 5 sec) [ -15600.1480] [ 2322] [depth= 1] . ( 5 sec) [ -15565.0373] [ 2315] [depth= 7] . ( 5 sec) [ -15528.7931] [ 2308] [depth= 12] . ( 5 sec) [ -15370.6259] [ 2286] [depth= 11] . ( 5 sec) [ -15249.5362] [ 2273] [depth= 6] . ( 6 sec) [ -15192.4606] [ 2261] [depth= 8] . ( 6 sec) [ -15127.6741] [ 2240] [depth= 3] . ( 6 sec) [ -15121.4536] [ 2238] [depth= 1] . ( 6 sec) [ -15113.3588] [ 2241] [depth= 3] . ( 6 sec) [ -15097.3445] [ 2236] [depth= 10] . ( 6 sec) [ -15039.7212] [ 2230] [depth= 1] . ( 6 sec) [ -14897.3531] [ 2210] [depth= 18] . ( 6 sec) [ -14589.2319] [ 2215] [depth= 15] . ( 6 sec) [ -14509.1443] [ 2210] [depth= 9] . ( 7 sec) [ -14394.2923] [ 2198] [depth= 9] . ( 7 sec) [ -14350.0671] [ 2193] [depth= 1] . ( 7 sec) [ -14346.3128] [ 2195] [depth= 10] . ( 7 sec) [ -14309.0117] [ 2189] [depth= 6] . ( 7 sec) [ -14290.5245] [ 2180] [depth= 4] . ( 7 sec) [ -14231.3708] [ 2180] [depth= 1] . ( 7 sec) [ -14226.1898] [ 2182] [depth= 1] . ( 7 sec) [ -14174.9319] [ 2180] [depth= 2] . ( 7 sec) [ -14038.5116] [ 2154] [depth= 9] . ( 7 sec) [ -14035.1477] [ 2150] [depth= 10] . ( 8 sec) [ -13985.8282] [ 2141] [depth= 3] . ( 8 sec) [ -13978.5268] [ 2138] [depth= 1] . ( 8 sec) [ -13955.2362] [ 2133] [depth= 5] . ( 8 sec) [ -13885.3258] [ 2133] [depth= 1] . ( 8 sec) [ -13778.8136] [ 2107] [depth= 15] . ( 8 sec) [ -13770.6384] [ 2106] [depth= 4] . ( 8 sec) [ -13740.3270] [ 2105] [depth= 3] . ( 8 sec) [ -13715.4161] [ 2104] [depth= 12] . ( 8 sec) [ -13686.2917] [ 2103] [depth= 2] . ( 8 sec) [ -13614.0641] [ 2091] [depth= 4] . ( 8 sec) [ -13565.7537] [ 2082] [depth= 1] . ( 9 sec) [ -13520.5702] [ 2082] [depth= 20] . ( 9 sec) [ -13417.6457] [ 2054] [depth= 17] . ( 9 sec) [ -13374.9182] [ 2059] [depth= 1] . ( 9 sec) [ -13316.8641] [ 2056] [depth= 14] . ( 9 sec) [ -13256.5732] [ 2038] [depth= 9] . ( 9 sec) [ -13227.4955] [ 2029] [depth= 1] . ( 9 sec) [ -13205.0583] [ 2029] [depth= 1] . ( 9 sec) [ -13153.4546] [ 2015] [depth= 9] . ( 9 sec) [ -13107.8116] [ 2006] [depth= 13] . ( 9 sec) [ -13075.2738] [ 1991] [depth= 4] . ( 9 sec) [ -13072.7851] [ 1990] [depth= 1] . ( 10 sec) [ -12951.8608] [ 1961] [depth= 11] . ( 10 sec) [ -12917.2752] [ 1952] [depth= 16] . ( 10 sec) [ -12866.3403] [ 1953] [depth= 1] . ( 10 sec) [ -12854.7389] [ 1952] [depth= 1] . ( 10 sec) [ -12840.5372] [ 1948] [depth= 15] . ( 10 sec) [ -12814.1756] [ 1946] [depth= 14] . ( 10 sec) [ -12799.5831] [ 1944] [depth= 18] . ( 10 sec) [ -12735.4028] [ 1929] [depth= 10] . ( 10 sec) [ -12685.3397] [ 1917] [depth= 19] . ( 11 sec) [ -12658.7570] [ 1911] [depth= 4] . ( 11 sec) [ -12652.9058] [ 1910] [depth= 1] . ( 11 sec) [ -12633.8083] [ 1906] [depth= 4] . ( 11 sec) [ -12625.7962] [ 1906] [depth= 1] . ( 11 sec) [ -12583.6322] [ 1898] [depth= 5] . ( 11 sec) [ -12412.3914] [ 1872] [depth= 8] . ( 11 sec) [ -12308.6062] [ 1872] [depth= 2] . ( 11 sec) [ -12272.1860] [ 1864] [depth= 1] . ( 11 sec) [ -12123.7092] [ 1842] [depth= 10] . ( 11 sec) [ -12027.6952] [ 1826] [depth= 15] . ( 11 sec) [ -12021.4150] [ 1827] [depth= 1] . ( 12 sec) [ -11920.3728] [ 1804] [depth= 9] . ( 12 sec) [ -11919.3357] [ 1806] [depth= 1] . ( 12 sec) [ -11840.1072] [ 1805] [depth= 6] . ( 12 sec) [ -11757.0293] [ 1812] [depth= 1] . ( 12 sec) [ -11685.7548] [ 1804] [depth= 5] . ( 12 sec) [ -11679.8729] [ 1803] [depth= 1] . ( 13 sec) [ -11679.7489] [ 1808] [depth= 2] . ( 13 sec) [ -11677.9186] [ 1809] [depth= 8] . ( 14 sec) [ -11654.8943] [ 1805] [depth= 7] . ( 14 sec) [ -11643.5096] [ 1802] [depth= 12] . ( 14 sec) [ -11546.0379] [ 1794] [depth= 6] . ( 14 sec) [ -11491.7601] [ 1777] [depth= 1] . ( 14 sec) [ -11436.2355] [ 1757] [depth= 7] . ( 14 sec) [ -11326.5419] [ 1724] [depth= 8] . ( 14 sec) [ -11320.1158] [ 1723] [depth= 1] . ( 14 sec) [ -11251.9228] [ 1708] [depth= 7] . ( 14 sec) [ -11244.9778] [ 1706] [depth= 2] . ( 15 sec) [ -11136.8215] [ 1690] [depth= 6] . ( 15 sec) [ -11058.9556] [ 1666] [depth= 4] . ( 15 sec) [ -11044.3795] [ 1662] [depth= 3] . ( 15 sec) [ -10952.0614] [ 1644] [depth= 1] . ( 15 sec) [ -10946.2908] [ 1640] [depth= 12] . ( 15 sec) [ -10910.4902] [ 1631] [depth= 3] . ( 15 sec) [ -10909.2924] [ 1628] [depth= 6] . ( 15 sec) [ -10890.6884] [ 1626] [depth= 1] . ( 15 sec) [ -10838.1648] [ 1612] [depth= 1] . ( 15 sec) [ -10825.7151] [ 1610] [depth= 3] . ( 16 sec) [ -10822.7947] [ 1606] [depth= 1] . ( 16 sec) [ -10723.5371] [ 1616] [depth= 1] . ( 16 sec) [ -10688.9899] [ 1606] [depth= 1] . ( 16 sec) [ -10665.4884] [ 1601] [depth= 2] . ( 16 sec) [ -10616.8092] [ 1587] [depth= 10] . ( 16 sec) [ -10598.7834] [ 1583] [depth= 1] . ( 16 sec) [ -10596.3180] [ 1582] [depth= 1] . ( 17 sec) [ -10589.0419] [ 1579] [depth= 1] . ( 17 sec) [ -10538.2354] [ 1570] [depth= 8] . ( 17 sec) [ -10434.8327] [ 1550] [depth= 9] . ( 17 sec) [ -10402.0873] [ 1545] [depth= 7] . ( 17 sec) [ -10388.5560] [ 1541] [depth= 2] . ( 17 sec) [ -10386.3774] [ 1540] [depth= 4] . ( 17 sec) [ -10383.4939] [ 1539] [depth= 4] . ( 17 sec) [ -10345.4157] [ 1526] [depth= 4] . ( 17 sec) [ -10342.2035] [ 1526] [depth= 1] . ( 17 sec) [ -10294.8117] [ 1521] [depth= 3] . ( 18 sec) [ -10282.6155] [ 1519] [depth= 1] . ( 18 sec) [ -10249.9362] [ 1500] [depth= 6] . ( 18 sec) [ -10249.8396] [ 1500] [depth= 1] . ( 18 sec) [ -10248.3954] [ 1500] [depth= 1] . ( 18 sec) [ -10246.7999] [ 1500] [depth= 1] . ( 18 sec) [ -10244.2548] [ 1498] [depth= 2] . ( 18 sec) [ -10243.8610] [ 1500] [depth= 2] . ( 18 sec) [ -10234.2986] [ 1501] [depth= 1] . ( 18 sec) [ -10233.5452] [ 1501] [depth= 1] . ( 18 sec) [ -10223.7766] [ 1499] [depth= 3] . ( 18 sec) [ -10207.3981] [ 1494] [depth= 3] . ( 19 sec) [ -10095.5968] [ 1463] [depth= 11] . ( 19 sec) [ -10083.2883] [ 1466] [depth= 7] . ( 19 sec) [ -10082.4809] [ 1466] [depth= 3] . ( 19 sec) [ -10028.6151] [ 1453] [depth= 8] . ( 19 sec) [ -10021.1531] [ 1451] [depth= 1] . ( 19 sec) [ -10019.9384] [ 1453] [depth= 1] . ( 19 sec) [ -10019.9142] [ 1456] [depth= 1] . ( 20 sec) [ -10017.3375] [ 1455] [depth= 1] . ( 20 sec) [ -10007.5822] [ 1447] [depth= 4] . ( 20 sec) [ -9976.7963] [ 1447] [depth= 1] . ( 20 sec) [ -9938.5218] [ 1441] [depth= 14] . ( 20 sec) [ -9931.9294] [ 1442] [depth= 2] . ( 20 sec) [ -9926.5260] [ 1441] [depth= 4] . ( 20 sec) [ -9923.6821] [ 1440] [depth= 2] . ( 20 sec) [ -9910.1465] [ 1436] [depth= 14] . ( 21 sec) [ -9870.1158] [ 1423] [depth= 1] . ( 21 sec) [ -9843.4402] [ 1412] [depth= 15] . ( 21 sec) [ -9842.1082] [ 1412] [depth= 3] . ( 22 sec) [ -9832.8060] [ 1411] [depth= 1] . ( 22 sec) [ -9733.9500] [ 1377] [depth= 2] . ( 22 sec) [ -9663.5264] [ 1359] [depth= 1] . ( 22 sec) [ -9659.1757] [ 1359] [depth= 2] . ( 22 sec) [ -9637.2064] [ 1358] [depth= 4] . ( 23 sec) [ -9532.5073] [Branch lengths ] . ( 27 sec) [ -9521.6304] [GTR parameters ] . ( 27 sec) [ -9486.4375] [Alpha ][ 0.302085] . ( 27 sec) [ -9450.6266] [ 1351] [depth= 1] . ( 27 sec) [ -9449.8262] [ 1352] [depth= 1] . ( 27 sec) [ -9435.0752] [ 1347] [depth= 1] . ( 27 sec) [ -9426.6000] [ 1341] [depth= 6] . ( 27 sec) [ -9397.1680] [ 1327] [depth= 1] . ( 27 sec) [ -9390.9452] [ 1325] [depth= 1] . ( 28 sec) [ -9388.1276] [ 1323] [depth= 3] . ( 28 sec) [ -9388.0891] [ 1322] [depth= 1] . ( 28 sec) [ -9386.1520] [ 1322] [depth= 1] . ( 29 sec) [ -9343.7119] [ 1306] [depth= 10] . ( 29 sec) [ -9330.1035] [ 1305] [depth= 2] . ( 29 sec) [ -9305.4284] [ 1298] [depth= 1] . ( 30 sec) [ -9304.6952] [ 1297] [depth= 3] . ( 30 sec) [ -9259.7601] [ 1293] [depth= 8] . ( 30 sec) [ -9249.0336] [ 1289] [depth= 4] . ( 30 sec) [ -9219.5518] [ 1285] [depth= 4] . ( 30 sec) [ -9217.0024] [ 1284] [depth= 1] . ( 30 sec) [ -9216.1729] [ 1280] [depth= 2] . ( 30 sec) [ -9210.2744] [ 1278] [depth= 2] . ( 31 sec) [ -9209.8157] [ 1278] [depth= 1] . ( 31 sec) [ -9209.0705] [ 1277] [depth= 1] . ( 31 sec) [ -9206.6897] [ 1277] [depth= 1] . ( 31 sec) [ -9204.2562] [ 1275] [depth= 4] . ( 31 sec) [ -9203.3957] [ 1276] [depth= 2] . ( 32 sec) [ -9171.1386] [ 1269] [depth= 1] . ( 32 sec) [ -9168.1941] [ 1271] [depth= 1] . ( 33 sec) [ -9164.9422] [ 1271] [depth= 2] . ( 35 sec) [ -9164.7478] [ 1271] [depth= 2] . ( 35 sec) [ -9164.0591] [ 1270] [depth= 2] . ( 35 sec) [ -9162.5023] [ 1271] [depth= 1] . ( 35 sec) [ -9161.5490] [ 1270] [depth= 2] . ( 35 sec) [ -9160.2989] [ 1270] [depth= 1] . ( 35 sec) [ -9158.5218] [ 1270] [depth= 1] . ( 35 sec) [ -9158.0756] [ 1270] [depth= 1] . ( 35 sec) [ -9122.8233] [ 1261] [depth= 4] . ( 36 sec) [ -9122.0424] [ 1261] [depth= 1] . ( 36 sec) [ -9114.2930] [ 1262] [depth= 1] . ( 37 sec) [ -9114.0967] [ 1262] [depth= 1] . ( 37 sec) [ -9113.6713] [ 1262] [depth= 1] . ( 37 sec) [ -9101.2107] [ 1258] [depth= 1] . ( 38 sec) [ -9084.8687] [ 1258] [depth= 1] . ( 38 sec) [ -9081.2580] [ 1257] [depth= 1] . ( 39 sec) [ -9080.8431] [ 1257] [depth= 1] . ( 39 sec) [ -9080.2413] [ 1257] [depth= 1] . ( 39 sec) [ -9079.2861] [ 1257] [depth= 1] . ( 39 sec) [ -9078.0152] [ 1256] [depth= 5] . ( 39 sec) [ -9070.0654] [ 1253] [depth= 2] . ( 39 sec) [ -9067.7946] [ 1253] [depth= 3] . ( 39 sec) [ -9067.3326] [ 1252] [depth= 1] . ( 40 sec) [ -9055.2420] [ 1248] [depth= 1] . ( 40 sec) [ -9055.1268] [ 1248] [depth= 1] . ( 40 sec) [ -9054.1787] [ 1248] [depth= 1] . ( 42 sec) [ -9052.8890] [ 1247] [depth= 1] . ( 42 sec) [ -9052.1182] [ 1247] [depth= 1] . ( 42 sec) [ -9052.0928] [ 1247] [depth= 1] . ( 43 sec) [ -9038.0890] [ 1242] [depth= 2] . ( 44 sec) [ -9036.0337] [ 1247] [depth= 1] . ( 46 sec) [ -9034.9596] [ 1247] [depth= 1] . ( 46 sec) [ -9034.8025] [ 1247] [depth= 1] . ( 47 sec) [ -9034.5409] [ 1247] [depth= 1] . ( 47 sec) [ -9034.1949] [ 1248] [depth= 3] . ( 48 sec) [ -9033.4389] [ 1247] [depth= 1] . ( 50 sec) [ -9031.2066] [ 1247] [depth= 1] . ( 50 sec) [ -9028.6476] [ 1247] [depth= 1] . ( 50 sec) [ -9028.6043] [ 1247] [depth= 1] . ( 51 sec) [ -9028.5210] [ 1247] [depth= 2] . ( 51 sec) [ -9028.4941] [ 1247] [depth= 1] . ( 51 sec) [ -9027.9930] [ 1247] [depth= 1] . ( 52 sec) [ -9027.8955] [ 1248] [depth= 1] . ( 53 sec) [ -9027.1789] [ 1248] [depth= 1] . ( 55 sec) [ -9027.0836] [ 1250] [depth= 1] . ( 56 sec) [ -9024.8967] [ 1248] [depth= 1] . ( 57 sec) [ -9008.9691] [Branch lengths ] . ( 60 sec) [ -9007.2890] [GTR parameters ] . ( 60 sec) [ -9007.1254] [Alpha ][ 0.312440] . ( 61 sec) [ -9003.8246] [ 1245] [depth= 1] . ( 65 sec) [ -9003.5539] [ 1244] [depth= 2] . ( 66 sec) [ -9002.6572] [ 1245] [depth= 6] . ( 67 sec) [ -9002.4883] [ 1245] [depth= 1] . ( 77 sec) [ -9002.4051] [ 1245] [depth= 2] . ( 88 sec) [ -9001.2930] [ 1245] [depth= 1] . ( 95 sec) [ -9001.1372] [ 1245] [depth= 2] . ( 96 sec) [ -8997.7356] [Branch lengths ] . ( 97 sec) [ -8997.7257] [GTR parameters ] . ( 97 sec) [ -8997.7257] [Alpha ][ 0.312752] . ( 114 sec) [ -8996.9339] [ 1245] [depth= 1] . ( 115 sec) [ -8996.7853] [ 1244] [depth= 3] . ( 117 sec) [ -8996.7328] [ 1244] [depth= 1] . ( 125 sec) [ -8996.6020] [ 1241] [depth= 1] . ( 128 sec) [ -8996.5197] [ 1242] [depth= 1] . ( 129 sec) [ -8995.6461] [ 1241] [depth= 1] . ( 136 sec) [ -8991.9975] [Branch lengths ] . ( 137 sec) [ -8991.9431] [GTR parameters ] . ( 137 sec) [ -8991.9417] [Alpha ][ 0.313706] . ( 149 sec) [ -8991.7124] [ 1241] [depth= 2] . ( 160 sec) [ -8991.5654] [ 1241] [depth= 1] . ( 176 sec) [ -8990.9235] [Branch lengths ] . ( 177 sec) [ -8990.9233] [GTR parameters ] . ( 177 sec) [ -8990.9233] [Alpha ][ 0.313706] . ( 222 sec) [ -8990.8898] [Branch lengths ] . ( 314 sec) [ -8990.8814] [Branch lengths ] . ( 314 sec) [ -8990.8814] [Topology ] . ( 316 sec) [ -8990.8798] [Topology ] . ( 318 sec) [ -8990.8791] [Topology ] . ( 320 sec) [ -8990.8625] [GTR parameters ] . ( 320 sec) [ -8990.8625] [Alpha ][ 0.313706] . ( 320 sec) [ -8990.8625] [Topology ] . ( 322 sec) [ -8990.8621] [Topology ] . ( 323 sec) [ -8990.8621] [GTR parameters ] . ( 323 sec) [ -8990.8621] [Alpha ][ 0.313706] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8990.862056. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -18601.6802] [GTR parameters ] . ( 3 sec) [ -18211.3421] [Alpha ][ 0.500960] . ( 4 sec) [ -17868.4126] [ 2636] [depth= 6] . ( 4 sec) [ -17517.4280] [ 2594] [depth= 13] . ( 4 sec) [ -17437.3408] [ 2573] [depth= 10] . ( 4 sec) [ -17294.6054] [ 2561] [depth= 1] . ( 4 sec) [ -17087.8267] [ 2554] [depth= 5] . ( 4 sec) [ -17020.4676] [ 2548] [depth= 2] . ( 4 sec) [ -17006.9914] [ 2545] [depth= 2] . ( 4 sec) [ -16957.6028] [ 2528] [depth= 2] . ( 4 sec) [ -16846.6173] [ 2527] [depth= 1] . ( 5 sec) [ -16828.4855] [ 2520] [depth= 8] . ( 5 sec) [ -16793.4860] [ 2518] [depth= 5] . ( 5 sec) [ -16682.9372] [ 2505] [depth= 1] . ( 5 sec) [ -16674.9384] [ 2504] [depth= 1] . ( 5 sec) [ -16465.2397] [ 2475] [depth= 5] . ( 5 sec) [ -16459.3091] [ 2478] [depth= 1] . ( 5 sec) [ -16358.1929] [ 2474] [depth= 12] . ( 5 sec) [ -16338.3632] [ 2471] [depth= 1] . ( 5 sec) [ -16158.4435] [ 2451] [depth= 8] . ( 5 sec) [ -15972.2586] [ 2390] [depth= 11] . ( 6 sec) [ -15960.7268] [ 2390] [depth= 2] . ( 6 sec) [ -15953.3571] [ 2390] [depth= 1] . ( 6 sec) [ -15937.8353] [ 2388] [depth= 2] . ( 6 sec) [ -15880.9491] [ 2388] [depth= 2] . ( 6 sec) [ -15841.6286] [ 2383] [depth= 20] . ( 6 sec) [ -15810.5948] [ 2381] [depth= 1] . ( 6 sec) [ -15596.1398] [ 2358] [depth= 19] . ( 6 sec) [ -15475.9877] [ 2345] [depth= 18] . ( 6 sec) [ -15434.5042] [ 2339] [depth= 4] . ( 6 sec) [ -15319.1069] [ 2328] [depth= 11] . ( 7 sec) [ -15245.3037] [ 2323] [depth= 11] . ( 7 sec) [ -15160.6078] [ 2315] [depth= 8] . ( 7 sec) [ -15030.2044] [ 2291] [depth= 1] . ( 7 sec) [ -15010.9388] [ 2288] [depth= 16] . ( 7 sec) [ -14967.0524] [ 2264] [depth= 5] . ( 7 sec) [ -14938.3416] [ 2266] [depth= 1] . ( 7 sec) [ -14868.7796] [ 2255] [depth= 4] . ( 7 sec) [ -14853.7867] [ 2253] [depth= 10] . ( 7 sec) [ -14772.8777] [ 2237] [depth= 5] . ( 8 sec) [ -14724.8090] [ 2231] [depth= 1] . ( 8 sec) [ -14592.2940] [ 2209] [depth= 15] . ( 8 sec) [ -14445.2899] [ 2193] [depth= 7] . ( 8 sec) [ -14438.8817] [ 2195] [depth= 1] . ( 8 sec) [ -14342.5695] [ 2183] [depth= 14] . ( 8 sec) [ -14291.1780] [ 2179] [depth= 10] . ( 8 sec) [ -14285.4309] [ 2180] [depth= 9] . ( 8 sec) [ -14268.7680] [ 2174] [depth= 2] . ( 9 sec) [ -14209.0158] [ 2166] [depth= 11] . ( 9 sec) [ -14160.3661] [ 2156] [depth= 1] . ( 9 sec) [ -14157.2238] [ 2154] [depth= 1] . ( 9 sec) [ -13801.9894] [ 2103] [depth= 10] . ( 9 sec) [ -13777.1026] [ 2112] [depth= 1] . ( 9 sec) [ -13647.6690] [ 2094] [depth= 2] . ( 10 sec) [ -13511.0611] [ 2084] [depth= 9] . ( 10 sec) [ -13439.4281] [ 2074] [depth= 6] . ( 10 sec) [ -13439.0941] [ 2074] [depth= 1] . ( 10 sec) [ -13405.8935] [ 2068] [depth= 20] . ( 10 sec) [ -13405.1311] [ 2071] [depth= 11] . ( 10 sec) [ -13401.5871] [ 2068] [depth= 2] . ( 10 sec) [ -13394.2598] [ 2067] [depth= 2] . ( 10 sec) [ -13363.9949] [ 2071] [depth= 16] . ( 10 sec) [ -13280.2730] [ 2067] [depth= 5] . ( 11 sec) [ -13280.0977] [ 2067] [depth= 4] . ( 11 sec) [ -13272.3147] [ 2064] [depth= 6] . ( 11 sec) [ -13137.7034] [ 2062] [depth= 2] . ( 11 sec) [ -13062.7837] [ 2047] [depth= 12] . ( 11 sec) [ -13061.8893] [ 2046] [depth= 5] . ( 11 sec) [ -13053.2797] [ 2045] [depth= 16] . ( 11 sec) [ -13017.8795] [ 2045] [depth= 4] . ( 11 sec) [ -13016.8947] [ 2044] [depth= 2] . ( 11 sec) [ -13013.5957] [ 2044] [depth= 10] . ( 12 sec) [ -13002.8173] [ 2019] [depth= 2] . ( 12 sec) [ -12981.0798] [ 2019] [depth= 3] . ( 12 sec) [ -12940.4272] [ 2015] [depth= 8] . ( 12 sec) [ -12937.2928] [ 2013] [depth= 1] . ( 12 sec) [ -12890.4047] [ 2005] [depth= 2] . ( 12 sec) [ -12867.1196] [ 2002] [depth= 22] . ( 12 sec) [ -12858.9359] [ 1999] [depth= 6] . ( 13 sec) [ -12839.8481] [ 1998] [depth= 14] . ( 13 sec) [ -12795.7242] [ 1993] [depth= 15] . ( 13 sec) [ -12781.6021] [ 1994] [depth= 9] . ( 13 sec) [ -12657.9738] [ 1991] [depth= 7] . ( 13 sec) [ -12538.0256] [ 1974] [depth= 2] . ( 13 sec) [ -12403.7165] [ 1947] [depth= 5] . ( 13 sec) [ -12356.8333] [ 1936] [depth= 4] . ( 13 sec) [ -12298.1920] [ 1914] [depth= 6] . ( 14 sec) [ -12173.2858] [ 1912] [depth= 24] . ( 14 sec) [ -12149.2623] [ 1901] [depth= 1] . ( 14 sec) [ -12135.6345] [ 1906] [depth= 22] . ( 14 sec) [ -12109.0904] [ 1902] [depth= 24] . ( 14 sec) [ -12107.8715] [ 1901] [depth= 1] . ( 14 sec) [ -12104.5847] [ 1902] [depth= 2] . ( 14 sec) [ -12091.7165] [ 1880] [depth= 16] . ( 15 sec) [ -12091.6009] [ 1886] [depth= 1] . ( 15 sec) [ -12089.8122] [ 1886] [depth= 1] . ( 15 sec) [ -12068.4195] [ 1874] [depth= 20] . ( 15 sec) [ -12006.9357] [ 1892] [depth= 1] . ( 15 sec) [ -11929.8325] [ 1891] [depth= 23] . ( 15 sec) [ -11856.7611] [ 1854] [depth= 2] . ( 16 sec) [ -11763.7709] [ 1831] [depth= 1] . ( 16 sec) [ -11691.9563] [ 1814] [depth= 5] . ( 16 sec) [ -11630.7974] [ 1798] [depth= 3] . ( 16 sec) [ -11599.6206] [ 1795] [depth= 1] . ( 16 sec) [ -11554.9415] [ 1783] [depth= 11] . ( 16 sec) [ -11541.5903] [ 1781] [depth= 3] . ( 17 sec) [ -11529.4397] [ 1780] [depth= 2] . ( 17 sec) [ -11495.0511] [ 1772] [depth= 3] . ( 17 sec) [ -11417.8411] [ 1750] [depth= 5] . ( 17 sec) [ -11417.4107] [ 1749] [depth= 2] . ( 17 sec) [ -11334.2718] [ 1734] [depth= 2] . ( 18 sec) [ -11325.4863] [ 1732] [depth= 1] . ( 18 sec) [ -11322.0175] [ 1730] [depth= 1] . ( 18 sec) [ -11236.3343] [ 1710] [depth= 7] . ( 18 sec) [ -11231.8566] [ 1709] [depth= 6] . ( 18 sec) [ -11170.2361] [ 1692] [depth= 2] . ( 18 sec) [ -11108.4052] [ 1667] [depth= 2] . ( 18 sec) [ -11095.5334] [ 1662] [depth= 9] . ( 19 sec) [ -11057.7036] [ 1649] [depth= 1] . ( 19 sec) [ -11041.8858] [ 1646] [depth= 7] . ( 19 sec) [ -10975.3796] [ 1634] [depth= 1] . ( 19 sec) [ -10974.7440] [ 1632] [depth= 9] . ( 19 sec) [ -10884.1009] [ 1607] [depth= 5] . ( 19 sec) [ -10867.4422] [ 1606] [depth= 2] . ( 19 sec) [ -10856.1192] [ 1601] [depth= 5] . ( 19 sec) [ -10849.8915] [ 1599] [depth= 2] . ( 19 sec) [ -10812.0917] [ 1593] [depth= 1] . ( 19 sec) [ -10788.7199] [ 1584] [depth= 9] . ( 20 sec) [ -10769.6545] [ 1589] [depth= 5] . ( 20 sec) [ -10745.1173] [ 1584] [depth= 1] . ( 20 sec) [ -10736.7234] [ 1582] [depth= 3] . ( 20 sec) [ -10720.9586] [ 1580] [depth= 1] . ( 21 sec) [ -10692.1067] [ 1573] [depth= 12] . ( 21 sec) [ -10688.4488] [ 1573] [depth= 1] . ( 21 sec) [ -10646.8555] [ 1573] [depth= 2] . ( 21 sec) [ -10549.6990] [ 1554] [depth= 1] . ( 21 sec) [ -10520.3359] [ 1556] [depth= 5] . ( 21 sec) [ -10517.8777] [ 1555] [depth= 1] . ( 21 sec) [ -10428.2547] [ 1527] [depth= 6] . ( 21 sec) [ -10427.9004] [ 1527] [depth= 2] . ( 22 sec) [ -10420.6586] [ 1528] [depth= 15] . ( 22 sec) [ -10413.5512] [ 1525] [depth= 4] . ( 22 sec) [ -10413.1177] [ 1525] [depth= 1] . ( 22 sec) [ -10412.2484] [ 1525] [depth= 1] . ( 22 sec) [ -10410.5741] [ 1525] [depth= 1] . ( 22 sec) [ -10409.1082] [ 1525] [depth= 4] . ( 22 sec) [ -10405.0512] [ 1523] [depth= 3] . ( 23 sec) [ -10402.9360] [ 1523] [depth= 1] . ( 23 sec) [ -10396.6983] [ 1521] [depth= 2] . ( 23 sec) [ -10396.0423] [ 1525] [depth= 1] . ( 23 sec) [ -10387.8527] [ 1526] [depth= 1] . ( 24 sec) [ -10387.4796] [ 1527] [depth= 1] . ( 24 sec) [ -10387.4652] [ 1527] [depth= 1] . ( 24 sec) [ -10383.3226] [ 1525] [depth= 1] . ( 24 sec) [ -10383.0894] [ 1524] [depth= 2] . ( 24 sec) [ -10378.7900] [ 1523] [depth= 2] . ( 24 sec) [ -10372.0703] [ 1521] [depth= 3] . ( 25 sec) [ -10367.4678] [ 1521] [depth= 1] . ( 25 sec) [ -10365.6907] [ 1527] [depth= 1] . ( 26 sec) [ -10351.8064] [ 1524] [depth= 1] . ( 26 sec) [ -10342.7798] [ 1526] [depth= 8] . ( 26 sec) [ -10340.9118] [ 1522] [depth= 4] . ( 26 sec) [ -10330.4255] [ 1510] [depth= 8] . ( 26 sec) [ -10325.7837] [ 1506] [depth= 1] . ( 26 sec) [ -10291.0783] [ 1490] [depth= 20] . ( 27 sec) [ -10290.6126] [ 1495] [depth= 13] . ( 27 sec) [ -10213.2514] [ 1470] [depth= 16] . ( 27 sec) [ -10024.5925] [ 1442] [depth= 8] . ( 27 sec) [ -10014.9081] [ 1441] [depth= 2] . ( 28 sec) [ -9950.5720] [ 1433] [depth= 4] . ( 28 sec) [ -9946.5236] [ 1433] [depth= 1] . ( 29 sec) [ -9943.4930] [ 1433] [depth= 1] . ( 29 sec) [ -9943.0724] [ 1433] [depth= 1] . ( 29 sec) [ -9926.2970] [ 1428] [depth= 11] . ( 29 sec) [ -9925.5905] [ 1429] [depth= 1] . ( 29 sec) [ -9813.7852] [ 1403] [depth= 15] . ( 29 sec) [ -9756.0702] [ 1392] [depth= 4] . ( 29 sec) [ -9736.8205] [ 1387] [depth= 2] . ( 30 sec) [ -9730.2188] [ 1389] [depth= 2] . ( 31 sec) [ -9599.0272] [Branch lengths ] . ( 35 sec) [ -9586.4050] [GTR parameters ] . ( 35 sec) [ -9541.7902] [Alpha ][ 0.288386] . ( 35 sec) [ -9537.2100] [ 1388] [depth= 2] . ( 38 sec) [ -9533.6603] [ 1389] [depth= 1] . ( 38 sec) [ -9527.7315] [ 1388] [depth= 1] . ( 38 sec) [ -9407.5208] [ 1358] [depth= 5] . ( 39 sec) [ -9406.0036] [ 1353] [depth= 2] . ( 40 sec) [ -9401.8865] [ 1349] [depth= 1] . ( 40 sec) [ -9338.7310] [ 1330] [depth= 4] . ( 40 sec) [ -9331.7383] [ 1330] [depth= 1] . ( 41 sec) [ -9329.9325] [ 1332] [depth= 1] . ( 42 sec) [ -9270.1352] [ 1309] [depth= 16] . ( 43 sec) [ -9264.6389] [ 1302] [depth= 1] . ( 44 sec) [ -9263.4536] [ 1301] [depth= 1] . ( 45 sec) [ -9216.5882] [ 1288] [depth= 4] . ( 45 sec) [ -9216.3622] [ 1288] [depth= 1] . ( 46 sec) [ -9216.1728] [ 1288] [depth= 1] . ( 46 sec) [ -9216.0942] [ 1288] [depth= 1] . ( 46 sec) [ -9214.9756] [ 1288] [depth= 1] . ( 47 sec) [ -9212.1596] [ 1286] [depth= 1] . ( 47 sec) [ -9211.9624] [ 1286] [depth= 1] . ( 47 sec) [ -9126.1016] [ 1265] [depth= 15] . ( 48 sec) [ -9125.1713] [ 1266] [depth= 1] . ( 48 sec) [ -9120.2973] [ 1265] [depth= 4] . ( 48 sec) [ -9119.8568] [ 1265] [depth= 2] . ( 48 sec) [ -9112.3334] [ 1262] [depth= 1] . ( 49 sec) [ -9111.7758] [ 1262] [depth= 1] . ( 49 sec) [ -9110.4148] [ 1263] [depth= 1] . ( 49 sec) [ -9103.7407] [ 1264] [depth= 2] . ( 49 sec) [ -9086.1344] [ 1259] [depth= 3] . ( 50 sec) [ -9077.8551] [ 1258] [depth= 1] . ( 50 sec) [ -9072.3190] [ 1252] [depth= 3] . ( 51 sec) [ -9069.6538] [ 1252] [depth= 3] . ( 51 sec) [ -9069.4218] [ 1252] [depth= 1] . ( 52 sec) [ -9067.6476] [ 1251] [depth= 1] . ( 52 sec) [ -9066.3292] [ 1250] [depth= 1] . ( 53 sec) [ -9065.6324] [ 1251] [depth= 1] . ( 53 sec) [ -9065.6066] [ 1251] [depth= 1] . ( 54 sec) [ -9065.5814] [ 1251] [depth= 1] . ( 54 sec) [ -9050.4521] [ 1248] [depth= 2] . ( 55 sec) [ -9049.5501] [ 1248] [depth= 1] . ( 57 sec) [ -9047.9092] [ 1249] [depth= 1] . ( 57 sec) [ -9047.0958] [ 1249] [depth= 1] . ( 58 sec) [ -9023.7543] [ 1246] [depth= 1] . ( 61 sec) [ -9022.6011] [ 1245] [depth= 2] . ( 61 sec) [ -9022.3341] [ 1245] [depth= 6] . ( 61 sec) [ -9020.5502] [ 1244] [depth= 1] . ( 62 sec) [ -9020.4265] [ 1244] [depth= 1] . ( 62 sec) [ -9017.5043] [ 1244] [depth= 1] . ( 63 sec) [ -9017.4798] [ 1245] [depth= 3] . ( 63 sec) [ -9015.6801] [ 1244] [depth= 1] . ( 63 sec) [ -9015.1397] [ 1243] [depth= 1] . ( 64 sec) [ -9015.0115] [ 1243] [depth= 1] . ( 67 sec) [ -9011.7181] [ 1240] [depth= 1] . ( 69 sec) [ -8997.0255] [Branch lengths ] . ( 76 sec) [ -8995.6714] [GTR parameters ] . ( 76 sec) [ -8994.6256] [Alpha ][ 0.313405] . ( 78 sec) [ -8994.5021] [ 1240] [depth= 1] . ( 84 sec) [ -8993.8879] [ 1241] [depth= 2] . ( 97 sec) [ -8993.7905] [ 1241] [depth= 1] . ( 103 sec) [ -8992.5144] [ 1240] [depth= 1] . ( 107 sec) [ -8992.4391] [ 1240] [depth= 1] . ( 118 sec) [ -8991.5830] [Branch lengths ] . ( 119 sec) [ -8991.5782] [GTR parameters ] . ( 119 sec) [ -8991.5779] [Alpha ][ 0.313747] . ( 160 sec) [ -8990.5747] [Branch lengths ] . ( 248 sec) [ -8989.6601] [Branch lengths ] . ( 248 sec) [ -8989.6601] [Topology ] . ( 250 sec) [ -8989.6574] [Topology ] . ( 252 sec) [ -8989.6563] [Topology ] . ( 254 sec) [ -8989.6555] [Topology ] . ( 255 sec) [ -8989.6541] [GTR parameters ] . ( 255 sec) [ -8989.6540] [Alpha ][ 0.313423] . ( 255 sec) [ -8989.6540] [Topology ] . ( 257 sec) [ -8989.6534] [Topology ] . ( 258 sec) [ -8989.6534] [GTR parameters ] . ( 258 sec) [ -8989.6534] [Alpha ][ 0.313423] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8989.653358. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -18740.8048] [GTR parameters ] . ( 3 sec) [ -18354.3028] [Alpha ][ 0.500960] . ( 4 sec) [ -18035.5385] [ 2609] [depth= 8] . ( 4 sec) [ -17673.2979] [ 2564] [depth= 14] . ( 4 sec) [ -17558.3918] [ 2544] [depth= 3] . ( 4 sec) [ -17523.0442] [ 2542] [depth= 11] . ( 4 sec) [ -17457.1729] [ 2539] [depth= 6] . ( 4 sec) [ -17376.3325] [ 2541] [depth= 2] . ( 4 sec) [ -17208.5052] [ 2512] [depth= 14] . ( 4 sec) [ -17085.4973] [ 2500] [depth= 14] . ( 5 sec) [ -16947.1309] [ 2476] [depth= 13] . ( 5 sec) [ -16811.0663] [ 2442] [depth= 1] . ( 5 sec) [ -16742.9454] [ 2434] [depth= 13] . ( 5 sec) [ -16686.8193] [ 2419] [depth= 10] . ( 5 sec) [ -16660.3351] [ 2416] [depth= 1] . ( 5 sec) [ -16494.8312] [ 2395] [depth= 6] . ( 5 sec) [ -16480.6274] [ 2391] [depth= 4] . ( 5 sec) [ -16471.6178] [ 2390] [depth= 3] . ( 5 sec) [ -16460.2722] [ 2385] [depth= 8] . ( 6 sec) [ -16367.0062] [ 2384] [depth= 1] . ( 6 sec) [ -16352.3537] [ 2368] [depth= 3] . ( 6 sec) [ -16349.6336] [ 2368] [depth= 1] . ( 6 sec) [ -16289.2842] [ 2363] [depth= 3] . ( 6 sec) [ -16203.1832] [ 2363] [depth= 1] . ( 6 sec) [ -16186.2472] [ 2362] [depth= 2] . ( 6 sec) [ -16180.1187] [ 2364] [depth= 3] . ( 6 sec) [ -16050.1346] [ 2350] [depth= 10] . ( 6 sec) [ -15864.7819] [ 2344] [depth= 1] . ( 6 sec) [ -15632.5335] [ 2332] [depth= 29] . ( 7 sec) [ -15589.5572] [ 2318] [depth= 28] . ( 7 sec) [ -15501.6146] [ 2295] [depth= 11] . ( 7 sec) [ -15452.8095] [ 2289] [depth= 4] . ( 7 sec) [ -15349.9904] [ 2271] [depth= 1] . ( 7 sec) [ -15300.4281] [ 2274] [depth= 1] . ( 7 sec) [ -15243.9801] [ 2257] [depth= 1] . ( 7 sec) [ -14925.3697] [ 2235] [depth= 8] . ( 7 sec) [ -14796.2781] [ 2208] [depth= 11] . ( 8 sec) [ -14770.4710] [ 2209] [depth= 27] . ( 8 sec) [ -14738.5758] [ 2197] [depth= 3] . ( 8 sec) [ -14586.0522] [ 2192] [depth= 3] . ( 8 sec) [ -14575.1224] [ 2191] [depth= 2] . ( 8 sec) [ -14569.2257] [ 2193] [depth= 2] . ( 8 sec) [ -14435.6503] [ 2148] [depth= 13] . ( 8 sec) [ -14303.3006] [ 2141] [depth= 17] . ( 8 sec) [ -14239.8135] [ 2142] [depth= 1] . ( 8 sec) [ -14153.7249] [ 2137] [depth= 20] . ( 9 sec) [ -13897.7881] [ 2095] [depth= 17] . ( 9 sec) [ -13840.7103] [ 2095] [depth= 15] . ( 9 sec) [ -13737.2698] [ 2087] [depth= 14] . ( 9 sec) [ -13580.5958] [ 2059] [depth= 14] . ( 9 sec) [ -13576.1720] [ 2059] [depth= 3] . ( 9 sec) [ -13556.8512] [ 2056] [depth= 7] . ( 9 sec) [ -13529.3075] [ 2051] [depth= 5] . ( 9 sec) [ -13516.8258] [ 2052] [depth= 1] . ( 9 sec) [ -13514.8866] [ 2051] [depth= 1] . ( 9 sec) [ -13509.1954] [ 2052] [depth= 1] . ( 10 sec) [ -13508.9756] [ 2053] [depth= 1] . ( 10 sec) [ -13503.8831] [ 2048] [depth= 2] . ( 10 sec) [ -13472.9089] [ 2041] [depth= 10] . ( 10 sec) [ -13444.7761] [ 2035] [depth= 11] . ( 10 sec) [ -13438.5440] [ 2035] [depth= 1] . ( 10 sec) [ -13424.0644] [ 2035] [depth= 1] . ( 10 sec) [ -13336.2541] [ 2013] [depth= 16] . ( 11 sec) [ -13320.5677] [ 2010] [depth= 1] . ( 11 sec) [ -13175.6854] [ 1980] [depth= 1] . ( 11 sec) [ -13103.1107] [ 1961] [depth= 5] . ( 11 sec) [ -13022.5520] [ 1948] [depth= 14] . ( 11 sec) [ -13018.3789] [ 1951] [depth= 1] . ( 11 sec) [ -13001.7330] [ 1948] [depth= 2] . ( 11 sec) [ -12899.1708] [ 1940] [depth= 18] . ( 11 sec) [ -12888.9127] [ 1937] [depth= 1] . ( 11 sec) [ -12822.9817] [ 1922] [depth= 8] . ( 12 sec) [ -12805.6696] [ 1921] [depth= 1] . ( 12 sec) [ -12677.9255] [ 1902] [depth= 6] . ( 12 sec) [ -12579.7342] [ 1877] [depth= 11] . ( 12 sec) [ -12462.3100] [ 1845] [depth= 9] . ( 12 sec) [ -12420.3506] [ 1837] [depth= 4] . ( 12 sec) [ -12387.6935] [ 1839] [depth= 1] . ( 12 sec) [ -12333.6650] [ 1820] [depth= 8] . ( 12 sec) [ -12299.4430] [ 1821] [depth= 1] . ( 12 sec) [ -12265.8613] [ 1810] [depth= 1] . ( 13 sec) [ -12258.1378] [ 1808] [depth= 1] . ( 13 sec) [ -12177.4278] [ 1791] [depth= 3] . ( 13 sec) [ -12081.0075] [ 1774] [depth= 1] . ( 13 sec) [ -12080.9848] [ 1768] [depth= 9] . ( 13 sec) [ -12075.7300] [ 1768] [depth= 1] . ( 13 sec) [ -12022.2708] [ 1765] [depth= 13] . ( 13 sec) [ -11856.7638] [ 1742] [depth= 4] . ( 13 sec) [ -11646.0478] [ 1740] [depth= 13] . ( 14 sec) [ -11406.3570] [ 1726] [depth= 3] . ( 14 sec) [ -11406.2490] [ 1728] [depth= 17] . ( 14 sec) [ -11381.8285] [ 1723] [depth= 6] . ( 14 sec) [ -11295.1551] [ 1703] [depth= 6] . ( 14 sec) [ -11263.1102] [ 1692] [depth= 4] . ( 14 sec) [ -11253.1849] [ 1692] [depth= 1] . ( 14 sec) [ -11244.6642] [ 1688] [depth= 1] . ( 14 sec) [ -11199.6871] [ 1688] [depth= 15] . ( 14 sec) [ -11185.9816] [ 1688] [depth= 1] . ( 15 sec) [ -11137.3841] [ 1685] [depth= 2] . ( 15 sec) [ -11106.6063] [ 1683] [depth= 2] . ( 15 sec) [ -11075.4121] [ 1685] [depth= 11] . ( 15 sec) [ -11058.7880] [ 1684] [depth= 2] . ( 15 sec) [ -11016.3013] [ 1670] [depth= 6] . ( 15 sec) [ -10972.0207] [ 1657] [depth= 7] . ( 15 sec) [ -10897.6171] [ 1638] [depth= 10] . ( 15 sec) [ -10869.7577] [ 1637] [depth= 5] . ( 15 sec) [ -10866.9560] [ 1636] [depth= 1] . ( 15 sec) [ -10853.2697] [ 1627] [depth= 7] . ( 16 sec) [ -10850.1310] [ 1625] [depth= 19] . ( 16 sec) [ -10849.9587] [ 1625] [depth= 1] . ( 16 sec) [ -10781.1956] [ 1604] [depth= 3] . ( 16 sec) [ -10647.3886] [ 1591] [depth= 26] . ( 16 sec) [ -10605.1444] [ 1581] [depth= 7] . ( 16 sec) [ -10591.6018] [ 1578] [depth= 1] . ( 16 sec) [ -10552.8884] [ 1568] [depth= 11] . ( 16 sec) [ -10542.2910] [ 1564] [depth= 6] . ( 17 sec) [ -10532.2442] [ 1564] [depth= 1] . ( 17 sec) [ -10527.9999] [ 1562] [depth= 1] . ( 17 sec) [ -10488.0885] [ 1553] [depth= 22] . ( 17 sec) [ -10468.6632] [ 1544] [depth= 1] . ( 17 sec) [ -10415.2133] [ 1531] [depth= 14] . ( 17 sec) [ -10394.6014] [ 1526] [depth= 9] . ( 17 sec) [ -10285.3876] [ 1504] [depth= 14] . ( 17 sec) [ -10257.7811] [ 1498] [depth= 3] . ( 18 sec) [ -10253.1084] [ 1498] [depth= 2] . ( 18 sec) [ -10156.5106] [ 1477] [depth= 12] . ( 18 sec) [ -10153.1748] [ 1477] [depth= 1] . ( 18 sec) [ -10144.4549] [ 1477] [depth= 1] . ( 18 sec) [ -10143.1600] [ 1477] [depth= 1] . ( 18 sec) [ -10124.3798] [ 1475] [depth= 10] . ( 18 sec) [ -10120.0635] [ 1474] [depth= 1] . ( 18 sec) [ -10119.0113] [ 1474] [depth= 1] . ( 19 sec) [ -10048.0763] [ 1456] [depth= 7] . ( 19 sec) [ -10046.0057] [ 1461] [depth= 5] . ( 19 sec) [ -10039.8971] [ 1457] [depth= 2] . ( 19 sec) [ -10034.4218] [ 1456] [depth= 2] . ( 19 sec) [ -10032.3393] [ 1457] [depth= 4] . ( 20 sec) [ -10022.5935] [ 1454] [depth= 4] . ( 20 sec) [ -10013.1009] [ 1452] [depth= 3] . ( 20 sec) [ -10004.0090] [ 1451] [depth= 1] . ( 20 sec) [ -10003.7455] [ 1452] [depth= 1] . ( 20 sec) [ -9898.9344] [ 1428] [depth= 5] . ( 20 sec) [ -9896.0827] [ 1428] [depth= 1] . ( 20 sec) [ -9891.4788] [ 1428] [depth= 1] . ( 20 sec) [ -9889.3024] [ 1427] [depth= 1] . ( 21 sec) [ -9889.2457] [ 1428] [depth= 9] . ( 21 sec) [ -9888.1327] [ 1430] [depth= 1] . ( 21 sec) [ -9885.1981] [ 1431] [depth= 1] . ( 21 sec) [ -9880.7673] [ 1428] [depth= 2] . ( 22 sec) [ -9878.7914] [ 1429] [depth= 1] . ( 22 sec) [ -9869.7850] [ 1426] [depth= 7] . ( 22 sec) [ -9868.9232] [ 1425] [depth= 1] . ( 22 sec) [ -9854.0794] [ 1424] [depth= 1] . ( 22 sec) [ -9848.5651] [ 1418] [depth= 6] . ( 22 sec) [ -9837.7241] [ 1414] [depth= 10] . ( 22 sec) [ -9830.7726] [ 1412] [depth= 1] . ( 23 sec) [ -9821.3190] [ 1403] [depth= 2] . ( 23 sec) [ -9820.9721] [ 1404] [depth= 5] . ( 23 sec) [ -9777.7650] [ 1395] [depth= 5] . ( 23 sec) [ -9771.3431] [ 1394] [depth= 1] . ( 23 sec) [ -9767.3107] [ 1393] [depth= 1] . ( 23 sec) [ -9711.9386] [ 1382] [depth= 6] . ( 24 sec) [ -9704.0720] [ 1379] [depth= 1] . ( 24 sec) [ -9697.8470] [ 1378] [depth= 1] . ( 24 sec) [ -9650.2441] [ 1370] [depth= 1] . ( 24 sec) [ -9629.5525] [ 1368] [depth= 2] . ( 24 sec) [ -9626.2950] [ 1368] [depth= 2] . ( 24 sec) [ -9623.4229] [ 1366] [depth= 1] . ( 24 sec) [ -9622.1425] [ 1366] [depth= 1] . ( 24 sec) [ -9603.0472] [ 1361] [depth= 3] . ( 24 sec) [ -9599.9821] [ 1360] [depth= 1] . ( 25 sec) [ -9599.6542] [ 1356] [depth= 1] . ( 25 sec) [ -9598.3571] [ 1356] [depth= 1] . ( 25 sec) [ -9596.3010] [ 1355] [depth= 1] . ( 25 sec) [ -9593.2675] [ 1354] [depth= 1] . ( 27 sec) [ -9588.3701] [ 1355] [depth= 7] . ( 27 sec) [ -9586.7107] [ 1357] [depth= 2] . ( 27 sec) [ -9566.3724] [ 1352] [depth= 9] . ( 27 sec) [ -9539.5916] [ 1347] [depth= 5] . ( 28 sec) [ -9533.2702] [ 1347] [depth= 1] . ( 29 sec) [ -9428.5709] [Branch lengths ] . ( 33 sec) [ -9420.5350] [GTR parameters ] . ( 33 sec) [ -9383.7888] [Alpha ][ 0.297204] . ( 35 sec) [ -9374.0903] [ 1346] [depth= 3] . ( 35 sec) [ -9372.2160] [ 1345] [depth= 1] . ( 36 sec) [ -9368.0477] [ 1343] [depth= 4] . ( 36 sec) [ -9359.8921] [ 1339] [depth= 1] . ( 36 sec) [ -9358.9784] [ 1338] [depth= 4] . ( 36 sec) [ -9358.4419] [ 1334] [depth= 2] . ( 36 sec) [ -9335.2426] [ 1325] [depth= 9] . ( 37 sec) [ -9334.8557] [ 1327] [depth= 1] . ( 37 sec) [ -9309.3665] [ 1323] [depth= 3] . ( 37 sec) [ -9270.8769] [ 1322] [depth= 16] . ( 37 sec) [ -9262.6534] [ 1317] [depth= 3] . ( 38 sec) [ -9262.5226] [ 1317] [depth= 1] . ( 38 sec) [ -9248.0784] [ 1323] [depth= 7] . ( 38 sec) [ -9185.6307] [ 1288] [depth= 6] . ( 38 sec) [ -9169.4835] [ 1282] [depth= 1] . ( 39 sec) [ -9165.4478] [ 1281] [depth= 2] . ( 40 sec) [ -9164.6209] [ 1280] [depth= 1] . ( 41 sec) [ -9162.7841] [ 1281] [depth= 3] . ( 41 sec) [ -9160.7255] [ 1281] [depth= 1] . ( 41 sec) [ -9160.4567] [ 1282] [depth= 1] . ( 41 sec) [ -9160.2634] [ 1282] [depth= 1] . ( 42 sec) [ -9154.1127] [ 1279] [depth= 2] . ( 42 sec) [ -9153.8237] [ 1279] [depth= 1] . ( 43 sec) [ -9149.1088] [ 1275] [depth= 1] . ( 43 sec) [ -9147.0239] [ 1276] [depth= 1] . ( 45 sec) [ -9147.0037] [ 1276] [depth= 1] . ( 45 sec) [ -9146.8576] [ 1276] [depth= 1] . ( 46 sec) [ -9146.8093] [ 1275] [depth= 1] . ( 46 sec) [ -9140.8682] [ 1268] [depth= 2] . ( 46 sec) [ -9140.4239] [ 1268] [depth= 1] . ( 47 sec) [ -9122.0268] [ 1266] [depth= 2] . ( 47 sec) [ -9120.8373] [ 1265] [depth= 3] . ( 48 sec) [ -9103.8655] [ 1259] [depth= 1] . ( 48 sec) [ -9085.9225] [ 1254] [depth= 1] . ( 49 sec) [ -9085.2933] [ 1255] [depth= 3] . ( 52 sec) [ -9081.4814] [ 1253] [depth= 2] . ( 52 sec) [ -9081.4577] [ 1254] [depth= 1] . ( 52 sec) [ -9080.4471] [ 1253] [depth= 1] . ( 52 sec) [ -9078.3213] [ 1252] [depth= 3] . ( 55 sec) [ -9073.9807] [ 1254] [depth= 3] . ( 56 sec) [ -9070.0682] [ 1255] [depth= 1] . ( 56 sec) [ -9069.5883] [ 1256] [depth= 1] . ( 56 sec) [ -9068.8051] [ 1256] [depth= 1] . ( 58 sec) [ -9068.7827] [ 1256] [depth= 1] . ( 59 sec) [ -9067.9569] [ 1255] [depth= 3] . ( 60 sec) [ -9066.1448] [ 1255] [depth= 1] . ( 60 sec) [ -9065.9990] [ 1256] [depth= 1] . ( 60 sec) [ -9056.9346] [ 1252] [depth= 1] . ( 62 sec) [ -9054.8458] [ 1253] [depth= 2] . ( 63 sec) [ -9053.6134] [ 1252] [depth= 1] . ( 63 sec) [ -9052.2544] [ 1249] [depth= 1] . ( 66 sec) [ -9052.1525] [ 1249] [depth= 3] . ( 66 sec) [ -9051.7827] [ 1246] [depth= 1] . ( 67 sec) [ -9051.2905] [ 1250] [depth= 2] . ( 68 sec) [ -9029.5640] [Branch lengths ] . ( 72 sec) [ -9027.8432] [GTR parameters ] . ( 72 sec) [ -9027.5832] [Alpha ][ 0.309859] . ( 74 sec) [ -9025.6045] [ 1250] [depth= 2] . ( 75 sec) [ -9017.1668] [ 1244] [depth= 1] . ( 75 sec) [ -9017.0553] [ 1245] [depth= 1] . ( 77 sec) [ -9017.0053] [ 1245] [depth= 1] . ( 78 sec) [ -9014.4648] [ 1243] [depth= 1] . ( 78 sec) [ -9013.6135] [ 1243] [depth= 2] . ( 81 sec) [ -9012.1255] [ 1242] [depth= 1] . ( 82 sec) [ -9010.1683] [ 1240] [depth= 1] . ( 82 sec) [ -9009.3638] [ 1240] [depth= 1] . ( 91 sec) [ -9009.2313] [ 1239] [depth= 1] . ( 92 sec) [ -9007.0284] [ 1239] [depth= 4] . ( 93 sec) [ -9006.5753] [ 1237] [depth= 1] . ( 93 sec) [ -9006.3578] [ 1237] [depth= 1] . ( 104 sec) [ -9005.9454] [ 1239] [depth= 1] . ( 106 sec) [ -9005.9244] [ 1240] [depth= 1] . ( 108 sec) [ -9005.6713] [ 1240] [depth= 1] . ( 112 sec) [ -9005.2367] [ 1239] [depth= 1] . ( 112 sec) [ -8998.4987] [Branch lengths ] . ( 114 sec) [ -8998.4704] [GTR parameters ] . ( 114 sec) [ -8998.4535] [Alpha ][ 0.313273] . ( 119 sec) [ -8998.2579] [ 1240] [depth= 1] . ( 124 sec) [ -8998.0312] [ 1240] [depth= 1] . ( 154 sec) [ -8997.6531] [ 1240] [depth= 1] . ( 155 sec) [ -8995.0158] [Branch lengths ] . ( 156 sec) [ -8995.0076] [GTR parameters ] . ( 156 sec) [ -8995.0076] [Alpha ][ 0.312960] . ( 191 sec) [ -8994.9287] [ 1240] [depth= 1] . ( 196 sec) [ -8994.7976] [Branch lengths ] . ( 197 sec) [ -8994.7965] [GTR parameters ] . ( 197 sec) [ -8994.7965] [Alpha ][ 0.312960] . ( 281 sec) [ -8994.7840] [Branch lengths ] . ( 281 sec) [ -8994.7840] [Topology ] . ( 283 sec) [ -8994.7818] [Topology ] . ( 286 sec) [ -8994.7807] [Topology ] . ( 287 sec) [ -8994.7800] [Topology ] . ( 288 sec) [ -8994.7798] [GTR parameters ] . ( 289 sec) [ -8994.7798] [Alpha ][ 0.312960] . ( 289 sec) [ -8994.7798] [Topology ] . ( 291 sec) [ -8994.7793] [Topology ] . ( 292 sec) [ -8994.7792] [GTR parameters ] . ( 293 sec) [ -8994.7792] [Alpha ][ 0.312960] . Checking for NNIs, optimizing five branches... . ( 305 sec) [ -8994.7791] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8994.779099. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -19090.7500] [GTR parameters ] . ( 2 sec) [ -18682.0167] [Alpha ][ 0.500960] . ( 2 sec) [ -18414.3626] [ 2705] [depth= 10] . ( 2 sec) [ -18155.5119] [ 2663] [depth= 12] . ( 2 sec) [ -18067.4428] [ 2658] [depth= 7] . ( 3 sec) [ -18039.2041] [ 2658] [depth= 2] . ( 3 sec) [ -17860.5644] [ 2644] [depth= 2] . ( 3 sec) [ -17835.0500] [ 2643] [depth= 2] . ( 3 sec) [ -17798.0550] [ 2633] [depth= 6] . ( 3 sec) [ -17794.0001] [ 2634] [depth= 1] . ( 3 sec) [ -17728.8979] [ 2627] [depth= 10] . ( 3 sec) [ -17689.8965] [ 2626] [depth= 5] . ( 3 sec) [ -17667.3790] [ 2625] [depth= 1] . ( 3 sec) [ -17646.3329] [ 2619] [depth= 14] . ( 4 sec) [ -17238.3202] [ 2597] [depth= 9] . ( 4 sec) [ -17159.6075] [ 2573] [depth= 6] . ( 4 sec) [ -16935.4062] [ 2537] [depth= 8] . ( 4 sec) [ -16916.2960] [ 2535] [depth= 6] . ( 4 sec) [ -16898.5828] [ 2532] [depth= 17] . ( 4 sec) [ -16842.4142] [ 2530] [depth= 12] . ( 4 sec) [ -16619.2953] [ 2493] [depth= 9] . ( 5 sec) [ -16568.8343] [ 2492] [depth= 16] . ( 5 sec) [ -16465.9730] [ 2472] [depth= 1] . ( 5 sec) [ -16366.7508] [ 2466] [depth= 17] . ( 5 sec) [ -16265.7307] [ 2459] [depth= 22] . ( 5 sec) [ -16135.7569] [ 2430] [depth= 1] . ( 5 sec) [ -16121.5573] [ 2428] [depth= 15] . ( 5 sec) [ -16038.5459] [ 2423] [depth= 11] . ( 5 sec) [ -15942.3792] [ 2423] [depth= 1] . ( 5 sec) [ -15775.1336] [ 2420] [depth= 2] . ( 6 sec) [ -15751.1789] [ 2417] [depth= 15] . ( 6 sec) [ -15709.4676] [ 2385] [depth= 15] . ( 6 sec) [ -15593.7347] [ 2386] [depth= 1] . ( 6 sec) [ -15514.4329] [ 2369] [depth= 5] . ( 6 sec) [ -15422.1620] [ 2359] [depth= 4] . ( 6 sec) [ -15349.2929] [ 2344] [depth= 15] . ( 6 sec) [ -15323.1579] [ 2344] [depth= 23] . ( 7 sec) [ -15164.3778] [ 2326] [depth= 20] . ( 7 sec) [ -15062.0380] [ 2299] [depth= 14] . ( 7 sec) [ -14910.3014] [ 2294] [depth= 12] . ( 7 sec) [ -14881.9277] [ 2288] [depth= 1] . ( 7 sec) [ -14851.8320] [ 2286] [depth= 9] . ( 7 sec) [ -14682.2217] [ 2255] [depth= 10] . ( 7 sec) [ -14657.5917] [ 2251] [depth= 3] . ( 7 sec) [ -14629.9281] [ 2246] [depth= 2] . ( 7 sec) [ -14481.1887] [ 2227] [depth= 13] . ( 8 sec) [ -14284.6176] [ 2226] [depth= 16] . ( 8 sec) [ -14199.6067] [ 2199] [depth= 7] . ( 8 sec) [ -14118.9085] [ 2182] [depth= 7] . ( 8 sec) [ -14010.2417] [ 2160] [depth= 11] . ( 8 sec) [ -13982.5341] [ 2156] [depth= 12] . ( 8 sec) [ -13981.5619] [ 2146] [depth= 10] . ( 8 sec) [ -13934.5544] [ 2136] [depth= 1] . ( 8 sec) [ -13878.1698] [ 2125] [depth= 8] . ( 9 sec) [ -13870.3124] [ 2126] [depth= 1] . ( 9 sec) [ -13853.3287] [ 2123] [depth= 1] . ( 9 sec) [ -13764.5543] [ 2130] [depth= 1] . ( 9 sec) [ -13713.9122] [ 2076] [depth= 6] . ( 9 sec) [ -13671.1962] [ 2071] [depth= 5] . ( 9 sec) [ -13663.7830] [ 2069] [depth= 1] . ( 9 sec) [ -13556.1416] [ 2055] [depth= 1] . ( 9 sec) [ -13551.2697] [ 2058] [depth= 1] . ( 10 sec) [ -13469.0526] [ 2035] [depth= 12] . ( 10 sec) [ -13462.7791] [ 2032] [depth= 1] . ( 10 sec) [ -13431.6014] [ 2026] [depth= 9] . ( 10 sec) [ -13417.7061] [ 2024] [depth= 7] . ( 10 sec) [ -13416.4096] [ 2025] [depth= 1] . ( 10 sec) [ -13323.1582] [ 1995] [depth= 15] . ( 10 sec) [ -13268.2862] [ 1980] [depth= 10] . ( 11 sec) [ -13179.4233] [ 1960] [depth= 7] . ( 11 sec) [ -13060.4448] [ 1940] [depth= 8] . ( 11 sec) [ -13030.1665] [ 1940] [depth= 11] . ( 11 sec) [ -13004.6950] [ 1930] [depth= 3] . ( 11 sec) [ -12986.0425] [ 1930] [depth= 2] . ( 11 sec) [ -12918.8718] [ 1917] [depth= 2] . ( 11 sec) [ -12783.4355] [ 1884] [depth= 1] . ( 11 sec) [ -12783.4049] [ 1884] [depth= 1] . ( 11 sec) [ -12760.7205] [ 1886] [depth= 2] . ( 11 sec) [ -12619.8660] [ 1853] [depth= 8] . ( 12 sec) [ -12587.1381] [ 1843] [depth= 17] . ( 12 sec) [ -12583.0109] [ 1845] [depth= 2] . ( 12 sec) [ -12511.9914] [ 1830] [depth= 11] . ( 12 sec) [ -12484.4358] [ 1822] [depth= 1] . ( 12 sec) [ -12446.0481] [ 1808] [depth= 15] . ( 12 sec) [ -12391.0635] [ 1828] [depth= 11] . ( 12 sec) [ -12390.5956] [ 1828] [depth= 1] . ( 13 sec) [ -12371.5832] [ 1831] [depth= 5] . ( 13 sec) [ -12268.9351] [ 1808] [depth= 7] . ( 13 sec) [ -12245.3416] [ 1809] [depth= 1] . ( 13 sec) [ -12234.5368] [ 1808] [depth= 1] . ( 13 sec) [ -12211.3762] [ 1806] [depth= 16] . ( 13 sec) [ -12205.1193] [ 1805] [depth= 1] . ( 13 sec) [ -12196.7509] [ 1804] [depth= 12] . ( 13 sec) [ -12180.5019] [ 1785] [depth= 13] . ( 14 sec) [ -11949.6396] [ 1784] [depth= 1] . ( 14 sec) [ -11771.3586] [ 1712] [depth= 10] . ( 14 sec) [ -11742.9468] [ 1709] [depth= 3] . ( 14 sec) [ -11680.4770] [ 1698] [depth= 9] . ( 14 sec) [ -11670.0530] [ 1699] [depth= 7] . ( 14 sec) [ -11661.2843] [ 1697] [depth= 1] . ( 14 sec) [ -11659.8760] [ 1697] [depth= 1] . ( 15 sec) [ -11650.3268] [ 1694] [depth= 1] . ( 15 sec) [ -11617.4279] [ 1698] [depth= 2] . ( 15 sec) [ -11598.2606] [ 1694] [depth= 1] . ( 15 sec) [ -11590.8305] [ 1694] [depth= 3] . ( 15 sec) [ -11559.6585] [ 1683] [depth= 1] . ( 15 sec) [ -11483.9922] [ 1675] [depth= 6] . ( 15 sec) [ -11453.4506] [ 1676] [depth= 14] . ( 15 sec) [ -11396.5934] [ 1662] [depth= 7] . ( 16 sec) [ -11384.0171] [ 1665] [depth= 1] . ( 16 sec) [ -11377.4588] [ 1664] [depth= 1] . ( 16 sec) [ -11274.4828] [ 1646] [depth= 5] . ( 16 sec) [ -11271.0137] [ 1649] [depth= 1] . ( 16 sec) [ -11205.3062] [ 1634] [depth= 2] . ( 16 sec) [ -11178.9194] [ 1628] [depth= 14] . ( 17 sec) [ -11174.1412] [ 1625] [depth= 2] . ( 17 sec) [ -11158.6982] [ 1625] [depth= 1] . ( 17 sec) [ -11132.3174] [ 1613] [depth= 4] . ( 17 sec) [ -10943.0668] [ 1620] [depth= 12] . ( 17 sec) [ -10935.8612] [ 1619] [depth= 1] . ( 17 sec) [ -10904.2871] [ 1615] [depth= 9] . ( 17 sec) [ -10829.1558] [ 1590] [depth= 14] . ( 17 sec) [ -10810.5817] [ 1584] [depth= 2] . ( 17 sec) [ -10780.8408] [ 1578] [depth= 12] . ( 18 sec) [ -10771.8077] [ 1569] [depth= 4] . ( 18 sec) [ -10768.2960] [ 1568] [depth= 1] . ( 18 sec) [ -10755.5101] [ 1562] [depth= 8] . ( 18 sec) [ -10743.3538] [ 1562] [depth= 1] . ( 18 sec) [ -10742.3332] [ 1561] [depth= 1] . ( 18 sec) [ -10678.7457] [ 1550] [depth= 3] . ( 18 sec) [ -10665.8812] [ 1552] [depth= 1] . ( 19 sec) [ -10624.3215] [ 1543] [depth= 11] . ( 19 sec) [ -10613.5216] [ 1542] [depth= 1] . ( 19 sec) [ -10607.2073] [ 1539] [depth= 1] . ( 19 sec) [ -10602.7769] [ 1540] [depth= 1] . ( 19 sec) [ -10598.2735] [ 1539] [depth= 1] . ( 19 sec) [ -10565.0395] [ 1534] [depth= 3] . ( 19 sec) [ -10563.0731] [ 1533] [depth= 1] . ( 20 sec) [ -10510.5208] [ 1518] [depth= 8] . ( 21 sec) [ -10502.4934] [ 1517] [depth= 12] . ( 21 sec) [ -10496.4651] [ 1514] [depth= 3] . ( 21 sec) [ -10495.3821] [ 1513] [depth= 1] . ( 21 sec) [ -10493.7911] [ 1517] [depth= 1] . ( 21 sec) [ -10491.0961] [ 1516] [depth= 1] . ( 21 sec) [ -10251.4725] [ 1500] [depth= 8] . ( 22 sec) [ -10249.9307] [ 1501] [depth= 1] . ( 22 sec) [ -10229.2235] [ 1497] [depth= 4] . ( 22 sec) [ -10206.8028] [ 1496] [depth= 7] . ( 22 sec) [ -10164.5316] [ 1486] [depth= 2] . ( 22 sec) [ -10162.6470] [ 1480] [depth= 6] . ( 22 sec) [ -10144.8686] [ 1473] [depth= 3] . ( 22 sec) [ -10097.2295] [ 1465] [depth= 7] . ( 23 sec) [ -10060.6996] [ 1453] [depth= 2] . ( 23 sec) [ -10054.6533] [ 1451] [depth= 2] . ( 23 sec) [ -10054.2394] [ 1452] [depth= 1] . ( 23 sec) [ -10050.0167] [ 1448] [depth= 1] . ( 24 sec) [ -10046.7737] [ 1448] [depth= 1] . ( 24 sec) [ -10044.5158] [ 1447] [depth= 1] . ( 24 sec) [ -10041.4412] [ 1469] [depth= 1] . ( 24 sec) [ -10041.1066] [ 1469] [depth= 1] . ( 24 sec) [ -10017.9529] [ 1462] [depth= 1] . ( 24 sec) [ -9931.8704] [ 1451] [depth= 4] . ( 24 sec) [ -9885.8333] [ 1426] [depth= 8] . ( 24 sec) [ -9871.1667] [ 1425] [depth= 1] . ( 24 sec) [ -9869.0220] [ 1424] [depth= 6] . ( 24 sec) [ -9856.0084] [ 1421] [depth= 1] . ( 25 sec) [ -9850.0485] [ 1421] [depth= 1] . ( 25 sec) [ -9828.3784] [ 1421] [depth= 3] . ( 25 sec) [ -9756.5308] [ 1403] [depth= 1] . ( 25 sec) [ -9756.4948] [ 1400] [depth= 3] . ( 25 sec) [ -9755.9815] [ 1400] [depth= 1] . ( 25 sec) [ -9753.3128] [ 1402] [depth= 3] . ( 25 sec) [ -9740.5660] [ 1398] [depth= 4] . ( 26 sec) [ -9734.2288] [ 1397] [depth= 1] . ( 26 sec) [ -9641.7019] [ 1365] [depth= 7] . ( 26 sec) [ -9638.4809] [ 1363] [depth= 4] . ( 26 sec) [ -9613.0266] [ 1357] [depth= 1] . ( 26 sec) [ -9606.6889] [ 1356] [depth= 2] . ( 26 sec) [ -9586.4078] [ 1355] [depth= 1] . ( 26 sec) [ -9584.4658] [ 1357] [depth= 1] . ( 26 sec) [ -9583.7775] [ 1356] [depth= 1] . ( 27 sec) [ -9440.0369] [Branch lengths ] . ( 30 sec) [ -9422.5580] [GTR parameters ] . ( 31 sec) [ -9382.0249] [Alpha ][ 0.292526] . ( 31 sec) [ -9335.8154] [ 1340] [depth= 1] . ( 32 sec) [ -9335.4925] [ 1337] [depth= 5] . ( 32 sec) [ -9334.0836] [ 1337] [depth= 1] . ( 33 sec) [ -9330.4834] [ 1335] [depth= 3] . ( 33 sec) [ -9309.7239] [ 1324] [depth= 1] . ( 34 sec) [ -9243.3935] [ 1304] [depth= 6] . ( 34 sec) [ -9198.0289] [ 1288] [depth= 1] . ( 34 sec) [ -9197.8692] [ 1288] [depth= 1] . ( 34 sec) [ -9182.2034] [ 1284] [depth= 2] . ( 35 sec) [ -9182.0232] [ 1285] [depth= 1] . ( 35 sec) [ -9162.8950] [ 1275] [depth= 1] . ( 36 sec) [ -9160.3289] [ 1273] [depth= 1] . ( 36 sec) [ -9154.3348] [ 1273] [depth= 3] . ( 39 sec) [ -9116.7487] [ 1263] [depth= 1] . ( 39 sec) [ -9116.6943] [ 1264] [depth= 1] . ( 39 sec) [ -9112.3236] [ 1263] [depth= 1] . ( 40 sec) [ -9108.1314] [ 1266] [depth= 1] . ( 40 sec) [ -9107.1376] [ 1265] [depth= 2] . ( 41 sec) [ -9106.6129] [ 1264] [depth= 2] . ( 41 sec) [ -9101.9657] [ 1262] [depth= 2] . ( 41 sec) [ -9098.2274] [ 1256] [depth= 2] . ( 41 sec) [ -9094.6812] [ 1256] [depth= 3] . ( 42 sec) [ -9093.9292] [ 1255] [depth= 2] . ( 45 sec) [ -9093.3418] [ 1254] [depth= 1] . ( 45 sec) [ -9093.0623] [ 1255] [depth= 1] . ( 46 sec) [ -9088.3301] [ 1253] [depth= 1] . ( 48 sec) [ -9084.5503] [ 1252] [depth= 1] . ( 49 sec) [ -9065.9318] [ 1244] [depth= 4] . ( 49 sec) [ -9056.7735] [ 1248] [depth= 1] . ( 50 sec) [ -9055.7783] [ 1248] [depth= 3] . ( 52 sec) [ -9055.5930] [ 1248] [depth= 1] . ( 53 sec) [ -9054.7335] [ 1251] [depth= 3] . ( 54 sec) [ -9054.5970] [ 1252] [depth= 3] . ( 54 sec) [ -9052.3822] [ 1252] [depth= 1] . ( 54 sec) [ -9049.7377] [ 1253] [depth= 1] . ( 55 sec) [ -9046.3340] [ 1247] [depth= 1] . ( 55 sec) [ -9044.8808] [ 1247] [depth= 1] . ( 56 sec) [ -9044.5858] [ 1247] [depth= 2] . ( 57 sec) [ -9040.8179] [ 1246] [depth= 4] . ( 57 sec) [ -9036.4471] [ 1245] [depth= 1] . ( 59 sec) [ -9034.6021] [ 1244] [depth= 1] . ( 59 sec) [ -9034.0532] [ 1244] [depth= 1] . ( 59 sec) [ -9033.8485] [ 1244] [depth= 1] . ( 59 sec) [ -9030.7768] [ 1248] [depth= 1] . ( 60 sec) [ -9028.5643] [ 1248] [depth= 1] . ( 60 sec) [ -9028.2558] [ 1249] [depth= 1] . ( 61 sec) [ -9027.9355] [ 1250] [depth= 1] . ( 61 sec) [ -9020.6749] [ 1244] [depth= 1] . ( 63 sec) [ -9004.8568] [Branch lengths ] . ( 65 sec) [ -9004.1788] [GTR parameters ] . ( 66 sec) [ -9003.5225] [Alpha ][ 0.312470] . ( 68 sec) [ -9001.9134] [ 1245] [depth= 2] . ( 70 sec) [ -8999.8316] [ 1244] [depth= 4] . ( 70 sec) [ -8999.5363] [ 1243] [depth= 1] . ( 77 sec) [ -8998.8778] [ 1242] [depth= 1] . ( 78 sec) [ -8996.2616] [ 1240] [depth= 1] . ( 82 sec) [ -8995.7855] [ 1239] [depth= 1] . ( 83 sec) [ -8995.4263] [ 1238] [depth= 1] . ( 83 sec) [ -8993.5787] [ 1237] [depth= 1] . ( 89 sec) [ -8993.3346] [ 1238] [depth= 3] . ( 89 sec) [ -8992.8243] [ 1239] [depth= 1] . ( 94 sec) [ -8992.6574] [ 1239] [depth= 1] . ( 102 sec) [ -8990.0590] [Branch lengths ] . ( 104 sec) [ -8990.0368] [GTR parameters ] . ( 105 sec) [ -8990.0345] [Alpha ][ 0.313687] . ( 143 sec) [ -8990.0071] [Branch lengths ] . ( 166 sec) [ -8989.9412] [ 1239] [depth= 1] . ( 223 sec) [ -8989.8722] [Branch lengths ] . ( 224 sec) [ -8989.8722] [GTR parameters ] . ( 224 sec) [ -8989.8722] [Alpha ][ 0.313687] . ( 224 sec) [ -8989.8722] [Topology ] . ( 226 sec) [ -8989.5747] [Topology ] . ( 227 sec) [ -8989.0910] [Topology ] . ( 229 sec) [ -8989.0685] [Topology ] . ( 231 sec) [ -8989.0656] [Topology ] . ( 233 sec) [ -8989.0650] [Topology ] . ( 237 sec) [ -8989.0500] [GTR parameters ] . ( 237 sec) [ -8989.0497] [Alpha ][ 0.314065] . ( 237 sec) [ -8989.0497] [Topology ] . ( 239 sec) [ -8989.0495] [Topology ] . ( 239 sec) [ -8989.0495] [GTR parameters ] . ( 239 sec) [ -8989.0495] [Alpha ][ 0.314065] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8989.049540. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -9336.8033] [GTR parameters ] . ( 4 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 4 sec) [ -9236.3667] [Topology ] . ( 6 sec) [ -9106.7265] [Topology ] . ( 8 sec) [ -9073.5495] [Topology ] . ( 9 sec) [ -9062.8635] [Topology ] . ( 11 sec) [ -9058.7107] [Topology ] . ( 13 sec) [ -9056.6216] [Topology ] . ( 15 sec) [ -9055.9627] [Topology ] . ( 17 sec) [ -9055.6109] [Topology ] . ( 19 sec) [ -9055.0866] [Topology ] . ( 20 sec) [ -9053.7351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -9052.4667] [GTR parameters ] . ( 37 sec) [ -9024.8575] [Alpha ][ 0.313875] . ( 37 sec) [ -9024.8575] [Topology ] . ( 39 sec) [ -9024.3363] [Topology ] . ( 41 sec) [ -9024.0852] [Topology ] . ( 43 sec) [ -9023.9339] [Topology ] . ( 44 sec) [ -9023.8381] [Topology ] . ( 46 sec) [ -9023.7762] [Topology ] . ( 48 sec) [ -9023.7359] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -9023.4456] [GTR parameters ] . ( 63 sec) [ -9023.4363] [Alpha ][ 0.311241] . ( 63 sec) [ -9023.4363] [Topology ] . ( 64 sec) [ -9023.4001] [Topology ] . ( 66 sec) [ -9023.3767] [Topology ] . ( 68 sec) [ -9023.3613] [Topology ] . ( 70 sec) [ -9023.3512] [Topology ] . ( 72 sec) [ -9023.3445] [Topology ] . ( 73 sec) [ -9023.3401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -9023.3391] [GTR parameters ] . ( 86 sec) [ -9023.3390] [Alpha ][ 0.310868] . ( 87 sec) [ -9023.3390] [Topology ] . ( 88 sec) [ -9023.3357] [Topology ] . ( 90 sec) [ -9023.3336] [Topology ] . ( 92 sec) [ -9023.3322] [Topology ] . ( 94 sec) [ -9023.3312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -9023.3306] [GTR parameters ] . ( 107 sec) [ -9023.3306] [Alpha ][ 0.310868] . ( 107 sec) [ -9023.3306] [Topology ] . ( 109 sec) [ -9023.3300] [Topology ] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -9023.3299] [GTR parameters ] . ( 122 sec) [ -9023.3299] [Alpha ][ 0.310868] . ( 122 sec) [ -9023.3299] [Topology ] . ( 123 sec) [ -9023.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 153 sec) [ -9336.8033] [GTR parameters ] . ( 153 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 154 sec) [ -9234.6589] [ 1259] [depth= 1] . ( 154 sec) [ -9230.9702] [ 1259] [depth= 1] . ( 155 sec) [ -9228.1890] [ 1256] [depth= 1] . ( 155 sec) [ -9227.9857] [ 1257] [depth= 1] . ( 155 sec) [ -9225.8774] [ 1257] [depth= 1] . ( 155 sec) [ -9225.2595] [ 1257] [depth= 1] . ( 155 sec) [ -9222.6440] [ 1256] [depth= 1] . ( 155 sec) [ -9219.7109] [ 1257] [depth= 1] . ( 156 sec) [ -9218.8532] [ 1256] [depth= 1] . ( 157 sec) [ -9218.4006] [ 1255] [depth= 1] . ( 157 sec) [ -9212.6493] [ 1254] [depth= 1] . ( 158 sec) [ -9212.2838] [ 1255] [depth= 1] . ( 158 sec) [ -9208.1121] [ 1254] [depth= 1] . ( 158 sec) [ -9207.8081] [ 1255] [depth= 1] . ( 158 sec) [ -9206.2989] [ 1254] [depth= 1] . ( 159 sec) [ -9205.5922] [ 1254] [depth= 1] . ( 159 sec) [ -9203.7407] [ 1253] [depth= 2] . ( 160 sec) [ -9198.4128] [ 1251] [depth= 1] . ( 160 sec) [ -9197.9473] [ 1251] [depth= 1] . ( 160 sec) [ -9194.8922] [ 1253] [depth= 4] . ( 160 sec) [ -9194.1529] [ 1253] [depth= 1] . ( 161 sec) [ -9194.0345] [ 1254] [depth= 1] . ( 161 sec) [ -9193.9770] [ 1255] [depth= 1] . ( 161 sec) [ -9190.8641] [ 1255] [depth= 1] . ( 161 sec) [ -9190.1195] [ 1255] [depth= 1] . ( 162 sec) [ -9186.4363] [ 1254] [depth= 1] . ( 162 sec) [ -9186.4252] [ 1254] [depth= 1] . ( 162 sec) [ -9184.3388] [ 1254] [depth= 1] . ( 162 sec) [ -9184.1906] [ 1254] [depth= 1] . ( 162 sec) [ -9179.8249] [ 1255] [depth= 3] . ( 164 sec) [ -9173.4594] [ 1253] [depth= 1] . ( 165 sec) [ -9173.2643] [ 1253] [depth= 1] . ( 165 sec) [ -9172.8667] [ 1252] [depth= 1] . ( 165 sec) [ -9171.3737] [ 1252] [depth= 4] . ( 165 sec) [ -9166.4254] [ 1250] [depth= 3] . ( 165 sec) [ -9164.5478] [ 1250] [depth= 2] . ( 166 sec) [ -9157.2810] [ 1248] [depth= 2] . ( 166 sec) [ -9156.6451] [ 1248] [depth= 1] . ( 166 sec) [ -9155.3311] [ 1250] [depth= 2] . ( 167 sec) [ -9154.9412] [ 1250] [depth= 1] . ( 167 sec) [ -9154.9160] [ 1250] [depth= 1] . ( 168 sec) [ -9154.5267] [ 1251] [depth= 1] . ( 168 sec) [ -9153.4468] [ 1250] [depth= 1] . ( 169 sec) [ -9136.8895] [ 1253] [depth= 1] . ( 170 sec) [ -9111.0896] [ 1247] [depth= 2] . ( 171 sec) [ -9103.5037] [ 1246] [depth= 2] . ( 172 sec) [ -9102.0583] [ 1246] [depth= 1] . ( 173 sec) [ -9098.5560] [ 1245] [depth= 2] . ( 174 sec) [ -9096.5242] [ 1245] [depth= 1] . ( 175 sec) [ -9094.9666] [ 1245] [depth= 1] . ( 176 sec) [ -9094.7728] [ 1245] [depth= 1] . ( 176 sec) [ -9094.4759] [ 1245] [depth= 1] . ( 176 sec) [ -9091.9699] [ 1244] [depth= 4] . ( 177 sec) [ -9091.8945] [ 1245] [depth= 6] . ( 179 sec) [ -9091.6959] [ 1245] [depth= 1] . ( 180 sec) [ -9090.6316] [ 1245] [depth= 1] . ( 181 sec) [ -9089.6504] [ 1244] [depth= 5] . ( 182 sec) [ -9089.1977] [ 1244] [depth= 1] . ( 184 sec) [ -9037.4453] [Branch lengths ] . ( 186 sec) [ -9036.9712] [GTR parameters ] . ( 187 sec) [ -9010.3820] [Alpha ][ 0.310787] . ( 189 sec) [ -9009.8194] [ 1243] [depth= 1] . ( 192 sec) [ -9008.7390] [ 1241] [depth= 1] . ( 196 sec) [ -9008.5657] [ 1241] [depth= 3] . ( 196 sec) [ -9007.6255] [ 1241] [depth= 1] . ( 201 sec) [ -9006.0591] [ 1241] [depth= 4] . ( 203 sec) [ -9006.0276] [ 1241] [depth= 1] . ( 204 sec) [ -9005.9448] [ 1241] [depth= 1] . ( 205 sec) [ -9005.8222] [ 1241] [depth= 1] . ( 207 sec) [ -9005.7829] [ 1242] [depth= 1] . ( 211 sec) [ -9005.7502] [ 1243] [depth= 2] . ( 216 sec) [ -9005.4718] [ 1243] [depth= 3] . ( 217 sec) [ -9005.1910] [ 1243] [depth= 2] . ( 217 sec) [ -9004.7966] [ 1244] [depth= 1] . ( 218 sec) [ -9002.4169] [ 1243] [depth= 1] . ( 218 sec) [ -9002.3837] [ 1243] [depth= 1] . ( 218 sec) [ -9002.3174] [ 1243] [depth= 1] . ( 219 sec) [ -9002.2916] [ 1243] [depth= 1] . ( 220 sec) [ -9002.1439] [ 1243] [depth= 1] . ( 224 sec) [ -8993.9006] [Branch lengths ] . ( 226 sec) [ -8993.4244] [GTR parameters ] . ( 226 sec) [ -8993.4054] [Alpha ][ 0.314504] . ( 249 sec) [ -8993.3373] [ 1243] [depth= 1] . ( 264 sec) [ -8991.8159] [Branch lengths ] . ( 264 sec) [ -8991.8158] [GTR parameters ] . ( 265 sec) [ -8991.8157] [Alpha ][ 0.314190] . ( 303 sec) [ -8991.4819] [Branch lengths ] . ( 354 sec) [ -8991.4406] [ 1240] [depth= 2] . ( 354 sec) [ -8991.1315] [ 1240] [depth= 1] . ( 355 sec) [ -8991.0860] [ 1239] [depth= 1] . ( 356 sec) [ -8991.0359] [ 1240] [depth= 1] . ( 393 sec) [ -8989.7562] [Branch lengths ] . ( 395 sec) [ -8989.7255] [GTR parameters ] . ( 395 sec) [ -8989.7255] [Alpha ][ 0.314190] . ( 484 sec) [ -8989.6755] [Branch lengths ] . ( 484 sec) [ -8989.6755] [Topology ] . ( 486 sec) [ -8989.6664] [Topology ] . ( 488 sec) [ -8989.6619] [Topology ] . ( 491 sec) [ -8989.6590] [Topology ] . ( 493 sec) [ -8989.6571] [Topology ] . ( 494 sec) [ -8989.6559] [Topology ] . ( 496 sec) [ -8989.6550] [Topology ] . ( 498 sec) [ -8989.6541] [GTR parameters ] . ( 498 sec) [ -8989.6536] [Alpha ][ 0.313531] . ( 498 sec) [ -8989.6536] [Topology ] . ( 500 sec) [ -8989.6529] [Topology ] . ( 500 sec) [ -8989.6528] [GTR parameters ] . ( 500 sec) [ -8989.6528] [Alpha ][ 0.313531] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9023.329451 . Log likelihood obtained after SPR moves : -8989.652837 . Log likelihood of the current tree: -8989.652837. . Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'... . Best log likelihood : -8989.049540 . Time used 0h8m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1859.40user 0.00system 32:44.49elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps