.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2752_106x1292_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 . 11 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 427 patterns found. (out of a total of 1292 sites) . 807 sites without polymorphism (62.46%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29877.8308] [GTR parameters ] . ( 2 sec) [ -29317.8646] [Alpha ][ 0.500960] . ( 2 sec) [ -29070.4772] [ 3540] [depth= 8] . ( 2 sec) [ -28319.7162] [ 3469] [depth= 8] . ( 2 sec) [ -28153.3017] [ 3454] [depth= 6] . ( 2 sec) [ -28047.4417] [ 3454] [depth= 1] . ( 2 sec) [ -27948.6614] [ 3449] [depth= 2] . ( 2 sec) [ -27608.3694] [ 3449] [depth= 4] . ( 2 sec) [ -27568.2194] [ 3407] [depth= 3] . ( 2 sec) [ -27417.4291] [ 3405] [depth= 8] . ( 3 sec) [ -27328.1886] [ 3402] [depth= 3] . ( 3 sec) [ -27218.9086] [ 3402] [depth= 3] . ( 3 sec) [ -26937.2133] [ 3380] [depth= 10] . ( 3 sec) [ -26742.4059] [ 3346] [depth= 3] . ( 3 sec) [ -26673.9923] [ 3338] [depth= 7] . ( 3 sec) [ -26516.0485] [ 3338] [depth= 1] . ( 3 sec) [ -26358.0688] [ 3309] [depth= 22] . ( 3 sec) [ -26235.4629] [ 3289] [depth= 5] . ( 3 sec) [ -26159.3353] [ 3276] [depth= 24] . ( 4 sec) [ -26094.4629] [ 3274] [depth= 4] . ( 4 sec) [ -25977.8419] [ 3257] [depth= 18] . ( 4 sec) [ -25860.7229] [ 3243] [depth= 7] . ( 4 sec) [ -25734.5316] [ 3229] [depth= 17] . ( 4 sec) [ -25701.4253] [ 3229] [depth= 13] . ( 4 sec) [ -25510.0183] [ 3181] [depth= 9] . ( 4 sec) [ -25421.6060] [ 3163] [depth= 2] . ( 5 sec) [ -25333.0946] [ 3160] [depth= 8] . ( 5 sec) [ -25178.4541] [ 3148] [depth= 12] . ( 5 sec) [ -25117.9002] [ 3140] [depth= 5] . ( 5 sec) [ -25058.5840] [ 3110] [depth= 14] . ( 5 sec) [ -24895.6405] [ 3111] [depth= 1] . ( 5 sec) [ -24648.9066] [ 3067] [depth= 20] . ( 5 sec) [ -24611.3520] [ 3067] [depth= 2] . ( 5 sec) [ -24599.3369] [ 3064] [depth= 1] . ( 5 sec) [ -24527.2466] [ 3064] [depth= 3] . ( 5 sec) [ -24519.2428] [ 3065] [depth= 1] . ( 5 sec) [ -24365.6600] [ 3064] [depth= 18] . ( 6 sec) [ -24206.0126] [ 3039] [depth= 12] . ( 6 sec) [ -23999.1092] [ 2990] [depth= 2] . ( 6 sec) [ -23943.3573] [ 2985] [depth= 2] . ( 6 sec) [ -23284.5927] [ 2979] [depth= 19] . ( 6 sec) [ -23241.2061] [ 2976] [depth= 5] . ( 6 sec) [ -22878.2731] [ 2972] [depth= 7] . ( 6 sec) [ -22837.5231] [ 2967] [depth= 12] . ( 6 sec) [ -22781.8355] [ 2960] [depth= 5] . ( 6 sec) [ -21781.8376] [ 2961] [depth= 11] . ( 7 sec) [ -21609.9755] [ 2945] [depth= 7] . ( 7 sec) [ -21603.6153] [ 2945] [depth= 11] . ( 7 sec) [ -21560.1027] [ 2939] [depth= 14] . ( 7 sec) [ -21555.2207] [ 2939] [depth= 1] . ( 7 sec) [ -21468.4692] [ 2927] [depth= 8] . ( 7 sec) [ -21383.2419] [ 2875] [depth= 1] . ( 7 sec) [ -20704.0677] [ 2807] [depth= 14] . ( 7 sec) [ -20701.1579] [ 2806] [depth= 3] . ( 7 sec) [ -20515.3806] [ 2777] [depth= 8] . ( 7 sec) [ -20436.2781] [ 2759] [depth= 16] . ( 8 sec) [ -20210.7242] [ 2757] [depth= 2] . ( 8 sec) [ -19987.0683] [ 2758] [depth= 10] . ( 8 sec) [ -19816.8523] [ 2757] [depth= 7] . ( 8 sec) [ -19714.9293] [ 2740] [depth= 4] . ( 8 sec) [ -19708.0882] [ 2740] [depth= 18] . ( 8 sec) [ -19581.7815] [ 2688] [depth= 2] . ( 8 sec) [ -19383.2204] [ 2666] [depth= 11] . ( 8 sec) [ -19302.1347] [ 2666] [depth= 15] . ( 8 sec) [ -19233.4735] [ 2663] [depth= 5] . ( 8 sec) [ -19195.0806] [ 2659] [depth= 5] . ( 9 sec) [ -18822.2148] [ 2661] [depth= 1] . ( 9 sec) [ -18689.8100] [ 2660] [depth= 10] . ( 9 sec) [ -18685.0237] [ 2674] [depth= 2] . ( 9 sec) [ -18650.5979] [ 2669] [depth= 9] . ( 9 sec) [ -18527.6387] [ 2674] [depth= 4] . ( 9 sec) [ -18523.1764] [ 2669] [depth= 1] . ( 9 sec) [ -18521.6321] [ 2669] [depth= 1] . ( 10 sec) [ -18516.1381] [ 2668] [depth= 6] . ( 10 sec) [ -17921.4521] [ 2573] [depth= 7] . ( 10 sec) [ -17811.0293] [ 2573] [depth= 6] . ( 10 sec) [ -17733.9416] [ 2567] [depth= 9] . ( 10 sec) [ -17733.1566] [ 2567] [depth= 2] . ( 10 sec) [ -17710.1475] [ 2582] [depth= 1] . ( 10 sec) [ -17509.9377] [ 2580] [depth= 6] . ( 10 sec) [ -17506.7440] [ 2580] [depth= 1] . ( 11 sec) [ -17482.5137] [ 2585] [depth= 8] . ( 11 sec) [ -17436.1190] [ 2558] [depth= 10] . ( 11 sec) [ -17234.9318] [ 2519] [depth= 15] . ( 11 sec) [ -17136.1528] [ 2512] [depth= 1] . ( 11 sec) [ -16847.7110] [ 2511] [depth= 13] . ( 11 sec) [ -16840.9450] [ 2511] [depth= 1] . ( 11 sec) [ -16837.1874] [ 2509] [depth= 1] . ( 12 sec) [ -16624.7397] [ 2511] [depth= 1] . ( 12 sec) [ -16505.7967] [ 2508] [depth= 10] . ( 12 sec) [ -16504.6859] [ 2507] [depth= 13] . ( 12 sec) [ -16327.3598] [ 2445] [depth= 8] . ( 12 sec) [ -16113.4232] [ 2441] [depth= 12] . ( 12 sec) [ -16111.2734] [ 2440] [depth= 8] . ( 12 sec) [ -16076.1438] [ 2443] [depth= 15] . ( 12 sec) [ -16014.5479] [ 2437] [depth= 7] . ( 13 sec) [ -16013.4738] [ 2437] [depth= 1] . ( 13 sec) [ -15961.2880] [ 2430] [depth= 9] . ( 13 sec) [ -15953.7431] [ 2430] [depth= 12] . ( 13 sec) [ -15949.1540] [ 2427] [depth= 6] . ( 13 sec) [ -15946.0871] [ 2427] [depth= 2] . ( 13 sec) [ -15928.7275] [ 2425] [depth= 12] . ( 13 sec) [ -15911.1650] [ 2425] [depth= 1] . ( 13 sec) [ -15825.8379] [ 2420] [depth= 12] . ( 13 sec) [ -15783.2047] [ 2420] [depth= 3] . ( 14 sec) [ -15616.2373] [ 2409] [depth= 12] . ( 14 sec) [ -15475.6002] [ 2390] [depth= 10] . ( 14 sec) [ -15422.0648] [ 2372] [depth= 1] . ( 14 sec) [ -15373.7458] [ 2363] [depth= 1] . ( 14 sec) [ -15257.8951] [ 2336] [depth= 9] . ( 14 sec) [ -15257.7794] [ 2338] [depth= 1] . ( 14 sec) [ -15040.3324] [ 2342] [depth= 24] . ( 14 sec) [ -15040.3154] [ 2338] [depth= 6] . ( 14 sec) [ -15022.8081] [ 2338] [depth= 3] . ( 15 sec) [ -15011.9645] [ 2337] [depth= 1] . ( 15 sec) [ -14969.5532] [ 2335] [depth= 1] . ( 15 sec) [ -14961.0094] [ 2334] [depth= 10] . ( 15 sec) [ -14834.9857] [ 2335] [depth= 4] . ( 15 sec) [ -14789.7038] [ 2325] [depth= 17] . ( 15 sec) [ -14759.3887] [ 2321] [depth= 21] . ( 15 sec) [ -14740.2898] [ 2306] [depth= 13] . ( 15 sec) [ -14733.7588] [ 2306] [depth= 1] . ( 15 sec) [ -14662.0162] [ 2303] [depth= 6] . ( 15 sec) [ -14540.4030] [ 2284] [depth= 6] . ( 16 sec) [ -14088.0215] [ 2241] [depth= 8] . ( 16 sec) [ -13902.5076] [ 2192] [depth= 11] . ( 16 sec) [ -13892.5912] [ 2188] [depth= 16] . ( 16 sec) [ -13839.3333] [ 2176] [depth= 6] . ( 16 sec) [ -13820.4820] [ 2177] [depth= 1] . ( 16 sec) [ -13807.4977] [ 2172] [depth= 6] . ( 16 sec) [ -13753.0379] [ 2164] [depth= 2] . ( 16 sec) [ -13733.0862] [ 2158] [depth= 10] . ( 17 sec) [ -13692.8747] [ 2154] [depth= 15] . ( 17 sec) [ -13334.4365] [ 2093] [depth= 20] . ( 17 sec) [ -13232.8883] [ 2093] [depth= 19] . ( 17 sec) [ -13011.5072] [ 2071] [depth= 18] . ( 17 sec) [ -13011.0985] [ 2072] [depth= 1] . ( 17 sec) [ -13010.4805] [ 2070] [depth= 3] . ( 17 sec) [ -13008.3749] [ 2070] [depth= 1] . ( 17 sec) [ -13001.0127] [ 2069] [depth= 2] . ( 18 sec) [ -12974.4314] [ 2065] [depth= 10] . ( 18 sec) [ -12972.7477] [ 2066] [depth= 1] . ( 18 sec) [ -12916.2626] [ 2064] [depth= 5] . ( 18 sec) [ -12902.2391] [ 2047] [depth= 2] . ( 18 sec) [ -12654.7206] [ 2009] [depth= 12] . ( 18 sec) [ -12629.5668] [ 2005] [depth= 7] . ( 18 sec) [ -12562.7434] [ 2006] [depth= 1] . ( 18 sec) [ -12533.1072] [ 2006] [depth= 16] . ( 18 sec) [ -12520.3946] [ 2006] [depth= 14] . ( 18 sec) [ -12444.7188] [ 2002] [depth= 12] . ( 19 sec) [ -12417.8085] [ 2004] [depth= 1] . ( 19 sec) [ -12396.4966] [ 1958] [depth= 1] . ( 19 sec) [ -12234.3973] [ 1899] [depth= 10] . ( 19 sec) [ -12215.0639] [ 1899] [depth= 13] . ( 19 sec) [ -12172.9773] [ 1894] [depth= 1] . ( 19 sec) [ -11992.7391] [ 1840] [depth= 11] . ( 19 sec) [ -11919.0934] [ 1825] [depth= 21] . ( 19 sec) [ -11918.6100] [ 1825] [depth= 1] . ( 19 sec) [ -11900.5675] [ 1824] [depth= 8] . ( 19 sec) [ -11881.1102] [ 1823] [depth= 2] . ( 20 sec) [ -11872.6139] [ 1818] [depth= 2] . ( 20 sec) [ -11853.3540] [ 1814] [depth= 2] . ( 20 sec) [ -11835.5131] [ 1810] [depth= 5] . ( 21 sec) [ -11733.4322] [ 1777] [depth= 5] . ( 21 sec) [ -11708.2556] [ 1763] [depth= 3] . ( 21 sec) [ -11528.5534] [ 1717] [depth= 3] . ( 22 sec) [ -11361.9562] [ 1700] [depth= 13] . ( 22 sec) [ -11355.8068] [ 1700] [depth= 2] . ( 22 sec) [ -11352.6759] [ 1700] [depth= 3] . ( 22 sec) [ -11297.5689] [ 1658] [depth= 14] . ( 22 sec) [ -11280.5291] [ 1661] [depth= 18] . ( 22 sec) [ -11257.9940] [ 1648] [depth= 3] . ( 22 sec) [ -11250.2451] [ 1647] [depth= 3] . ( 22 sec) [ -11237.2206] [ 1642] [depth= 1] . ( 23 sec) [ -11146.0900] [ 1641] [depth= 2] . ( 23 sec) [ -10944.6244] [ 1628] [depth= 7] . ( 23 sec) [ -10941.6834] [ 1627] [depth= 1] . ( 23 sec) [ -10785.0207] [ 1580] [depth= 12] . ( 23 sec) [ -10784.6419] [ 1580] [depth= 1] . ( 23 sec) [ -10744.1647] [ 1576] [depth= 8] . ( 24 sec) [ -10743.5677] [ 1575] [depth= 2] . ( 24 sec) [ -10480.6779] [ 1536] [depth= 1] . ( 24 sec) [ -10441.2022] [ 1508] [depth= 9] . ( 24 sec) [ -10430.5576] [ 1515] [depth= 1] . ( 24 sec) [ -10259.8415] [ 1487] [depth= 4] . ( 25 sec) [ -10257.5389] [ 1487] [depth= 6] . ( 25 sec) [ -10257.4500] [ 1487] [depth= 1] . ( 25 sec) [ -10242.0924] [ 1483] [depth= 3] . ( 25 sec) [ -10195.1111] [ 1478] [depth= 3] . ( 25 sec) [ -10195.1004] [ 1478] [depth= 1] . ( 25 sec) [ -10186.5097] [ 1473] [depth= 7] . ( 25 sec) [ -10173.6837] [ 1474] [depth= 1] . ( 25 sec) [ -10123.3722] [ 1469] [depth= 5] . ( 25 sec) [ -10019.1626] [ 1440] [depth= 4] . ( 25 sec) [ -9994.1203] [ 1432] [depth= 2] . ( 26 sec) [ -9901.1845] [ 1420] [depth= 5] . ( 26 sec) [ -9889.0122] [ 1420] [depth= 2] . ( 26 sec) [ -9882.4682] [ 1419] [depth= 10] . ( 26 sec) [ -9877.7874] [ 1432] [depth= 1] . ( 26 sec) [ -9860.4130] [ 1432] [depth= 9] . ( 26 sec) [ -9836.0870] [ 1418] [depth= 4] . ( 26 sec) [ -9830.6692] [ 1417] [depth= 1] . ( 26 sec) [ -9784.4565] [ 1405] [depth= 3] . ( 26 sec) [ -9779.8103] [ 1405] [depth= 2] . ( 26 sec) [ -9760.8419] [ 1398] [depth= 1] . ( 27 sec) [ -9748.2748] [ 1397] [depth= 2] . ( 27 sec) [ -9707.2808] [ 1390] [depth= 2] . ( 27 sec) [ -9643.9651] [ 1385] [depth= 6] . ( 27 sec) [ -9629.7576] [ 1385] [depth= 2] . ( 27 sec) [ -9627.9563] [ 1385] [depth= 1] . ( 27 sec) [ -9627.7998] [ 1385] [depth= 1] . ( 27 sec) [ -9614.0437] [ 1385] [depth= 2] . ( 28 sec) [ -9612.7758] [ 1385] [depth= 1] . ( 28 sec) [ -9610.4599] [ 1385] [depth= 2] . ( 28 sec) [ -9579.2463] [ 1378] [depth= 1] . ( 28 sec) [ -9566.9253] [ 1380] [depth= 3] . ( 28 sec) [ -9488.3554] [ 1352] [depth= 13] . ( 29 sec) [ -9468.9124] [ 1350] [depth= 2] . ( 29 sec) [ -9441.9934] [ 1347] [depth= 8] . ( 29 sec) [ -9426.8470] [ 1343] [depth= 1] . ( 29 sec) [ -9420.8002] [ 1342] [depth= 1] . ( 29 sec) [ -9420.4907] [ 1342] [depth= 1] . ( 29 sec) [ -9396.3007] [ 1342] [depth= 1] . ( 29 sec) [ -9389.2193] [ 1342] [depth= 1] . ( 30 sec) [ -9383.3615] [ 1342] [depth= 4] . ( 30 sec) [ -9376.2727] [ 1340] [depth= 3] . ( 30 sec) [ -9375.8235] [ 1342] [depth= 1] . ( 30 sec) [ -9372.6324] [ 1339] [depth= 2] . ( 30 sec) [ -9372.5696] [ 1340] [depth= 1] . ( 30 sec) [ -9186.7283] [ 1285] [depth= 19] . ( 30 sec) [ -9166.7674] [ 1283] [depth= 5] . ( 31 sec) [ -9134.1221] [ 1272] [depth= 2] . ( 31 sec) [ -9098.4400] [ 1267] [depth= 1] . ( 31 sec) [ -9097.3673] [ 1267] [depth= 1] . ( 31 sec) [ -9084.7440] [ 1266] [depth= 1] . ( 31 sec) [ -9082.4717] [ 1265] [depth= 1] . ( 31 sec) [ -9082.3319] [ 1266] [depth= 1] . ( 31 sec) [ -9075.0392] [ 1262] [depth= 3] . ( 32 sec) [ -9043.5529] [ 1255] [depth= 1] . ( 32 sec) [ -9042.0714] [ 1256] [depth= 1] . ( 33 sec) [ -8910.7040] [Branch lengths ] . ( 36 sec) [ -8776.1795] [GTR parameters ] . ( 36 sec) [ -8755.5044] [Alpha ][ 0.331889] . ( 36 sec) [ -8751.2397] [ 1254] [depth= 1] . ( 37 sec) [ -8738.3212] [ 1252] [depth= 12] . ( 37 sec) [ -8738.2887] [ 1252] [depth= 1] . ( 38 sec) [ -8737.6894] [ 1252] [depth= 2] . ( 38 sec) [ -8736.4122] [ 1251] [depth= 1] . ( 39 sec) [ -8723.2175] [ 1247] [depth= 6] . ( 39 sec) [ -8720.3445] [ 1246] [depth= 1] . ( 39 sec) [ -8718.9444] [ 1246] [depth= 3] . ( 41 sec) [ -8717.6632] [ 1246] [depth= 1] . ( 41 sec) [ -8717.0828] [ 1234] [depth= 1] . ( 42 sec) [ -8710.4216] [ 1233] [depth= 11] . ( 42 sec) [ -8709.7445] [ 1232] [depth= 1] . ( 43 sec) [ -8708.0745] [ 1231] [depth= 3] . ( 43 sec) [ -8704.4204] [ 1225] [depth= 1] . ( 43 sec) [ -8704.3531] [ 1225] [depth= 1] . ( 43 sec) [ -8704.3428] [ 1225] [depth= 1] . ( 44 sec) [ -8699.3597] [ 1224] [depth= 4] . ( 45 sec) [ -8696.6516] [ 1223] [depth= 3] . ( 45 sec) [ -8694.0633] [ 1221] [depth= 2] . ( 45 sec) [ -8513.8481] [ 1165] [depth= 5] . ( 45 sec) [ -8507.6063] [ 1164] [depth= 4] . ( 46 sec) [ -8507.5641] [ 1164] [depth= 1] . ( 46 sec) [ -8463.9740] [ 1146] [depth= 6] . ( 46 sec) [ -8463.9140] [ 1146] [depth= 4] . ( 46 sec) [ -8449.5859] [ 1142] [depth= 3] . ( 47 sec) [ -8436.1771] [ 1142] [depth= 1] . ( 47 sec) [ -8316.9116] [ 1105] [depth= 7] . ( 47 sec) [ -8287.4537] [ 1099] [depth= 7] . ( 48 sec) [ -8254.5850] [ 1100] [depth= 2] . ( 48 sec) [ -8254.5724] [ 1100] [depth= 1] . ( 48 sec) [ -8253.5197] [ 1100] [depth= 1] . ( 49 sec) [ -8241.8384] [ 1096] [depth= 3] . ( 50 sec) [ -8241.8164] [ 1096] [depth= 1] . ( 50 sec) [ -8235.7609] [ 1096] [depth= 8] . ( 51 sec) [ -8234.8159] [ 1096] [depth= 1] . ( 51 sec) [ -8151.2239] [ 1073] [depth= 9] . ( 51 sec) [ -8148.7757] [ 1072] [depth= 2] . ( 51 sec) [ -8148.7347] [ 1072] [depth= 1] . ( 51 sec) [ -8146.7898] [ 1072] [depth= 2] . ( 52 sec) [ -8137.4973] [ 1072] [depth= 3] . ( 52 sec) [ -8137.0770] [ 1072] [depth= 3] . ( 53 sec) [ -8137.0524] [ 1072] [depth= 1] . ( 53 sec) [ -8137.0277] [ 1072] [depth= 1] . ( 53 sec) [ -8135.3449] [ 1071] [depth= 1] . ( 53 sec) [ -8135.0015] [ 1071] [depth= 4] . ( 54 sec) [ -8133.5797] [ 1071] [depth= 3] . ( 54 sec) [ -8131.7803] [ 1071] [depth= 1] . ( 55 sec) [ -8131.6597] [ 1071] [depth= 1] . ( 55 sec) [ -8121.6851] [ 1069] [depth= 2] . ( 55 sec) [ -8109.9485] [ 1063] [depth= 6] . ( 55 sec) [ -8094.0530] [ 1060] [depth= 2] . ( 55 sec) [ -8090.9043] [ 1059] [depth= 3] . ( 55 sec) [ -8088.7272] [ 1058] [depth= 1] . ( 55 sec) [ -8087.8741] [ 1058] [depth= 1] . ( 56 sec) [ -8059.7735] [ 1051] [depth= 2] . ( 56 sec) [ -8032.4484] [ 1045] [depth= 3] . ( 56 sec) [ -8024.2625] [ 1043] [depth= 6] . ( 56 sec) [ -7974.5718] [ 1019] [depth= 8] . ( 57 sec) [ -7939.2690] [ 1012] [depth= 5] . ( 58 sec) [ -7939.2161] [ 1013] [depth= 1] . ( 58 sec) [ -7939.1643] [ 1013] [depth= 1] . ( 58 sec) [ -7939.1293] [ 1013] [depth= 6] . ( 58 sec) [ -7936.9961] [ 1013] [depth= 1] . ( 59 sec) [ -7936.9243] [ 1013] [depth= 1] . ( 60 sec) [ -7936.7930] [ 1013] [depth= 2] . ( 60 sec) [ -7936.7460] [ 1013] [depth= 1] . ( 62 sec) [ -7936.0149] [ 1014] [depth= 2] . ( 65 sec) [ -7935.4457] [ 1014] [depth= 4] . ( 66 sec) [ -7930.7417] [ 1009] [depth= 1] . ( 66 sec) [ -7930.7309] [ 1009] [depth= 1] . ( 66 sec) [ -7925.1954] [ 1006] [depth= 1] . ( 68 sec) [ -7925.0945] [ 1007] [depth= 1] . ( 68 sec) [ -7925.0265] [ 1007] [depth= 1] . ( 68 sec) [ -7924.6877] [ 1007] [depth= 1] . ( 69 sec) [ -7924.4535] [ 1007] [depth= 1] . ( 69 sec) [ -7921.7310] [ 1006] [depth= 1] . ( 69 sec) [ -7921.7206] [ 1005] [depth= 1] . ( 71 sec) [ -7921.7089] [ 1005] [depth= 2] . ( 73 sec) [ -7921.6879] [ 1005] [depth= 2] . ( 75 sec) [ -7920.7294] [ 1005] [depth= 1] . ( 77 sec) [ -7920.7182] [ 1005] [depth= 1] . ( 80 sec) [ -7920.6691] [ 1005] [depth= 1] . ( 80 sec) [ -7920.4248] [ 1005] [depth= 1] . ( 80 sec) [ -7919.4272] [ 1003] [depth= 6] . ( 82 sec) [ -7897.2249] [Branch lengths ] . ( 83 sec) [ -7895.2929] [GTR parameters ] . ( 83 sec) [ -7885.2956] [Alpha ][ 0.465275] . ( 90 sec) [ -7883.4416] [ 1003] [depth= 1] . ( 101 sec) [ -7882.9362] [ 1004] [depth= 3] . ( 102 sec) [ -7882.9103] [ 1004] [depth= 2] . ( 102 sec) [ -7881.6826] [ 1004] [depth= 3] . ( 102 sec) [ -7881.6396] [ 1004] [depth= 2] . ( 102 sec) [ -7881.5280] [ 1004] [depth= 1] . ( 102 sec) [ -7881.4888] [ 1004] [depth= 2] . ( 104 sec) [ -7881.3290] [ 1004] [depth= 4] . ( 104 sec) [ -7881.0478] [ 1004] [depth= 1] . ( 105 sec) [ -7880.8004] [ 1004] [depth= 2] . ( 109 sec) [ -7880.6910] [ 1004] [depth= 1] . ( 111 sec) [ -7879.9618] [ 1004] [depth= 1] . ( 111 sec) [ -7879.8895] [ 1004] [depth= 1] . ( 113 sec) [ -7879.7582] [ 1004] [depth= 1] . ( 114 sec) [ -7879.6481] [ 1003] [depth= 1] . ( 119 sec) [ -7879.5350] [ 1003] [depth= 1] . ( 120 sec) [ -7879.5227] [ 1003] [depth= 3] . ( 123 sec) [ -7879.5090] [ 1003] [depth= 2] . ( 126 sec) [ -7878.2760] [ 1003] [depth= 4] . ( 126 sec) [ -7878.2259] [ 1003] [depth= 1] . ( 135 sec) [ -7878.0774] [ 1003] [depth= 3] . ( 137 sec) [ -7873.2782] [Branch lengths ] . ( 138 sec) [ -7873.1507] [GTR parameters ] . ( 138 sec) [ -7873.1347] [Alpha ][ 0.472305] . ( 197 sec) [ -7870.3073] [Branch lengths ] . ( 288 sec) [ -7869.0862] [Branch lengths ] . ( 288 sec) [ -7869.0862] [Topology ] . ( 290 sec) [ -7869.0827] [Topology ] . ( 292 sec) [ -7869.0817] [Topology ] . ( 293 sec) [ -7869.0794] [GTR parameters ] . ( 293 sec) [ -7869.0792] [Alpha ][ 0.473035] . ( 293 sec) [ -7869.0792] [Topology ] . ( 295 sec) [ -7869.0786] [Topology ] . ( 295 sec) [ -7869.0786] [GTR parameters ] . ( 296 sec) [ -7869.0786] [Alpha ][ 0.473035] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7869.078643. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -32863.2390] [GTR parameters ] . ( 2 sec) [ -32222.4054] [Alpha ][ 0.500960] . ( 2 sec) [ -31032.9335] [ 3740] [depth= 16] . ( 2 sec) [ -30443.6825] [ 3673] [depth= 21] . ( 2 sec) [ -30397.7180] [ 3670] [depth= 1] . ( 2 sec) [ -30194.4533] [ 3621] [depth= 10] . ( 2 sec) [ -30152.6339] [ 3621] [depth= 2] . ( 2 sec) [ -30021.3918] [ 3621] [depth= 14] . ( 2 sec) [ -29470.5009] [ 3576] [depth= 7] . ( 2 sec) [ -29469.7157] [ 3576] [depth= 1] . ( 3 sec) [ -29406.1317] [ 3573] [depth= 14] . ( 3 sec) [ -29376.5395] [ 3566] [depth= 1] . ( 3 sec) [ -29343.2166] [ 3566] [depth= 2] . ( 3 sec) [ -29307.4388] [ 3562] [depth= 1] . ( 3 sec) [ -29264.2721] [ 3560] [depth= 3] . ( 3 sec) [ -29255.9528] [ 3560] [depth= 8] . ( 3 sec) [ -29223.1190] [ 3560] [depth= 2] . ( 3 sec) [ -29066.5306] [ 3554] [depth= 5] . ( 3 sec) [ -29064.2822] [ 3554] [depth= 2] . ( 3 sec) [ -29020.5676] [ 3512] [depth= 11] . ( 3 sec) [ -29014.0679] [ 3512] [depth= 2] . ( 4 sec) [ -28847.5539] [ 3506] [depth= 13] . ( 4 sec) [ -28809.4490] [ 3506] [depth= 1] . ( 4 sec) [ -28585.7070] [ 3497] [depth= 27] . ( 4 sec) [ -27490.0555] [ 3497] [depth= 1] . ( 4 sec) [ -27070.1741] [ 3493] [depth= 22] . ( 4 sec) [ -27046.2417] [ 3493] [depth= 1] . ( 4 sec) [ -27034.7323] [ 3492] [depth= 13] . ( 4 sec) [ -26697.8189] [ 3425] [depth= 5] . ( 4 sec) [ -26513.3656] [ 3405] [depth= 21] . ( 4 sec) [ -26488.4261] [ 3402] [depth= 12] . ( 5 sec) [ -26436.1384] [ 3400] [depth= 27] . ( 5 sec) [ -26258.2375] [ 3378] [depth= 11] . ( 5 sec) [ -26120.1022] [ 3378] [depth= 1] . ( 5 sec) [ -26081.1988] [ 3376] [depth= 31] . ( 5 sec) [ -25492.1918] [ 3315] [depth= 22] . ( 5 sec) [ -24920.7115] [ 3312] [depth= 23] . ( 5 sec) [ -24693.5129] [ 3258] [depth= 12] . ( 5 sec) [ -24425.9993] [ 3229] [depth= 12] . ( 5 sec) [ -24355.3057] [ 3213] [depth= 20] . ( 6 sec) [ -24339.4945] [ 3214] [depth= 13] . ( 6 sec) [ -24060.9173] [ 3209] [depth= 23] . ( 6 sec) [ -23140.2278] [ 3091] [depth= 17] . ( 6 sec) [ -22989.7881] [ 3106] [depth= 10] . ( 6 sec) [ -22874.5360] [ 3106] [depth= 2] . ( 6 sec) [ -22478.8127] [ 3040] [depth= 18] . ( 6 sec) [ -22402.0581] [ 3037] [depth= 2] . ( 6 sec) [ -22188.7590] [ 2985] [depth= 2] . ( 6 sec) [ -22114.8854] [ 2975] [depth= 9] . ( 7 sec) [ -22092.3135] [ 2973] [depth= 23] . ( 7 sec) [ -21957.1798] [ 2949] [depth= 7] . ( 7 sec) [ -21915.7298] [ 2944] [depth= 6] . ( 7 sec) [ -21840.5286] [ 2937] [depth= 7] . ( 7 sec) [ -21831.2514] [ 2936] [depth= 21] . ( 7 sec) [ -21778.2179] [ 2928] [depth= 1] . ( 7 sec) [ -21384.6584] [ 2886] [depth= 3] . ( 7 sec) [ -21381.3546] [ 2886] [depth= 1] . ( 7 sec) [ -21351.5694] [ 2883] [depth= 8] . ( 8 sec) [ -21350.4380] [ 2883] [depth= 1] . ( 8 sec) [ -21346.9259] [ 2883] [depth= 1] . ( 8 sec) [ -21310.5909] [ 2870] [depth= 1] . ( 8 sec) [ -21238.5267] [ 2866] [depth= 13] . ( 8 sec) [ -21104.6519] [ 2856] [depth= 3] . ( 8 sec) [ -21101.5618] [ 2856] [depth= 1] . ( 8 sec) [ -20902.1002] [ 2802] [depth= 10] . ( 8 sec) [ -20888.8389] [ 2802] [depth= 17] . ( 8 sec) [ -20866.0349] [ 2802] [depth= 3] . ( 8 sec) [ -20830.1425] [ 2796] [depth= 25] . ( 9 sec) [ -20792.9016] [ 2789] [depth= 2] . ( 9 sec) [ -20496.5935] [ 2788] [depth= 9] . ( 9 sec) [ -20460.8121] [ 2790] [depth= 13] . ( 9 sec) [ -20423.5876] [ 2743] [depth= 10] . ( 9 sec) [ -20332.2155] [ 2726] [depth= 2] . ( 9 sec) [ -20060.0766] [ 2725] [depth= 5] . ( 9 sec) [ -20028.1263] [ 2723] [depth= 11] . ( 9 sec) [ -19949.1181] [ 2723] [depth= 4] . ( 9 sec) [ -19664.4767] [ 2660] [depth= 9] . ( 10 sec) [ -19604.3290] [ 2648] [depth= 10] . ( 10 sec) [ -19602.8715] [ 2648] [depth= 1] . ( 10 sec) [ -19525.0316] [ 2639] [depth= 25] . ( 10 sec) [ -19462.5681] [ 2619] [depth= 8] . ( 10 sec) [ -19273.6407] [ 2619] [depth= 4] . ( 10 sec) [ -18121.9933] [ 2572] [depth= 7] . ( 10 sec) [ -18121.5645] [ 2573] [depth= 2] . ( 10 sec) [ -18071.6575] [ 2522] [depth= 4] . ( 10 sec) [ -18042.0342] [ 2522] [depth= 11] . ( 10 sec) [ -17997.1375] [ 2504] [depth= 2] . ( 11 sec) [ -17959.4203] [ 2503] [depth= 7] . ( 11 sec) [ -17940.1718] [ 2500] [depth= 5] . ( 11 sec) [ -17935.1748] [ 2500] [depth= 1] . ( 11 sec) [ -17803.2568] [ 2492] [depth= 2] . ( 11 sec) [ -17754.6888] [ 2482] [depth= 2] . ( 11 sec) [ -17613.2512] [ 2479] [depth= 12] . ( 11 sec) [ -17605.3685] [ 2480] [depth= 1] . ( 11 sec) [ -17458.0688] [ 2460] [depth= 25] . ( 11 sec) [ -17455.4866] [ 2461] [depth= 16] . ( 11 sec) [ -17439.5717] [ 2459] [depth= 20] . ( 12 sec) [ -17384.7190] [ 2445] [depth= 1] . ( 12 sec) [ -17375.0976] [ 2443] [depth= 15] . ( 12 sec) [ -16469.0467] [ 2441] [depth= 1] . ( 12 sec) [ -16386.0162] [ 2400] [depth= 15] . ( 12 sec) [ -15801.2650] [ 2315] [depth= 1] . ( 12 sec) [ -15691.1135] [ 2305] [depth= 1] . ( 12 sec) [ -15672.2202] [ 2304] [depth= 16] . ( 12 sec) [ -15575.3393] [ 2252] [depth= 1] . ( 12 sec) [ -15544.1565] [ 2246] [depth= 15] . ( 13 sec) [ -15515.9294] [ 2236] [depth= 5] . ( 13 sec) [ -15495.2880] [ 2234] [depth= 37] . ( 13 sec) [ -15476.4176] [ 2223] [depth= 17] . ( 13 sec) [ -14525.8581] [ 2187] [depth= 26] . ( 13 sec) [ -14471.8472] [ 2183] [depth= 14] . ( 13 sec) [ -14390.2982] [ 2175] [depth= 15] . ( 13 sec) [ -14308.2462] [ 2160] [depth= 20] . ( 13 sec) [ -14203.7809] [ 2164] [depth= 15] . ( 13 sec) [ -14048.6767] [ 2161] [depth= 3] . ( 14 sec) [ -13701.8882] [ 2153] [depth= 19] . ( 14 sec) [ -13341.6881] [ 2148] [depth= 19] . ( 14 sec) [ -13172.6561] [ 2082] [depth= 9] . ( 14 sec) [ -13168.6308] [ 2084] [depth= 1] . ( 14 sec) [ -13063.9303] [ 2083] [depth= 3] . ( 14 sec) [ -12897.5922] [ 2037] [depth= 12] . ( 14 sec) [ -12790.2784] [ 2017] [depth= 23] . ( 14 sec) [ -12782.7095] [ 2015] [depth= 1] . ( 14 sec) [ -12626.0712] [ 1965] [depth= 14] . ( 15 sec) [ -12596.8423] [ 1958] [depth= 9] . ( 15 sec) [ -12525.4635] [ 1945] [depth= 3] . ( 15 sec) [ -12258.0855] [ 1927] [depth= 7] . ( 15 sec) [ -11985.2546] [ 1846] [depth= 2] . ( 15 sec) [ -11984.0105] [ 1848] [depth= 1] . ( 15 sec) [ -11865.6671] [ 1810] [depth= 11] . ( 15 sec) [ -11761.4191] [ 1794] [depth= 1] . ( 16 sec) [ -11755.9598] [ 1792] [depth= 1] . ( 16 sec) [ -11707.3357] [ 1788] [depth= 9] . ( 16 sec) [ -11673.5422] [ 1786] [depth= 3] . ( 16 sec) [ -11671.2775] [ 1787] [depth= 1] . ( 16 sec) [ -11571.0172] [ 1761] [depth= 5] . ( 16 sec) [ -11546.9097] [ 1758] [depth= 12] . ( 16 sec) [ -11500.3326] [ 1758] [depth= 1] . ( 17 sec) [ -11465.3563] [ 1749] [depth= 13] . ( 17 sec) [ -11428.8202] [ 1741] [depth= 9] . ( 17 sec) [ -11428.6656] [ 1741] [depth= 3] . ( 17 sec) [ -11349.3286] [ 1727] [depth= 10] . ( 17 sec) [ -11323.3197] [ 1710] [depth= 5] . ( 17 sec) [ -11320.2874] [ 1710] [depth= 2] . ( 17 sec) [ -11300.5041] [ 1707] [depth= 1] . ( 18 sec) [ -11300.1538] [ 1707] [depth= 1] . ( 18 sec) [ -11298.9488] [ 1706] [depth= 1] . ( 18 sec) [ -11296.7541] [ 1706] [depth= 5] . ( 18 sec) [ -11296.4156] [ 1706] [depth= 1] . ( 18 sec) [ -11221.1480] [ 1690] [depth= 5] . ( 18 sec) [ -11207.4148] [ 1689] [depth= 1] . ( 18 sec) [ -11010.5871] [ 1628] [depth= 5] . ( 19 sec) [ -10991.5688] [ 1626] [depth= 5] . ( 19 sec) [ -10990.1596] [ 1626] [depth= 3] . ( 19 sec) [ -10978.7005] [ 1616] [depth= 4] . ( 19 sec) [ -10924.1708] [ 1618] [depth= 1] . ( 19 sec) [ -10834.0794] [ 1601] [depth= 10] . ( 19 sec) [ -10817.6125] [ 1601] [depth= 1] . ( 19 sec) [ -10816.3415] [ 1601] [depth= 1] . ( 19 sec) [ -10776.7152] [ 1596] [depth= 11] . ( 19 sec) [ -10677.2653] [ 1592] [depth= 10] . ( 20 sec) [ -10594.8265] [ 1563] [depth= 9] . ( 20 sec) [ -10594.5005] [ 1563] [depth= 1] . ( 20 sec) [ -10580.0921] [ 1562] [depth= 1] . ( 20 sec) [ -10578.5467] [ 1562] [depth= 1] . ( 20 sec) [ -10534.8729] [ 1556] [depth= 3] . ( 20 sec) [ -10530.4391] [ 1556] [depth= 1] . ( 20 sec) [ -10530.3872] [ 1556] [depth= 1] . ( 20 sec) [ -10530.2045] [ 1556] [depth= 1] . ( 21 sec) [ -10527.0239] [ 1556] [depth= 2] . ( 21 sec) [ -10518.9319] [ 1555] [depth= 8] . ( 21 sec) [ -10513.5709] [ 1554] [depth= 2] . ( 21 sec) [ -10499.4237] [ 1549] [depth= 12] . ( 21 sec) [ -10497.0552] [ 1548] [depth= 9] . ( 21 sec) [ -10441.0192] [ 1542] [depth= 1] . ( 21 sec) [ -10398.2274] [ 1525] [depth= 10] . ( 21 sec) [ -10376.7893] [ 1521] [depth= 2] . ( 22 sec) [ -10376.1863] [ 1525] [depth= 14] . ( 22 sec) [ -10376.1666] [ 1525] [depth= 3] . ( 22 sec) [ -10365.6059] [ 1522] [depth= 8] . ( 22 sec) [ -10365.5829] [ 1522] [depth= 1] . ( 22 sec) [ -10363.6808] [ 1522] [depth= 1] . ( 22 sec) [ -10363.2106] [ 1523] [depth= 1] . ( 22 sec) [ -10330.6320] [ 1507] [depth= 2] . ( 22 sec) [ -10328.0176] [ 1505] [depth= 1] . ( 23 sec) [ -10306.8870] [ 1501] [depth= 8] . ( 23 sec) [ -10300.3081] [ 1504] [depth= 2] . ( 23 sec) [ -10250.1913] [ 1488] [depth= 12] . ( 23 sec) [ -10250.1651] [ 1488] [depth= 1] . ( 23 sec) [ -10210.9935] [ 1482] [depth= 5] . ( 23 sec) [ -10210.5731] [ 1482] [depth= 1] . ( 24 sec) [ -10190.6693] [ 1479] [depth= 10] . ( 24 sec) [ -10174.6309] [ 1476] [depth= 1] . ( 24 sec) [ -10170.6066] [ 1474] [depth= 3] . ( 24 sec) [ -10145.9631] [ 1462] [depth= 6] . ( 24 sec) [ -10118.9000] [ 1453] [depth= 13] . ( 25 sec) [ -10014.7094] [ 1441] [depth= 4] . ( 25 sec) [ -10001.5776] [ 1431] [depth= 5] . ( 25 sec) [ -9871.8024] [ 1430] [depth= 9] . ( 25 sec) [ -9811.1210] [ 1415] [depth= 1] . ( 25 sec) [ -9803.9582] [ 1406] [depth= 5] . ( 25 sec) [ -9656.9419] [ 1380] [depth= 4] . ( 25 sec) [ -9607.9691] [ 1360] [depth= 9] . ( 26 sec) [ -9601.6789] [ 1360] [depth= 3] . ( 26 sec) [ -9439.9758] [ 1320] [depth= 14] . ( 26 sec) [ -9438.3497] [ 1320] [depth= 1] . ( 27 sec) [ -9437.6180] [ 1320] [depth= 7] . ( 27 sec) [ -9435.7845] [ 1320] [depth= 1] . ( 27 sec) [ -9434.5194] [ 1318] [depth= 8] . ( 27 sec) [ -9398.1021] [ 1312] [depth= 7] . ( 27 sec) [ -9383.3166] [ 1310] [depth= 4] . ( 27 sec) [ -9382.6883] [ 1310] [depth= 1] . ( 28 sec) [ -9338.0841] [ 1303] [depth= 14] . ( 28 sec) [ -9331.8871] [ 1303] [depth= 2] . ( 28 sec) [ -9325.1675] [ 1262] [depth= 3] . ( 28 sec) [ -9323.8984] [ 1262] [depth= 5] . ( 28 sec) [ -9168.4743] [ 1259] [depth= 10] . ( 28 sec) [ -9142.3450] [ 1250] [depth= 1] . ( 29 sec) [ -9141.1970] [ 1252] [depth= 1] . ( 29 sec) [ -9130.5723] [ 1251] [depth= 6] . ( 29 sec) [ -9066.9607] [ 1238] [depth= 5] . ( 30 sec) [ -9065.5604] [ 1238] [depth= 1] . ( 30 sec) [ -9065.5305] [ 1238] [depth= 6] . ( 31 sec) [ -9063.3973] [ 1238] [depth= 2] . ( 31 sec) [ -9057.2726] [ 1232] [depth= 12] . ( 31 sec) [ -8956.1940] [ 1205] [depth= 13] . ( 31 sec) [ -8945.6787] [ 1205] [depth= 1] . ( 31 sec) [ -8945.5490] [ 1205] [depth= 3] . ( 32 sec) [ -8865.5247] [ 1188] [depth= 13] . ( 32 sec) [ -8863.9891] [ 1188] [depth= 2] . ( 32 sec) [ -8850.5753] [ 1188] [depth= 1] . ( 32 sec) [ -8847.9664] [ 1188] [depth= 1] . ( 32 sec) [ -8840.3662] [ 1186] [depth= 2] . ( 32 sec) [ -8837.2536] [ 1185] [depth= 1] . ( 32 sec) [ -8830.2820] [ 1186] [depth= 2] . ( 33 sec) [ -8719.6338] [Branch lengths ] . ( 36 sec) [ -8562.2087] [GTR parameters ] . ( 36 sec) [ -8550.5126] [Alpha ][ 0.361347] . ( 36 sec) [ -8549.6279] [ 1185] [depth= 2] . ( 37 sec) [ -8549.5962] [ 1185] [depth= 3] . ( 37 sec) [ -8545.8708] [ 1184] [depth= 2] . ( 37 sec) [ -8545.3385] [ 1184] [depth= 2] . ( 37 sec) [ -8526.4546] [ 1181] [depth= 4] . ( 37 sec) [ -8511.4393] [ 1179] [depth= 8] . ( 38 sec) [ -8493.2524] [ 1175] [depth= 2] . ( 38 sec) [ -8493.0779] [ 1175] [depth= 2] . ( 38 sec) [ -8493.0073] [ 1175] [depth= 1] . ( 38 sec) [ -8325.1028] [ 1126] [depth= 7] . ( 38 sec) [ -8318.9684] [ 1125] [depth= 1] . ( 39 sec) [ -8318.9222] [ 1125] [depth= 1] . ( 39 sec) [ -8318.8976] [ 1125] [depth= 1] . ( 40 sec) [ -8313.9996] [ 1123] [depth= 1] . ( 40 sec) [ -8313.4471] [ 1123] [depth= 1] . ( 41 sec) [ -8313.3653] [ 1123] [depth= 5] . ( 41 sec) [ -8287.9667] [ 1114] [depth= 4] . ( 41 sec) [ -8248.7077] [ 1103] [depth= 1] . ( 41 sec) [ -8211.1512] [ 1085] [depth= 8] . ( 42 sec) [ -8211.0273] [ 1085] [depth= 2] . ( 42 sec) [ -8210.9676] [ 1085] [depth= 1] . ( 43 sec) [ -8210.9152] [ 1085] [depth= 1] . ( 43 sec) [ -8205.4018] [ 1083] [depth= 7] . ( 43 sec) [ -8187.7203] [ 1079] [depth= 7] . ( 43 sec) [ -8184.7433] [ 1078] [depth= 2] . ( 44 sec) [ -8183.8018] [ 1077] [depth= 4] . ( 45 sec) [ -8183.7917] [ 1077] [depth= 2] . ( 45 sec) [ -8181.3201] [ 1077] [depth= 1] . ( 48 sec) [ -8180.2661] [ 1076] [depth= 3] . ( 48 sec) [ -8174.0579] [ 1075] [depth= 4] . ( 48 sec) [ -8164.6836] [ 1073] [depth= 3] . ( 49 sec) [ -8162.8209] [ 1073] [depth= 2] . ( 49 sec) [ -8106.4182] [ 1056] [depth= 7] . ( 49 sec) [ -8102.5497] [ 1054] [depth= 4] . ( 51 sec) [ -8102.5359] [ 1054] [depth= 1] . ( 53 sec) [ -8079.0195] [ 1051] [depth= 3] . ( 53 sec) [ -8078.0285] [ 1050] [depth= 1] . ( 54 sec) [ -8076.0773] [ 1051] [depth= 1] . ( 54 sec) [ -8076.0509] [ 1051] [depth= 1] . ( 54 sec) [ -8075.1283] [ 1051] [depth= 1] . ( 54 sec) [ -8074.9988] [ 1051] [depth= 1] . ( 56 sec) [ -8074.9479] [ 1051] [depth= 4] . ( 56 sec) [ -8053.6725] [ 1045] [depth= 1] . ( 56 sec) [ -8053.6354] [ 1045] [depth= 1] . ( 57 sec) [ -8045.5214] [ 1046] [depth= 1] . ( 58 sec) [ -8040.2603] [ 1045] [depth= 3] . ( 59 sec) [ -8017.5963] [ 1037] [depth= 6] . ( 59 sec) [ -7997.4858] [ 1033] [depth= 9] . ( 59 sec) [ -7996.8530] [ 1033] [depth= 2] . ( 62 sec) [ -7989.7787] [ 1034] [depth= 4] . ( 63 sec) [ -7984.6814] [ 1033] [depth= 6] . ( 63 sec) [ -7984.5950] [ 1033] [depth= 4] . ( 64 sec) [ -7984.5772] [ 1033] [depth= 1] . ( 65 sec) [ -7984.5290] [ 1033] [depth= 1] . ( 65 sec) [ -7983.6544] [ 1033] [depth= 1] . ( 66 sec) [ -7943.8375] [ 1013] [depth= 1] . ( 66 sec) [ -7939.9159] [ 1011] [depth= 1] . ( 66 sec) [ -7927.9797] [ 1009] [depth= 4] . ( 67 sec) [ -7927.8015] [ 1009] [depth= 1] . ( 67 sec) [ -7927.7475] [ 1009] [depth= 1] . ( 67 sec) [ -7927.6931] [ 1009] [depth= 1] . ( 68 sec) [ -7927.5375] [ 1009] [depth= 1] . ( 71 sec) [ -7926.8169] [ 1009] [depth= 1] . ( 71 sec) [ -7926.7085] [ 1009] [depth= 4] . ( 72 sec) [ -7926.3854] [ 1009] [depth= 1] . ( 75 sec) [ -7926.3666] [ 1009] [depth= 2] . ( 76 sec) [ -7926.3433] [ 1009] [depth= 3] . ( 76 sec) [ -7926.3125] [ 1009] [depth= 1] . ( 77 sec) [ -7923.0860] [ 1008] [depth= 2] . ( 80 sec) [ -7913.5561] [ 1006] [depth= 1] . ( 81 sec) [ -7913.3166] [ 1007] [depth= 1] . ( 82 sec) [ -7911.4488] [ 1006] [depth= 1] . ( 84 sec) [ -7910.6386] [ 1006] [depth= 1] . ( 84 sec) [ -7910.6242] [ 1007] [depth= 1] . ( 85 sec) [ -7890.1820] [Branch lengths ] . ( 86 sec) [ -7888.0064] [GTR parameters ] . ( 86 sec) [ -7882.6684] [Alpha ][ 0.464181] . ( 92 sec) [ -7880.6119] [ 1006] [depth= 1] . ( 94 sec) [ -7879.1958] [ 1005] [depth= 1] . ( 108 sec) [ -7879.1585] [ 1005] [depth= 1] . ( 120 sec) [ -7878.6520] [ 1005] [depth= 2] . ( 124 sec) [ -7875.7641] [ 1004] [depth= 6] . ( 124 sec) [ -7875.6691] [ 1004] [depth= 2] . ( 128 sec) [ -7875.6178] [ 1004] [depth= 1] . ( 142 sec) [ -7875.4975] [ 1003] [depth= 1] . ( 145 sec) [ -7870.6133] [Branch lengths ] . ( 146 sec) [ -7870.4092] [GTR parameters ] . ( 146 sec) [ -7870.3861] [Alpha ][ 0.472678] . ( 205 sec) [ -7869.1111] [Branch lengths ] . ( 296 sec) [ -7869.0846] [Branch lengths ] . ( 296 sec) [ -7869.0846] [Topology ] . ( 298 sec) [ -7869.0827] [Topology ] . ( 300 sec) [ -7869.0822] [Topology ] . ( 301 sec) [ -7869.0791] [GTR parameters ] . ( 301 sec) [ -7869.0791] [Alpha ][ 0.473151] . ( 301 sec) [ -7869.0791] [Topology ] . ( 303 sec) [ -7869.0787] [Topology ] . ( 304 sec) [ -7869.0787] [GTR parameters ] . ( 304 sec) [ -7869.0787] [Alpha ][ 0.473151] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7869.078709. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -30681.1690] [GTR parameters ] . ( 2 sec) [ -30052.3839] [Alpha ][ 0.500960] . ( 2 sec) [ -29153.1198] [ 3799] [depth= 14] . ( 2 sec) [ -28300.0696] [ 3723] [depth= 9] . ( 2 sec) [ -27755.3739] [ 3706] [depth= 9] . ( 2 sec) [ -27635.2317] [ 3657] [depth= 1] . ( 2 sec) [ -27511.6622] [ 3650] [depth= 8] . ( 2 sec) [ -26285.4068] [ 3642] [depth= 2] . ( 3 sec) [ -26079.1308] [ 3621] [depth= 14] . ( 3 sec) [ -26065.9554] [ 3581] [depth= 3] . ( 3 sec) [ -25901.7701] [ 3568] [depth= 7] . ( 3 sec) [ -25465.4542] [ 3550] [depth= 8] . ( 3 sec) [ -25449.8090] [ 3549] [depth= 1] . ( 3 sec) [ -25280.8272] [ 3535] [depth= 2] . ( 3 sec) [ -25126.1322] [ 3514] [depth= 5] . ( 3 sec) [ -25109.5959] [ 3513] [depth= 2] . ( 3 sec) [ -25046.5027] [ 3505] [depth= 6] . ( 3 sec) [ -24531.6084] [ 3503] [depth= 9] . ( 4 sec) [ -24403.4051] [ 3502] [depth= 5] . ( 4 sec) [ -24326.3461] [ 3502] [depth= 2] . ( 4 sec) [ -24164.6146] [ 3459] [depth= 2] . ( 4 sec) [ -24160.7077] [ 3459] [depth= 2] . ( 4 sec) [ -24138.5007] [ 3455] [depth= 7] . ( 4 sec) [ -24119.7554] [ 3455] [depth= 1] . ( 4 sec) [ -23984.0820] [ 3451] [depth= 14] . ( 4 sec) [ -23980.5470] [ 3451] [depth= 2] . ( 4 sec) [ -23938.6767] [ 3449] [depth= 1] . ( 4 sec) [ -23925.4754] [ 3450] [depth= 1] . ( 4 sec) [ -23718.5007] [ 3427] [depth= 11] . ( 5 sec) [ -23549.6942] [ 3389] [depth= 17] . ( 5 sec) [ -23447.4612] [ 3385] [depth= 18] . ( 5 sec) [ -23205.0469] [ 3385] [depth= 5] . ( 5 sec) [ -22819.3571] [ 3304] [depth= 15] . ( 5 sec) [ -22635.5639] [ 3299] [depth= 17] . ( 5 sec) [ -22300.1102] [ 3268] [depth= 16] . ( 5 sec) [ -22283.2352] [ 3267] [depth= 4] . ( 5 sec) [ -22247.4580] [ 3257] [depth= 8] . ( 5 sec) [ -22143.2939] [ 3252] [depth= 12] . ( 6 sec) [ -22129.8911] [ 3250] [depth= 1] . ( 6 sec) [ -22001.0607] [ 3248] [depth= 7] . ( 6 sec) [ -21815.5535] [ 3242] [depth= 4] . ( 6 sec) [ -21745.7187] [ 3244] [depth= 1] . ( 6 sec) [ -21744.7935] [ 3244] [depth= 1] . ( 6 sec) [ -21601.5726] [ 3225] [depth= 13] . ( 6 sec) [ -21521.1511] [ 3210] [depth= 6] . ( 6 sec) [ -21429.5364] [ 3188] [depth= 10] . ( 6 sec) [ -21429.3881] [ 3188] [depth= 2] . ( 6 sec) [ -21144.1186] [ 3152] [depth= 6] . ( 7 sec) [ -21020.0753] [ 3153] [depth= 2] . ( 7 sec) [ -20524.1416] [ 3118] [depth= 13] . ( 7 sec) [ -20517.0993] [ 3118] [depth= 1] . ( 7 sec) [ -20516.3974] [ 3118] [depth= 1] . ( 7 sec) [ -20489.5299] [ 3118] [depth= 13] . ( 7 sec) [ -20345.6709] [ 3080] [depth= 6] . ( 7 sec) [ -20337.3452] [ 3080] [depth= 14] . ( 7 sec) [ -20199.4444] [ 3054] [depth= 8] . ( 7 sec) [ -19515.5353] [ 3031] [depth= 8] . ( 8 sec) [ -19377.5094] [ 2987] [depth= 6] . ( 8 sec) [ -19273.1912] [ 2985] [depth= 4] . ( 8 sec) [ -19196.4148] [ 2967] [depth= 1] . ( 8 sec) [ -19178.5923] [ 2965] [depth= 11] . ( 8 sec) [ -19013.0304] [ 2963] [depth= 9] . ( 8 sec) [ -18841.8126] [ 2944] [depth= 17] . ( 8 sec) [ -18690.1696] [ 2943] [depth= 1] . ( 8 sec) [ -18545.4507] [ 2934] [depth= 4] . ( 8 sec) [ -18346.4776] [ 2917] [depth= 11] . ( 9 sec) [ -18142.6181] [ 2865] [depth= 19] . ( 9 sec) [ -18050.4584] [ 2846] [depth= 7] . ( 9 sec) [ -17853.5425] [ 2814] [depth= 7] . ( 9 sec) [ -17758.1548] [ 2803] [depth= 11] . ( 9 sec) [ -17727.5797] [ 2789] [depth= 1] . ( 9 sec) [ -17711.6313] [ 2787] [depth= 3] . ( 9 sec) [ -17647.8734] [ 2786] [depth= 5] . ( 9 sec) [ -17600.0451] [ 2780] [depth= 12] . ( 9 sec) [ -17490.7286] [ 2778] [depth= 1] . ( 10 sec) [ -17142.7502] [ 2715] [depth= 10] . ( 10 sec) [ -16995.7805] [ 2715] [depth= 13] . ( 10 sec) [ -16886.7737] [ 2671] [depth= 8] . ( 10 sec) [ -16841.9070] [ 2672] [depth= 1] . ( 10 sec) [ -16734.1884] [ 2676] [depth= 16] . ( 10 sec) [ -16710.4210] [ 2666] [depth= 1] . ( 11 sec) [ -16583.5185] [ 2663] [depth= 11] . ( 11 sec) [ -16371.8616] [ 2600] [depth= 13] . ( 11 sec) [ -16299.6731] [ 2591] [depth= 8] . ( 11 sec) [ -16214.4996] [ 2576] [depth= 7] . ( 11 sec) [ -16199.1207] [ 2573] [depth= 1] . ( 11 sec) [ -16139.1312] [ 2543] [depth= 6] . ( 11 sec) [ -16040.8067] [ 2547] [depth= 8] . ( 12 sec) [ -16040.7629] [ 2546] [depth= 11] . ( 12 sec) [ -15935.8117] [ 2529] [depth= 13] . ( 12 sec) [ -15932.5456] [ 2529] [depth= 1] . ( 12 sec) [ -15911.6097] [ 2525] [depth= 12] . ( 12 sec) [ -15911.1220] [ 2525] [depth= 10] . ( 12 sec) [ -15790.2162] [ 2515] [depth= 7] . ( 12 sec) [ -15746.3760] [ 2508] [depth= 1] . ( 12 sec) [ -15744.7688] [ 2508] [depth= 1] . ( 12 sec) [ -15695.5229] [ 2504] [depth= 12] . ( 13 sec) [ -15499.5694] [ 2447] [depth= 3] . ( 13 sec) [ -15480.0947] [ 2447] [depth= 2] . ( 13 sec) [ -15449.9012] [ 2439] [depth= 12] . ( 13 sec) [ -15442.5705] [ 2437] [depth= 2] . ( 13 sec) [ -15435.5028] [ 2437] [depth= 3] . ( 13 sec) [ -15402.5288] [ 2437] [depth= 2] . ( 13 sec) [ -15402.0752] [ 2438] [depth= 2] . ( 13 sec) [ -15395.1771] [ 2437] [depth= 13] . ( 13 sec) [ -15388.2881] [ 2433] [depth= 16] . ( 13 sec) [ -15342.7081] [ 2390] [depth= 15] . ( 14 sec) [ -15321.4410] [ 2391] [depth= 4] . ( 14 sec) [ -15300.5691] [ 2386] [depth= 21] . ( 14 sec) [ -15277.5023] [ 2382] [depth= 1] . ( 14 sec) [ -15113.2187] [ 2325] [depth= 13] . ( 14 sec) [ -15018.6500] [ 2314] [depth= 8] . ( 14 sec) [ -14935.9063] [ 2263] [depth= 27] . ( 14 sec) [ -14840.0769] [ 2253] [depth= 18] . ( 14 sec) [ -14653.9290] [ 2191] [depth= 1] . ( 14 sec) [ -14180.4645] [ 2113] [depth= 7] . ( 15 sec) [ -14137.6802] [ 2123] [depth= 1] . ( 15 sec) [ -14091.1018] [ 2113] [depth= 7] . ( 15 sec) [ -13907.3231] [ 2069] [depth= 1] . ( 15 sec) [ -13772.5506] [ 2035] [depth= 24] . ( 15 sec) [ -13744.1211] [ 2034] [depth= 1] . ( 15 sec) [ -13662.1716] [ 2015] [depth= 5] . ( 15 sec) [ -13642.9321] [ 2010] [depth= 4] . ( 15 sec) [ -13566.5961] [ 2009] [depth= 1] . ( 15 sec) [ -13492.2328] [ 1988] [depth= 1] . ( 16 sec) [ -13490.8364] [ 1988] [depth= 1] . ( 16 sec) [ -13490.7270] [ 1988] [depth= 1] . ( 16 sec) [ -13275.2791] [ 1971] [depth= 5] . ( 16 sec) [ -13243.8426] [ 1977] [depth= 1] . ( 16 sec) [ -13166.1226] [ 1953] [depth= 8] . ( 16 sec) [ -13163.9544] [ 1955] [depth= 11] . ( 16 sec) [ -13152.1840] [ 1955] [depth= 19] . ( 16 sec) [ -13127.9966] [ 1946] [depth= 1] . ( 16 sec) [ -13122.5941] [ 1943] [depth= 6] . ( 17 sec) [ -13087.1863] [ 1943] [depth= 1] . ( 17 sec) [ -13006.8261] [ 1943] [depth= 1] . ( 17 sec) [ -12997.7718] [ 1942] [depth= 4] . ( 17 sec) [ -12983.1382] [ 1941] [depth= 7] . ( 17 sec) [ -12892.1151] [ 1925] [depth= 10] . ( 17 sec) [ -12885.3830] [ 1925] [depth= 12] . ( 17 sec) [ -12884.0337] [ 1925] [depth= 1] . ( 17 sec) [ -12884.0224] [ 1925] [depth= 1] . ( 17 sec) [ -12820.6634] [ 1887] [depth= 15] . ( 17 sec) [ -12817.0116] [ 1886] [depth= 4] . ( 18 sec) [ -12788.3377] [ 1881] [depth= 6] . ( 18 sec) [ -12774.2656] [ 1881] [depth= 4] . ( 18 sec) [ -12761.8267] [ 1880] [depth= 1] . ( 18 sec) [ -12720.0897] [ 1874] [depth= 9] . ( 18 sec) [ -12718.7797] [ 1874] [depth= 1] . ( 18 sec) [ -12717.6897] [ 1874] [depth= 1] . ( 19 sec) [ -12692.4391] [ 1878] [depth= 6] . ( 19 sec) [ -12654.3366] [ 1874] [depth= 13] . ( 19 sec) [ -12654.2599] [ 1874] [depth= 1] . ( 19 sec) [ -12654.1622] [ 1874] [depth= 1] . ( 19 sec) [ -12653.7472] [ 1874] [depth= 1] . ( 19 sec) [ -12573.6830] [ 1864] [depth= 8] . ( 19 sec) [ -12531.5548] [ 1852] [depth= 5] . ( 19 sec) [ -12510.2027] [ 1852] [depth= 1] . ( 19 sec) [ -12441.5383] [ 1831] [depth= 7] . ( 20 sec) [ -12353.6725] [ 1831] [depth= 18] . ( 20 sec) [ -12306.6202] [ 1830] [depth= 2] . ( 20 sec) [ -12278.1345] [ 1828] [depth= 17] . ( 20 sec) [ -12173.9118] [ 1796] [depth= 13] . ( 20 sec) [ -12147.7359] [ 1821] [depth= 1] . ( 20 sec) [ -11958.3421] [ 1764] [depth= 10] . ( 20 sec) [ -11954.8931] [ 1764] [depth= 6] . ( 20 sec) [ -11941.5001] [ 1758] [depth= 1] . ( 20 sec) [ -11892.7137] [ 1750] [depth= 4] . ( 21 sec) [ -11885.2933] [ 1751] [depth= 2] . ( 21 sec) [ -11875.9296] [ 1752] [depth= 9] . ( 21 sec) [ -11832.9786] [ 1748] [depth= 6] . ( 21 sec) [ -11832.7156] [ 1749] [depth= 2] . ( 22 sec) [ -11828.8063] [ 1748] [depth= 18] . ( 22 sec) [ -11819.9106] [ 1747] [depth= 1] . ( 22 sec) [ -11800.4962] [ 1737] [depth= 1] . ( 22 sec) [ -11780.4532] [ 1732] [depth= 1] . ( 22 sec) [ -11779.7750] [ 1732] [depth= 1] . ( 22 sec) [ -11736.1458] [ 1723] [depth= 23] . ( 22 sec) [ -11714.1227] [ 1719] [depth= 1] . ( 22 sec) [ -11714.0610] [ 1718] [depth= 3] . ( 22 sec) [ -11704.9450] [ 1716] [depth= 1] . ( 23 sec) [ -11446.3159] [ 1718] [depth= 21] . ( 23 sec) [ -11421.0902] [ 1723] [depth= 17] . ( 23 sec) [ -11304.9214] [ 1694] [depth= 18] . ( 23 sec) [ -11297.8760] [ 1693] [depth= 14] . ( 23 sec) [ -11281.9983] [ 1691] [depth= 1] . ( 23 sec) [ -11272.9218] [ 1691] [depth= 19] . ( 23 sec) [ -11269.6356] [ 1694] [depth= 3] . ( 23 sec) [ -11229.4948] [ 1684] [depth= 2] . ( 24 sec) [ -11102.7870] [ 1634] [depth= 8] . ( 24 sec) [ -11076.8220] [ 1630] [depth= 3] . ( 24 sec) [ -11076.3675] [ 1630] [depth= 3] . ( 24 sec) [ -11052.7184] [ 1626] [depth= 24] . ( 24 sec) [ -11001.6802] [ 1615] [depth= 4] . ( 24 sec) [ -10996.5066] [ 1616] [depth= 4] . ( 25 sec) [ -10966.2002] [ 1612] [depth= 4] . ( 25 sec) [ -10955.9975] [ 1610] [depth= 3] . ( 25 sec) [ -10920.7948] [ 1604] [depth= 29] . ( 25 sec) [ -10899.0255] [ 1607] [depth= 2] . ( 25 sec) [ -10846.4516] [ 1594] [depth= 23] . ( 25 sec) [ -10844.3691] [ 1594] [depth= 2] . ( 25 sec) [ -10802.9022] [ 1597] [depth= 16] . ( 25 sec) [ -10799.9601] [ 1597] [depth= 1] . ( 25 sec) [ -10791.8035] [ 1597] [depth= 1] . ( 26 sec) [ -10791.4438] [ 1597] [depth= 2] . ( 26 sec) [ -10785.1334] [ 1595] [depth= 2] . ( 26 sec) [ -10773.5263] [ 1593] [depth= 7] . ( 26 sec) [ -10706.9746] [ 1595] [depth= 2] . ( 26 sec) [ -10689.9380] [ 1593] [depth= 3] . ( 26 sec) [ -10677.6535] [ 1593] [depth= 4] . ( 26 sec) [ -10646.8012] [ 1593] [depth= 1] . ( 26 sec) [ -10634.1230] [ 1591] [depth= 1] . ( 27 sec) [ -10634.0039] [ 1591] [depth= 1] . ( 27 sec) [ -10633.7242] [ 1591] [depth= 3] . ( 27 sec) [ -10625.6049] [ 1594] [depth= 1] . ( 27 sec) [ -10617.3845] [ 1591] [depth= 3] . ( 27 sec) [ -10603.5952] [ 1589] [depth= 12] . ( 27 sec) [ -10603.5435] [ 1588] [depth= 3] . ( 27 sec) [ -10404.8062] [ 1540] [depth= 25] . ( 27 sec) [ -10041.8517] [ 1540] [depth= 1] . ( 27 sec) [ -10038.3825] [ 1540] [depth= 1] . ( 28 sec) [ -9993.4577] [ 1525] [depth= 33] . ( 28 sec) [ -9977.2725] [ 1520] [depth= 23] . ( 28 sec) [ -9975.0223] [ 1519] [depth= 1] . ( 28 sec) [ -9953.9926] [ 1517] [depth= 1] . ( 28 sec) [ -9942.3762] [ 1516] [depth= 4] . ( 28 sec) [ -9939.6545] [ 1516] [depth= 7] . ( 28 sec) [ -9899.6435] [ 1510] [depth= 11] . ( 28 sec) [ -9878.4138] [ 1507] [depth= 5] . ( 29 sec) [ -9877.9809] [ 1507] [depth= 6] . ( 29 sec) [ -9869.5509] [ 1504] [depth= 19] . ( 29 sec) [ -9671.7376] [ 1438] [depth= 25] . ( 29 sec) [ -9621.8027] [ 1412] [depth= 6] . ( 29 sec) [ -9602.1090] [ 1411] [depth= 1] . ( 29 sec) [ -9549.6868] [ 1392] [depth= 7] . ( 29 sec) [ -9401.5063] [ 1350] [depth= 4] . ( 29 sec) [ -9398.2443] [ 1353] [depth= 4] . ( 30 sec) [ -9398.1871] [ 1353] [depth= 3] . ( 30 sec) [ -9397.7008] [ 1353] [depth= 2] . ( 30 sec) [ -9361.3411] [ 1350] [depth= 3] . ( 30 sec) [ -9348.9740] [ 1348] [depth= 1] . ( 31 sec) [ -9338.7774] [ 1346] [depth= 4] . ( 31 sec) [ -9338.4503] [ 1346] [depth= 1] . ( 31 sec) [ -9337.6636] [ 1346] [depth= 2] . ( 31 sec) [ -9333.0354] [ 1345] [depth= 2] . ( 31 sec) [ -9332.7790] [ 1345] [depth= 1] . ( 31 sec) [ -9327.9249] [ 1344] [depth= 2] . ( 31 sec) [ -9318.3045] [ 1343] [depth= 2] . ( 32 sec) [ -9315.9622] [ 1343] [depth= 6] . ( 32 sec) [ -9315.5917] [ 1343] [depth= 1] . ( 32 sec) [ -9310.1852] [ 1343] [depth= 1] . ( 32 sec) [ -9223.1533] [ 1314] [depth= 1] . ( 32 sec) [ -9222.5773] [ 1314] [depth= 1] . ( 32 sec) [ -9219.0223] [ 1313] [depth= 1] . ( 33 sec) [ -9195.6025] [ 1313] [depth= 2] . ( 33 sec) [ -9181.7411] [ 1308] [depth= 5] . ( 33 sec) [ -9162.5362] [ 1310] [depth= 1] . ( 33 sec) [ -9162.4489] [ 1309] [depth= 1] . ( 33 sec) [ -9153.9275] [ 1308] [depth= 3] . ( 34 sec) [ -8974.1950] [Branch lengths ] . ( 38 sec) [ -8760.2710] [GTR parameters ] . ( 38 sec) [ -8741.6285] [Alpha ][ 0.336437] . ( 38 sec) [ -8679.4883] [ 1254] [depth= 1] . ( 38 sec) [ -8677.3974] [ 1254] [depth= 3] . ( 39 sec) [ -8674.4182] [ 1256] [depth= 18] . ( 39 sec) [ -8670.9335] [ 1253] [depth= 4] . ( 40 sec) [ -8670.5526] [ 1253] [depth= 1] . ( 40 sec) [ -8618.2882] [ 1239] [depth= 3] . ( 40 sec) [ -8383.4236] [ 1159] [depth= 2] . ( 42 sec) [ -8375.7544] [ 1154] [depth= 1] . ( 42 sec) [ -8339.6492] [ 1151] [depth= 13] . ( 42 sec) [ -8339.6286] [ 1151] [depth= 1] . ( 43 sec) [ -8334.0984] [ 1149] [depth= 2] . ( 43 sec) [ -8331.9225] [ 1148] [depth= 4] . ( 45 sec) [ -8331.7455] [ 1148] [depth= 1] . ( 46 sec) [ -8330.2670] [ 1147] [depth= 1] . ( 46 sec) [ -8330.1301] [ 1147] [depth= 3] . ( 47 sec) [ -8327.3591] [ 1143] [depth= 1] . ( 47 sec) [ -8327.3449] [ 1143] [depth= 2] . ( 49 sec) [ -8305.0299] [ 1137] [depth= 1] . ( 50 sec) [ -8303.2179] [ 1138] [depth= 3] . ( 51 sec) [ -8289.6477] [ 1136] [depth= 1] . ( 51 sec) [ -8289.5327] [ 1136] [depth= 2] . ( 51 sec) [ -8289.4757] [ 1136] [depth= 4] . ( 52 sec) [ -8289.4564] [ 1136] [depth= 1] . ( 52 sec) [ -8287.5354] [ 1137] [depth= 1] . ( 52 sec) [ -8286.3670] [ 1137] [depth= 1] . ( 54 sec) [ -8275.2405] [ 1135] [depth= 6] . ( 54 sec) [ -8275.1739] [ 1135] [depth= 1] . ( 54 sec) [ -8274.9479] [ 1134] [depth= 1] . ( 54 sec) [ -8272.9986] [ 1134] [depth= 1] . ( 54 sec) [ -8272.4862] [ 1134] [depth= 1] . ( 54 sec) [ -8271.8469] [ 1134] [depth= 2] . ( 57 sec) [ -8270.1078] [ 1133] [depth= 1] . ( 57 sec) [ -8257.6698] [ 1131] [depth= 2] . ( 57 sec) [ -8257.6490] [ 1131] [depth= 3] . ( 57 sec) [ -8248.7063] [ 1129] [depth= 1] . ( 57 sec) [ -8235.9094] [ 1127] [depth= 4] . ( 58 sec) [ -8234.5412] [ 1127] [depth= 1] . ( 58 sec) [ -8230.8536] [ 1126] [depth= 2] . ( 58 sec) [ -8230.4998] [ 1126] [depth= 1] . ( 59 sec) [ -8229.8335] [ 1126] [depth= 1] . ( 59 sec) [ -8229.2731] [ 1125] [depth= 1] . ( 60 sec) [ -8225.4856] [ 1124] [depth= 1] . ( 60 sec) [ -8225.3554] [ 1122] [depth= 1] . ( 60 sec) [ -8225.2329] [ 1123] [depth= 1] . ( 60 sec) [ -8223.3893] [ 1123] [depth= 1] . ( 60 sec) [ -8218.5482] [ 1123] [depth= 1] . ( 63 sec) [ -8198.3087] [ 1096] [depth= 12] . ( 64 sec) [ -8198.2875] [ 1096] [depth= 3] . ( 64 sec) [ -8198.2743] [ 1096] [depth= 3] . ( 64 sec) [ -8193.2777] [ 1092] [depth= 3] . ( 64 sec) [ -8193.0523] [ 1092] [depth= 1] . ( 64 sec) [ -8189.3966] [ 1092] [depth= 4] . ( 68 sec) [ -8189.3834] [ 1090] [depth= 1] . ( 68 sec) [ -8189.2753] [ 1090] [depth= 1] . ( 69 sec) [ -8182.0476] [ 1086] [depth= 9] . ( 70 sec) [ -8181.5849] [ 1087] [depth= 1] . ( 70 sec) [ -8165.2133] [ 1084] [depth= 8] . ( 71 sec) [ -8130.8996] [ 1076] [depth= 2] . ( 71 sec) [ -8129.7146] [ 1076] [depth= 1] . ( 72 sec) [ -8128.8149] [ 1075] [depth= 4] . ( 73 sec) [ -8083.3115] [ 1047] [depth= 3] . ( 73 sec) [ -8078.8179] [ 1045] [depth= 5] . ( 75 sec) [ -8077.9068] [ 1045] [depth= 1] . ( 75 sec) [ -8074.8561] [ 1044] [depth= 2] . ( 75 sec) [ -8066.3904] [ 1041] [depth= 3] . ( 76 sec) [ -8066.3538] [ 1041] [depth= 3] . ( 77 sec) [ -8066.3371] [ 1041] [depth= 1] . ( 78 sec) [ -8066.0993] [ 1041] [depth= 1] . ( 82 sec) [ -8066.0601] [ 1041] [depth= 1] . ( 82 sec) [ -8066.0236] [ 1041] [depth= 1] . ( 83 sec) [ -8064.6490] [ 1041] [depth= 2] . ( 85 sec) [ -8035.5111] [Branch lengths ] . ( 87 sec) [ -8033.8505] [GTR parameters ] . ( 87 sec) [ -8027.0579] [Alpha ][ 0.440786] . ( 89 sec) [ -8027.0475] [ 1041] [depth= 3] . ( 91 sec) [ -8025.8637] [ 1041] [depth= 1] . ( 91 sec) [ -8023.7684] [ 1041] [depth= 1] . ( 95 sec) [ -8023.6687] [ 1040] [depth= 1] . ( 96 sec) [ -7943.7659] [ 1018] [depth= 1] . ( 97 sec) [ -7942.8143] [ 1018] [depth= 1] . ( 97 sec) [ -7941.5637] [ 1018] [depth= 2] . ( 98 sec) [ -7940.0080] [ 1018] [depth= 1] . ( 100 sec) [ -7922.9030] [ 1014] [depth= 5] . ( 101 sec) [ -7922.7742] [ 1014] [depth= 2] . ( 101 sec) [ -7922.6434] [ 1014] [depth= 1] . ( 101 sec) [ -7922.6053] [ 1014] [depth= 1] . ( 102 sec) [ -7922.0768] [ 1016] [depth= 2] . ( 104 sec) [ -7919.6972] [ 1016] [depth= 5] . ( 104 sec) [ -7919.6869] [ 1016] [depth= 1] . ( 106 sec) [ -7889.1285] [ 1007] [depth= 1] . ( 110 sec) [ -7889.1115] [ 1007] [depth= 1] . ( 111 sec) [ -7886.8835] [ 1007] [depth= 1] . ( 111 sec) [ -7886.8618] [ 1007] [depth= 1] . ( 120 sec) [ -7886.8433] [ 1007] [depth= 2] . ( 121 sec) [ -7886.6568] [ 1007] [depth= 3] . ( 121 sec) [ -7884.9677] [ 1007] [depth= 1] . ( 123 sec) [ -7884.9269] [ 1007] [depth= 1] . ( 124 sec) [ -7884.9033] [ 1007] [depth= 1] . ( 127 sec) [ -7884.5291] [ 1007] [depth= 1] . ( 131 sec) [ -7884.4694] [ 1007] [depth= 1] . ( 134 sec) [ -7881.5793] [ 1005] [depth= 1] . ( 135 sec) [ -7881.5464] [ 1005] [depth= 1] . ( 140 sec) [ -7876.3687] [Branch lengths ] . ( 141 sec) [ -7875.8657] [GTR parameters ] . ( 142 sec) [ -7875.5638] [Alpha ][ 0.469212] . ( 144 sec) [ -7875.3483] [ 1005] [depth= 3] . ( 199 sec) [ -7874.5034] [Branch lengths ] . ( 200 sec) [ -7874.4922] [GTR parameters ] . ( 200 sec) [ -7874.4912] [Alpha ][ 0.470870] . ( 245 sec) [ -7874.3716] [ 1005] [depth= 1] . ( 257 sec) [ -7872.8034] [Branch lengths ] . ( 258 sec) [ -7872.7953] [GTR parameters ] . ( 258 sec) [ -7872.7952] [Alpha ][ 0.471340] . ( 259 sec) [ -7872.4983] [ 1005] [depth= 1] . ( 260 sec) [ -7872.4355] [ 1005] [depth= 2] . ( 277 sec) [ -7872.4125] [ 1005] [depth= 1] . ( 277 sec) [ -7872.3792] [ 1005] [depth= 1] . ( 283 sec) [ -7872.3661] [ 1005] [depth= 1] . ( 289 sec) [ -7872.3308] [ 1005] [depth= 1] . ( 295 sec) [ -7872.3135] [ 1005] [depth= 2] . ( 304 sec) [ -7872.2198] [ 1005] [depth= 3] . ( 313 sec) [ -7871.7732] [Branch lengths ] . ( 314 sec) [ -7871.7715] [GTR parameters ] . ( 314 sec) [ -7871.7715] [Alpha ][ 0.470771] . ( 371 sec) [ -7871.7564] [Branch lengths ] . ( 463 sec) [ -7871.7561] [Branch lengths ] . ( 463 sec) [ -7871.7561] [Topology ] . ( 465 sec) [ -7871.7561] [Topology ] . ( 465 sec) [ -7871.7561] [GTR parameters ] . ( 465 sec) [ -7871.7561] [Alpha ][ 0.470771] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7871.756133. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -32356.5843] [GTR parameters ] . ( 2 sec) [ -31734.8784] [Alpha ][ 0.500960] . ( 3 sec) [ -31571.1469] [ 3754] [depth= 8] . ( 3 sec) [ -30820.9798] [ 3685] [depth= 5] . ( 3 sec) [ -30789.4168] [ 3683] [depth= 4] . ( 3 sec) [ -30760.0353] [ 3682] [depth= 3] . ( 3 sec) [ -30689.1170] [ 3672] [depth= 7] . ( 3 sec) [ -30477.1968] [ 3670] [depth= 3] . ( 3 sec) [ -30387.9016] [ 3667] [depth= 5] . ( 3 sec) [ -30253.7658] [ 3667] [depth= 2] . ( 3 sec) [ -30055.8880] [ 3655] [depth= 12] . ( 3 sec) [ -29929.1410] [ 3655] [depth= 1] . ( 4 sec) [ -29903.6745] [ 3650] [depth= 22] . ( 4 sec) [ -29722.3884] [ 3650] [depth= 1] . ( 4 sec) [ -29259.9892] [ 3649] [depth= 2] . ( 4 sec) [ -29226.4215] [ 3649] [depth= 1] . ( 4 sec) [ -28897.2463] [ 3618] [depth= 10] . ( 4 sec) [ -28594.3265] [ 3594] [depth= 16] . ( 4 sec) [ -28126.5222] [ 3472] [depth= 11] . ( 4 sec) [ -28079.2419] [ 3465] [depth= 1] . ( 4 sec) [ -27926.5546] [ 3457] [depth= 17] . ( 5 sec) [ -27455.3634] [ 3391] [depth= 27] . ( 5 sec) [ -27412.1173] [ 3390] [depth= 5] . ( 5 sec) [ -27371.6591] [ 3389] [depth= 1] . ( 5 sec) [ -27079.6114] [ 3368] [depth= 5] . ( 5 sec) [ -26907.8687] [ 3358] [depth= 5] . ( 5 sec) [ -26706.3799] [ 3309] [depth= 13] . ( 5 sec) [ -26498.2492] [ 3287] [depth= 19] . ( 5 sec) [ -26437.7949] [ 3277] [depth= 6] . ( 5 sec) [ -26375.1038] [ 3273] [depth= 17] . ( 6 sec) [ -26296.7766] [ 3274] [depth= 4] . ( 6 sec) [ -26172.8619] [ 3275] [depth= 24] . ( 6 sec) [ -25833.8896] [ 3269] [depth= 14] . ( 6 sec) [ -24325.5775] [ 3268] [depth= 2] . ( 6 sec) [ -24058.8403] [ 3246] [depth= 14] . ( 6 sec) [ -24006.4612] [ 3246] [depth= 2] . ( 6 sec) [ -23868.3097] [ 3238] [depth= 2] . ( 6 sec) [ -23758.4211] [ 3219] [depth= 15] . ( 6 sec) [ -23656.0604] [ 3203] [depth= 15] . ( 6 sec) [ -23622.4531] [ 3188] [depth= 1] . ( 7 sec) [ -23549.1580] [ 3180] [depth= 6] . ( 7 sec) [ -23502.6279] [ 3181] [depth= 1] . ( 7 sec) [ -23281.4615] [ 3149] [depth= 20] . ( 7 sec) [ -23019.9963] [ 3051] [depth= 20] . ( 7 sec) [ -22922.2318] [ 3048] [depth= 17] . ( 7 sec) [ -22878.6473] [ 3049] [depth= 3] . ( 7 sec) [ -22802.6493] [ 3048] [depth= 21] . ( 7 sec) [ -21389.1495] [ 3048] [depth= 4] . ( 7 sec) [ -21105.4909] [ 3001] [depth= 17] . ( 7 sec) [ -21043.7417] [ 3001] [depth= 1] . ( 8 sec) [ -20798.4822] [ 3000] [depth= 11] . ( 8 sec) [ -20615.2660] [ 3039] [depth= 1] . ( 8 sec) [ -20415.6456] [ 2982] [depth= 7] . ( 8 sec) [ -20158.2212] [ 2965] [depth= 12] . ( 8 sec) [ -19778.7897] [ 2961] [depth= 6] . ( 8 sec) [ -19772.6102] [ 2960] [depth= 8] . ( 8 sec) [ -19761.9419] [ 2960] [depth= 2] . ( 8 sec) [ -19756.9298] [ 2956] [depth= 9] . ( 8 sec) [ -19720.4601] [ 2956] [depth= 1] . ( 8 sec) [ -19301.8157] [ 2888] [depth= 21] . ( 9 sec) [ -19275.2202] [ 2886] [depth= 15] . ( 9 sec) [ -19269.0359] [ 2903] [depth= 1] . ( 9 sec) [ -19156.2988] [ 2877] [depth= 15] . ( 9 sec) [ -19126.5412] [ 2874] [depth= 15] . ( 9 sec) [ -19078.7708] [ 2855] [depth= 7] . ( 9 sec) [ -18791.4911] [ 2848] [depth= 14] . ( 9 sec) [ -18783.3035] [ 2847] [depth= 14] . ( 10 sec) [ -18579.1045] [ 2851] [depth= 13] . ( 10 sec) [ -18396.2194] [ 2805] [depth= 6] . ( 10 sec) [ -18395.7855] [ 2805] [depth= 1] . ( 10 sec) [ -18384.0990] [ 2763] [depth= 14] . ( 10 sec) [ -18379.8779] [ 2762] [depth= 10] . ( 10 sec) [ -17484.7375] [ 2762] [depth= 1] . ( 10 sec) [ -17130.3683] [ 2655] [depth= 13] . ( 10 sec) [ -17082.2758] [ 2654] [depth= 8] . ( 11 sec) [ -17034.0349] [ 2608] [depth= 16] . ( 11 sec) [ -16883.7538] [ 2594] [depth= 4] . ( 11 sec) [ -16725.4009] [ 2584] [depth= 5] . ( 11 sec) [ -16554.8715] [ 2558] [depth= 13] . ( 11 sec) [ -16195.1655] [ 2555] [depth= 11] . ( 11 sec) [ -16097.0312] [ 2536] [depth= 15] . ( 11 sec) [ -15943.2120] [ 2482] [depth= 12] . ( 11 sec) [ -15685.6671] [ 2457] [depth= 18] . ( 11 sec) [ -15653.4919] [ 2454] [depth= 14] . ( 12 sec) [ -15495.2281] [ 2401] [depth= 11] . ( 12 sec) [ -15494.9489] [ 2401] [depth= 1] . ( 12 sec) [ -15470.9764] [ 2401] [depth= 1] . ( 12 sec) [ -15457.7566] [ 2401] [depth= 4] . ( 12 sec) [ -15267.8363] [ 2343] [depth= 21] . ( 12 sec) [ -15208.9421] [ 2327] [depth= 17] . ( 12 sec) [ -15182.9862] [ 2327] [depth= 1] . ( 12 sec) [ -15109.3250] [ 2327] [depth= 4] . ( 12 sec) [ -15100.1804] [ 2324] [depth= 9] . ( 13 sec) [ -14846.6445] [ 2324] [depth= 3] . ( 13 sec) [ -14780.9961] [ 2314] [depth= 2] . ( 13 sec) [ -14778.9244] [ 2314] [depth= 3] . ( 13 sec) [ -14760.6291] [ 2308] [depth= 6] . ( 13 sec) [ -14746.0767] [ 2308] [depth= 2] . ( 13 sec) [ -14702.6401] [ 2293] [depth= 13] . ( 13 sec) [ -14520.2408] [ 2293] [depth= 1] . ( 13 sec) [ -14249.4155] [ 2240] [depth= 21] . ( 13 sec) [ -14207.1985] [ 2245] [depth= 20] . ( 13 sec) [ -14182.0084] [ 2244] [depth= 4] . ( 14 sec) [ -13974.7520] [ 2266] [depth= 1] . ( 14 sec) [ -13830.8785] [ 2231] [depth= 7] . ( 14 sec) [ -13815.4006] [ 2231] [depth= 18] . ( 14 sec) [ -13812.8362] [ 2231] [depth= 2] . ( 14 sec) [ -13651.0713] [ 2182] [depth= 20] . ( 14 sec) [ -13612.7831] [ 2180] [depth= 4] . ( 14 sec) [ -13552.1108] [ 2172] [depth= 5] . ( 14 sec) [ -13537.4360] [ 2168] [depth= 2] . ( 14 sec) [ -13438.4797] [ 2164] [depth= 3] . ( 14 sec) [ -13396.1025] [ 2162] [depth= 2] . ( 15 sec) [ -13368.4505] [ 2162] [depth= 1] . ( 15 sec) [ -13299.4188] [ 2148] [depth= 10] . ( 15 sec) [ -13262.6438] [ 2149] [depth= 2] . ( 15 sec) [ -13232.8903] [ 2143] [depth= 9] . ( 15 sec) [ -13210.9506] [ 2131] [depth= 15] . ( 15 sec) [ -13171.6258] [ 2126] [depth= 3] . ( 15 sec) [ -13136.1622] [ 2128] [depth= 5] . ( 15 sec) [ -13094.6715] [ 2117] [depth= 1] . ( 16 sec) [ -13075.8055] [ 2115] [depth= 23] . ( 16 sec) [ -12969.2170] [ 2103] [depth= 13] . ( 16 sec) [ -12886.7608] [ 2102] [depth= 1] . ( 16 sec) [ -12867.3661] [ 2100] [depth= 15] . ( 16 sec) [ -12865.6210] [ 2100] [depth= 1] . ( 16 sec) [ -12778.9718] [ 2104] [depth= 14] . ( 16 sec) [ -12691.2814] [ 2088] [depth= 20] . ( 16 sec) [ -12690.3653] [ 2088] [depth= 1] . ( 17 sec) [ -12648.5439] [ 2082] [depth= 1] . ( 17 sec) [ -12641.7089] [ 2081] [depth= 18] . ( 17 sec) [ -12635.7269] [ 2080] [depth= 1] . ( 17 sec) [ -12612.2883] [ 2079] [depth= 7] . ( 17 sec) [ -12603.8306] [ 2079] [depth= 13] . ( 17 sec) [ -12566.8108] [ 2074] [depth= 15] . ( 17 sec) [ -12531.6582] [ 2063] [depth= 1] . ( 17 sec) [ -12481.3941] [ 2058] [depth= 13] . ( 17 sec) [ -12437.8301] [ 2048] [depth= 2] . ( 18 sec) [ -12403.8646] [ 2042] [depth= 13] . ( 18 sec) [ -12397.0656] [ 2041] [depth= 2] . ( 18 sec) [ -12332.5788] [ 2023] [depth= 4] . ( 18 sec) [ -12329.7929] [ 2023] [depth= 12] . ( 18 sec) [ -12329.2502] [ 2023] [depth= 1] . ( 18 sec) [ -12242.2014] [ 1997] [depth= 12] . ( 18 sec) [ -12230.0962] [ 1998] [depth= 4] . ( 18 sec) [ -12222.9672] [ 1997] [depth= 3] . ( 18 sec) [ -12222.1512] [ 1995] [depth= 15] . ( 19 sec) [ -12203.2100] [ 1994] [depth= 3] . ( 19 sec) [ -12203.1245] [ 1994] [depth= 1] . ( 19 sec) [ -12202.9118] [ 1994] [depth= 2] . ( 19 sec) [ -12191.9258] [ 1992] [depth= 4] . ( 19 sec) [ -12048.8059] [ 1950] [depth= 9] . ( 19 sec) [ -12019.6438] [ 1950] [depth= 1] . ( 20 sec) [ -11975.4767] [ 1942] [depth= 6] . ( 20 sec) [ -11969.9425] [ 1944] [depth= 3] . ( 20 sec) [ -11785.4034] [ 1891] [depth= 15] . ( 20 sec) [ -11777.1125] [ 1890] [depth= 1] . ( 20 sec) [ -11767.9787] [ 1881] [depth= 6] . ( 20 sec) [ -11740.0295] [ 1877] [depth= 8] . ( 20 sec) [ -11732.9690] [ 1877] [depth= 3] . ( 20 sec) [ -11645.4716] [ 1861] [depth= 2] . ( 21 sec) [ -11642.1526] [ 1861] [depth= 1] . ( 21 sec) [ -11633.7944] [ 1858] [depth= 9] . ( 21 sec) [ -11524.4096] [ 1797] [depth= 11] . ( 21 sec) [ -11352.9474] [ 1779] [depth= 9] . ( 21 sec) [ -11223.3401] [ 1779] [depth= 10] . ( 21 sec) [ -11217.6834] [ 1779] [depth= 1] . ( 21 sec) [ -11088.5828] [ 1779] [depth= 10] . ( 21 sec) [ -11082.1146] [ 1781] [depth= 1] . ( 21 sec) [ -11058.1978] [ 1779] [depth= 2] . ( 22 sec) [ -11057.4036] [ 1779] [depth= 11] . ( 22 sec) [ -11057.3570] [ 1779] [depth= 1] . ( 22 sec) [ -11046.1190] [ 1779] [depth= 1] . ( 22 sec) [ -10972.9848] [ 1770] [depth= 14] . ( 22 sec) [ -10968.0940] [ 1772] [depth= 16] . ( 22 sec) [ -10942.7631] [ 1757] [depth= 1] . ( 22 sec) [ -10921.5528] [ 1747] [depth= 20] . ( 22 sec) [ -10919.5339] [ 1747] [depth= 1] . ( 23 sec) [ -10905.2418] [ 1736] [depth= 4] . ( 23 sec) [ -10805.3142] [ 1706] [depth= 21] . ( 23 sec) [ -10796.2672] [ 1705] [depth= 3] . ( 23 sec) [ -10719.0882] [ 1681] [depth= 4] . ( 23 sec) [ -10705.0187] [ 1673] [depth= 17] . ( 23 sec) [ -10700.1876] [ 1684] [depth= 1] . ( 23 sec) [ -10671.9307] [ 1679] [depth= 6] . ( 23 sec) [ -10647.1748] [ 1674] [depth= 9] . ( 23 sec) [ -10641.8112] [ 1671] [depth= 1] . ( 23 sec) [ -10629.6838] [ 1670] [depth= 3] . ( 24 sec) [ -10626.6403] [ 1622] [depth= 21] . ( 24 sec) [ -10618.1656] [ 1621] [depth= 1] . ( 24 sec) [ -10554.0159] [ 1624] [depth= 1] . ( 24 sec) [ -10440.6422] [ 1609] [depth= 1] . ( 24 sec) [ -10424.4174] [ 1606] [depth= 1] . ( 24 sec) [ -10405.7171] [ 1599] [depth= 15] . ( 24 sec) [ -10335.6387] [ 1569] [depth= 1] . ( 24 sec) [ -10306.9430] [ 1560] [depth= 15] . ( 24 sec) [ -10293.9595] [ 1560] [depth= 13] . ( 24 sec) [ -10143.2478] [ 1559] [depth= 9] . ( 25 sec) [ -10133.1837] [ 1562] [depth= 1] . ( 25 sec) [ -10124.6284] [ 1559] [depth= 1] . ( 25 sec) [ -10117.8857] [ 1558] [depth= 3] . ( 25 sec) [ -10117.8137] [ 1558] [depth= 1] . ( 25 sec) [ -10117.7569] [ 1558] [depth= 1] . ( 25 sec) [ -10109.3640] [ 1552] [depth= 7] . ( 25 sec) [ -10089.7787] [ 1550] [depth= 3] . ( 26 sec) [ -10081.8427] [ 1553] [depth= 1] . ( 26 sec) [ -10012.4629] [ 1538] [depth= 11] . ( 26 sec) [ -9969.7486] [ 1520] [depth= 5] . ( 26 sec) [ -9963.6902] [ 1519] [depth= 1] . ( 26 sec) [ -9959.6673] [ 1495] [depth= 7] . ( 26 sec) [ -9959.4493] [ 1495] [depth= 18] . ( 26 sec) [ -9953.7943] [ 1495] [depth= 20] . ( 27 sec) [ -9953.7560] [ 1495] [depth= 2] . ( 27 sec) [ -9953.5826] [ 1495] [depth= 1] . ( 27 sec) [ -9951.6739] [ 1496] [depth= 1] . ( 27 sec) [ -9951.2751] [ 1495] [depth= 3] . ( 27 sec) [ -9950.5465] [ 1495] [depth= 12] . ( 27 sec) [ -9942.4087] [ 1494] [depth= 3] . ( 27 sec) [ -9936.3851] [ 1495] [depth= 7] . ( 28 sec) [ -9934.3956] [ 1495] [depth= 2] . ( 28 sec) [ -9930.7069] [ 1495] [depth= 2] . ( 28 sec) [ -9923.7097] [ 1495] [depth= 9] . ( 28 sec) [ -9919.5298] [ 1474] [depth= 1] . ( 29 sec) [ -9919.3101] [ 1475] [depth= 1] . ( 29 sec) [ -9816.5725] [ 1456] [depth= 1] . ( 29 sec) [ -9814.0096] [ 1453] [depth= 18] . ( 29 sec) [ -9800.0424] [ 1450] [depth= 1] . ( 29 sec) [ -9789.1027] [ 1450] [depth= 1] . ( 29 sec) [ -9788.9928] [ 1450] [depth= 1] . ( 29 sec) [ -9788.7025] [ 1450] [depth= 2] . ( 29 sec) [ -9778.1843] [ 1449] [depth= 2] . ( 29 sec) [ -9778.0831] [ 1449] [depth= 1] . ( 30 sec) [ -9778.0720] [ 1449] [depth= 1] . ( 30 sec) [ -9721.4630] [ 1442] [depth= 2] . ( 31 sec) [ -9720.4242] [ 1441] [depth= 2] . ( 31 sec) [ -9713.1822] [ 1441] [depth= 1] . ( 31 sec) [ -9713.1098] [ 1441] [depth= 1] . ( 32 sec) [ -9690.1074] [ 1438] [depth= 1] . ( 32 sec) [ -9670.7647] [ 1431] [depth= 1] . ( 32 sec) [ -9670.1145] [ 1430] [depth= 1] . ( 32 sec) [ -9601.0002] [ 1429] [depth= 6] . ( 32 sec) [ -9600.0306] [ 1429] [depth= 1] . ( 32 sec) [ -9585.8080] [ 1424] [depth= 5] . ( 34 sec) [ -9585.5996] [ 1424] [depth= 1] . ( 35 sec) [ -9386.7460] [Branch lengths ] . ( 37 sec) [ -9212.9649] [GTR parameters ] . ( 37 sec) [ -9169.4353] [Alpha ][ 0.289065] . ( 37 sec) [ -9107.2565] [ 1369] [depth= 2] . ( 38 sec) [ -9068.0244] [ 1348] [depth= 2] . ( 38 sec) [ -9067.1158] [ 1347] [depth= 2] . ( 38 sec) [ -9055.3425] [ 1345] [depth= 2] . ( 38 sec) [ -9039.7141] [ 1337] [depth= 1] . ( 41 sec) [ -9033.7768] [ 1336] [depth= 1] . ( 41 sec) [ -9027.1319] [ 1334] [depth= 3] . ( 41 sec) [ -9008.7784] [ 1328] [depth= 1] . ( 41 sec) [ -9008.3350] [ 1326] [depth= 1] . ( 41 sec) [ -8974.2909] [ 1317] [depth= 4] . ( 44 sec) [ -8933.0291] [ 1278] [depth= 4] . ( 44 sec) [ -8914.1898] [ 1275] [depth= 3] . ( 44 sec) [ -8913.5729] [ 1277] [depth= 1] . ( 45 sec) [ -8909.2380] [ 1276] [depth= 12] . ( 45 sec) [ -8908.9654] [ 1275] [depth= 1] . ( 45 sec) [ -8886.6632] [ 1269] [depth= 10] . ( 46 sec) [ -8886.1702] [ 1269] [depth= 4] . ( 46 sec) [ -8867.3896] [ 1267] [depth= 18] . ( 46 sec) [ -8849.5753] [ 1264] [depth= 2] . ( 47 sec) [ -8848.8585] [ 1263] [depth= 2] . ( 47 sec) [ -8848.8274] [ 1263] [depth= 2] . ( 47 sec) [ -8848.4946] [ 1263] [depth= 1] . ( 47 sec) [ -8844.1424] [ 1263] [depth= 1] . ( 47 sec) [ -8797.5869] [ 1253] [depth= 16] . ( 49 sec) [ -8796.4071] [ 1254] [depth= 1] . ( 50 sec) [ -8796.3048] [ 1254] [depth= 1] . ( 50 sec) [ -8796.0315] [ 1253] [depth= 2] . ( 50 sec) [ -8737.7382] [ 1226] [depth= 7] . ( 50 sec) [ -8559.7681] [ 1168] [depth= 21] . ( 51 sec) [ -8558.0643] [ 1168] [depth= 2] . ( 51 sec) [ -8557.3171] [ 1168] [depth= 2] . ( 51 sec) [ -8532.5184] [ 1163] [depth= 2] . ( 51 sec) [ -8522.9379] [ 1161] [depth= 5] . ( 51 sec) [ -8519.9691] [ 1158] [depth= 5] . ( 51 sec) [ -8519.7718] [ 1158] [depth= 6] . ( 52 sec) [ -8519.6001] [ 1158] [depth= 5] . ( 52 sec) [ -8519.5036] [ 1157] [depth= 3] . ( 52 sec) [ -8519.4691] [ 1157] [depth= 1] . ( 53 sec) [ -8519.4300] [ 1157] [depth= 3] . ( 53 sec) [ -8518.8445] [ 1156] [depth= 5] . ( 54 sec) [ -8509.5399] [ 1154] [depth= 1] . ( 54 sec) [ -8509.4110] [ 1154] [depth= 2] . ( 55 sec) [ -8489.0276] [ 1151] [depth= 6] . ( 55 sec) [ -8484.3085] [ 1151] [depth= 1] . ( 56 sec) [ -8483.0804] [ 1151] [depth= 1] . ( 57 sec) [ -8481.4072] [ 1150] [depth= 3] . ( 57 sec) [ -8480.9506] [ 1148] [depth= 1] . ( 57 sec) [ -8464.5590] [ 1145] [depth= 11] . ( 57 sec) [ -8440.2578] [ 1136] [depth= 1] . ( 58 sec) [ -8440.1960] [ 1136] [depth= 1] . ( 58 sec) [ -8437.3386] [ 1137] [depth= 6] . ( 58 sec) [ -8430.6354] [ 1135] [depth= 2] . ( 58 sec) [ -8428.9356] [ 1134] [depth= 4] . ( 59 sec) [ -8301.2459] [ 1119] [depth= 2] . ( 59 sec) [ -8181.3238] [ 1075] [depth= 6] . ( 59 sec) [ -8178.5008] [ 1074] [depth= 1] . ( 59 sec) [ -8178.4539] [ 1074] [depth= 1] . ( 59 sec) [ -8172.8773] [ 1073] [depth= 3] . ( 60 sec) [ -8172.8452] [ 1073] [depth= 1] . ( 60 sec) [ -8172.3287] [ 1072] [depth= 1] . ( 60 sec) [ -8172.2781] [ 1072] [depth= 2] . ( 62 sec) [ -8170.2552] [ 1072] [depth= 2] . ( 65 sec) [ -8131.7780] [ 1057] [depth= 11] . ( 66 sec) [ -8121.7516] [ 1054] [depth= 2] . ( 67 sec) [ -8116.9713] [ 1056] [depth= 1] . ( 67 sec) [ -7980.8093] [ 1017] [depth= 7] . ( 68 sec) [ -7980.5078] [ 1017] [depth= 2] . ( 68 sec) [ -7979.3104] [ 1017] [depth= 5] . ( 68 sec) [ -7971.4967] [ 1015] [depth= 4] . ( 68 sec) [ -7971.0542] [ 1015] [depth= 2] . ( 69 sec) [ -7966.3536] [ 1011] [depth= 1] . ( 70 sec) [ -7965.9373] [ 1011] [depth= 2] . ( 72 sec) [ -7965.4813] [ 1011] [depth= 3] . ( 72 sec) [ -7963.9031] [ 1011] [depth= 4] . ( 72 sec) [ -7960.7178] [ 1010] [depth= 2] . ( 74 sec) [ -7958.2248] [ 1009] [depth= 1] . ( 74 sec) [ -7957.9409] [ 1008] [depth= 1] . ( 75 sec) [ -7956.3344] [ 1008] [depth= 2] . ( 76 sec) [ -7955.8974] [ 1008] [depth= 2] . ( 77 sec) [ -7954.9342] [ 1008] [depth= 2] . ( 78 sec) [ -7953.5841] [ 1008] [depth= 1] . ( 78 sec) [ -7953.2293] [ 1008] [depth= 1] . ( 80 sec) [ -7951.7103] [ 1008] [depth= 1] . ( 81 sec) [ -7951.5341] [ 1008] [depth= 1] . ( 85 sec) [ -7921.2555] [Branch lengths ] . ( 86 sec) [ -7914.4002] [GTR parameters ] . ( 86 sec) [ -7894.4787] [Alpha ][ 0.456276] . ( 89 sec) [ -7894.4642] [ 1008] [depth= 2] . ( 91 sec) [ -7892.5548] [ 1008] [depth= 1] . ( 94 sec) [ -7892.5400] [ 1008] [depth= 3] . ( 95 sec) [ -7891.0502] [ 1006] [depth= 1] . ( 96 sec) [ -7890.3622] [ 1006] [depth= 1] . ( 97 sec) [ -7890.3483] [ 1006] [depth= 1] . ( 98 sec) [ -7884.7953] [ 1004] [depth= 4] . ( 98 sec) [ -7884.7346] [ 1004] [depth= 1] . ( 100 sec) [ -7884.0580] [ 1003] [depth= 3] . ( 102 sec) [ -7884.0232] [ 1004] [depth= 2] . ( 103 sec) [ -7883.9874] [ 1004] [depth= 1] . ( 113 sec) [ -7882.3568] [ 1003] [depth= 3] . ( 116 sec) [ -7880.9426] [ 1003] [depth= 3] . ( 116 sec) [ -7880.9008] [ 1003] [depth= 1] . ( 133 sec) [ -7880.8872] [ 1003] [depth= 1] . ( 142 sec) [ -7874.9692] [Branch lengths ] . ( 143 sec) [ -7874.6115] [GTR parameters ] . ( 143 sec) [ -7874.5397] [Alpha ][ 0.470445] . ( 202 sec) [ -7873.5066] [Branch lengths ] . ( 297 sec) [ -7872.0057] [Branch lengths ] . ( 297 sec) [ -7872.0057] [Topology ] . ( 299 sec) [ -7871.0849] [Topology ] . ( 301 sec) [ -7871.0431] [Topology ] . ( 303 sec) [ -7871.0386] [Topology ] . ( 306 sec) [ -7871.0377] [Topology ] . ( 306 sec) [ -7871.0315] [GTR parameters ] . ( 306 sec) [ -7871.0296] [Alpha ][ 0.472877] . ( 306 sec) [ -7871.0296] [Topology ] . ( 308 sec) [ -7871.0291] [Topology ] . ( 309 sec) [ -7871.0291] [GTR parameters ] . ( 309 sec) [ -7871.0291] [Alpha ][ 0.472877] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7871.029100. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -28973.9760] [GTR parameters ] . ( 2 sec) [ -28367.2535] [Alpha ][ 0.500960] . ( 2 sec) [ -27561.5473] [ 3732] [depth= 9] . ( 3 sec) [ -26838.1741] [ 3659] [depth= 8] . ( 3 sec) [ -26583.6316] [ 3614] [depth= 1] . ( 3 sec) [ -26531.9428] [ 3611] [depth= 2] . ( 3 sec) [ -26388.8080] [ 3566] [depth= 1] . ( 3 sec) [ -26186.7763] [ 3564] [depth= 6] . ( 3 sec) [ -26144.0948] [ 3563] [depth= 5] . ( 3 sec) [ -25974.1719] [ 3563] [depth= 5] . ( 3 sec) [ -25463.0550] [ 3555] [depth= 7] . ( 3 sec) [ -25336.7024] [ 3554] [depth= 2] . ( 3 sec) [ -25091.8978] [ 3514] [depth= 13] . ( 4 sec) [ -24880.9692] [ 3512] [depth= 7] . ( 4 sec) [ -24764.9757] [ 3512] [depth= 9] . ( 4 sec) [ -24662.7995] [ 3510] [depth= 17] . ( 4 sec) [ -24485.3235] [ 3479] [depth= 18] . ( 4 sec) [ -24441.0209] [ 3476] [depth= 20] . ( 4 sec) [ -24316.9279] [ 3451] [depth= 1] . ( 4 sec) [ -24153.9790] [ 3430] [depth= 1] . ( 4 sec) [ -24054.0335] [ 3419] [depth= 3] . ( 4 sec) [ -24053.7713] [ 3422] [depth= 1] . ( 4 sec) [ -24007.0864] [ 3414] [depth= 22] . ( 5 sec) [ -23967.3271] [ 3409] [depth= 20] . ( 5 sec) [ -23880.5544] [ 3399] [depth= 18] . ( 5 sec) [ -23788.6972] [ 3382] [depth= 13] . ( 5 sec) [ -23503.3128] [ 3359] [depth= 16] . ( 5 sec) [ -22811.1333] [ 3358] [depth= 1] . ( 5 sec) [ -22438.3882] [ 3329] [depth= 15] . ( 5 sec) [ -22407.6382] [ 3326] [depth= 17] . ( 5 sec) [ -22107.6604] [ 3251] [depth= 1] . ( 5 sec) [ -21988.8289] [ 3228] [depth= 21] . ( 5 sec) [ -21849.9469] [ 3164] [depth= 1] . ( 6 sec) [ -21605.3503] [ 3109] [depth= 6] . ( 6 sec) [ -21532.7600] [ 3109] [depth= 5] . ( 6 sec) [ -21490.1602] [ 3111] [depth= 11] . ( 6 sec) [ -21436.1246] [ 3106] [depth= 14] . ( 6 sec) [ -21428.6278] [ 3106] [depth= 1] . ( 6 sec) [ -21290.5032] [ 3074] [depth= 7] . ( 6 sec) [ -21232.5189] [ 3069] [depth= 19] . ( 6 sec) [ -21222.1827] [ 3068] [depth= 4] . ( 6 sec) [ -21150.7708] [ 3068] [depth= 1] . ( 6 sec) [ -20828.2621] [ 3056] [depth= 11] . ( 7 sec) [ -20813.6539] [ 3056] [depth= 1] . ( 7 sec) [ -20740.2494] [ 3055] [depth= 2] . ( 7 sec) [ -20706.8886] [ 3054] [depth= 2] . ( 7 sec) [ -20461.6520] [ 3026] [depth= 12] . ( 7 sec) [ -19900.9563] [ 2994] [depth= 16] . ( 7 sec) [ -19117.4857] [ 2885] [depth= 17] . ( 7 sec) [ -19087.0975] [ 2882] [depth= 5] . ( 7 sec) [ -18901.1556] [ 2877] [depth= 11] . ( 8 sec) [ -18842.4413] [ 2870] [depth= 13] . ( 8 sec) [ -18835.3152] [ 2866] [depth= 1] . ( 8 sec) [ -18706.3336] [ 2857] [depth= 8] . ( 8 sec) [ -18429.3507] [ 2837] [depth= 13] . ( 8 sec) [ -18245.5849] [ 2789] [depth= 19] . ( 8 sec) [ -18221.6109] [ 2789] [depth= 10] . ( 8 sec) [ -18135.3149] [ 2784] [depth= 16] . ( 8 sec) [ -18131.4388] [ 2782] [depth= 7] . ( 8 sec) [ -18092.2207] [ 2781] [depth= 1] . ( 9 sec) [ -18062.7788] [ 2774] [depth= 1] . ( 9 sec) [ -17805.3720] [ 2778] [depth= 9] . ( 9 sec) [ -17787.1601] [ 2773] [depth= 1] . ( 9 sec) [ -17705.9100] [ 2761] [depth= 10] . ( 9 sec) [ -17492.2094] [ 2714] [depth= 12] . ( 9 sec) [ -17479.9459] [ 2699] [depth= 9] . ( 9 sec) [ -17467.3119] [ 2700] [depth= 2] . ( 9 sec) [ -17368.6678] [ 2680] [depth= 7] . ( 9 sec) [ -17366.9480] [ 2680] [depth= 1] . ( 9 sec) [ -17348.0369] [ 2678] [depth= 1] . ( 10 sec) [ -17331.4854] [ 2675] [depth= 1] . ( 10 sec) [ -17125.4504] [ 2662] [depth= 12] . ( 10 sec) [ -17107.7879] [ 2661] [depth= 3] . ( 10 sec) [ -17085.7213] [ 2661] [depth= 21] . ( 10 sec) [ -16881.1199] [ 2593] [depth= 10] . ( 10 sec) [ -16779.2648] [ 2585] [depth= 7] . ( 10 sec) [ -16528.0626] [ 2561] [depth= 11] . ( 10 sec) [ -16395.5760] [ 2554] [depth= 7] . ( 10 sec) [ -16333.8384] [ 2550] [depth= 1] . ( 11 sec) [ -16315.6614] [ 2549] [depth= 10] . ( 11 sec) [ -15924.2647] [ 2548] [depth= 8] . ( 11 sec) [ -15911.9919] [ 2546] [depth= 1] . ( 11 sec) [ -15886.3545] [ 2546] [depth= 2] . ( 11 sec) [ -15770.1522] [ 2521] [depth= 17] . ( 11 sec) [ -15719.2340] [ 2507] [depth= 16] . ( 11 sec) [ -15674.1120] [ 2495] [depth= 14] . ( 11 sec) [ -15663.9289] [ 2493] [depth= 1] . ( 11 sec) [ -15568.6697] [ 2488] [depth= 10] . ( 12 sec) [ -15567.4121] [ 2495] [depth= 14] . ( 12 sec) [ -15548.5849] [ 2493] [depth= 4] . ( 12 sec) [ -15548.5016] [ 2493] [depth= 3] . ( 12 sec) [ -15194.1471] [ 2488] [depth= 11] . ( 12 sec) [ -14876.2256] [ 2403] [depth= 8] . ( 12 sec) [ -14808.7189] [ 2404] [depth= 1] . ( 12 sec) [ -14804.2074] [ 2404] [depth= 7] . ( 12 sec) [ -14728.5237] [ 2362] [depth= 4] . ( 12 sec) [ -14565.7659] [ 2309] [depth= 6] . ( 12 sec) [ -14500.4963] [ 2290] [depth= 7] . ( 13 sec) [ -14399.7508] [ 2270] [depth= 5] . ( 13 sec) [ -14312.8164] [ 2249] [depth= 6] . ( 13 sec) [ -14201.9973] [ 2248] [depth= 21] . ( 13 sec) [ -14141.0414] [ 2241] [depth= 5] . ( 13 sec) [ -14101.0324] [ 2245] [depth= 5] . ( 13 sec) [ -14013.8643] [ 2242] [depth= 4] . ( 13 sec) [ -14003.7632] [ 2241] [depth= 1] . ( 13 sec) [ -13824.1433] [ 2194] [depth= 15] . ( 14 sec) [ -13817.8984] [ 2194] [depth= 1] . ( 14 sec) [ -13814.8167] [ 2194] [depth= 25] . ( 14 sec) [ -13801.0158] [ 2189] [depth= 8] . ( 14 sec) [ -13793.6127] [ 2192] [depth= 8] . ( 14 sec) [ -13734.5560] [ 2145] [depth= 1] . ( 14 sec) [ -13670.3533] [ 2143] [depth= 5] . ( 14 sec) [ -13660.8925] [ 2143] [depth= 5] . ( 14 sec) [ -13641.9100] [ 2142] [depth= 5] . ( 14 sec) [ -13561.2974] [ 2141] [depth= 5] . ( 15 sec) [ -13554.6947] [ 2140] [depth= 6] . ( 15 sec) [ -13479.3514] [ 2135] [depth= 8] . ( 15 sec) [ -13401.8193] [ 2084] [depth= 11] . ( 15 sec) [ -13244.3249] [ 2081] [depth= 2] . ( 15 sec) [ -13234.7935] [ 2081] [depth= 1] . ( 16 sec) [ -13144.0844] [ 2073] [depth= 15] . ( 16 sec) [ -13130.1807] [ 2069] [depth= 2] . ( 16 sec) [ -13029.3182] [ 2059] [depth= 4] . ( 16 sec) [ -13028.4005] [ 2058] [depth= 1] . ( 16 sec) [ -13015.0805] [ 2055] [depth= 11] . ( 16 sec) [ -13013.2120] [ 2055] [depth= 1] . ( 16 sec) [ -12923.5373] [ 2051] [depth= 1] . ( 16 sec) [ -12919.6867] [ 2048] [depth= 9] . ( 16 sec) [ -12800.2364] [ 2027] [depth= 2] . ( 16 sec) [ -12720.6150] [ 2026] [depth= 1] . ( 17 sec) [ -12709.3046] [ 2020] [depth= 2] . ( 17 sec) [ -12706.9730] [ 2021] [depth= 1] . ( 17 sec) [ -12643.7197] [ 2017] [depth= 9] . ( 17 sec) [ -12638.7512] [ 2018] [depth= 2] . ( 17 sec) [ -12626.5019] [ 2018] [depth= 7] . ( 17 sec) [ -12550.3376] [ 2016] [depth= 8] . ( 17 sec) [ -12375.8357] [ 1953] [depth= 13] . ( 17 sec) [ -12374.7310] [ 1953] [depth= 2] . ( 18 sec) [ -12333.5071] [ 1947] [depth= 8] . ( 18 sec) [ -12319.7637] [ 1945] [depth= 2] . ( 18 sec) [ -12315.7307] [ 1944] [depth= 9] . ( 18 sec) [ -12271.9126] [ 1938] [depth= 4] . ( 18 sec) [ -12090.7355] [ 1884] [depth= 14] . ( 18 sec) [ -12082.6535] [ 1884] [depth= 3] . ( 18 sec) [ -12079.5234] [ 1884] [depth= 3] . ( 18 sec) [ -12079.5000] [ 1884] [depth= 2] . ( 18 sec) [ -12078.6287] [ 1884] [depth= 2] . ( 19 sec) [ -12060.9100] [ 1881] [depth= 4] . ( 19 sec) [ -11957.6222] [ 1857] [depth= 19] . ( 19 sec) [ -11922.6287] [ 1850] [depth= 6] . ( 19 sec) [ -11910.0647] [ 1850] [depth= 2] . ( 19 sec) [ -11861.8575] [ 1822] [depth= 9] . ( 19 sec) [ -11861.7592] [ 1822] [depth= 1] . ( 19 sec) [ -11834.2532] [ 1821] [depth= 2] . ( 19 sec) [ -11806.8332] [ 1822] [depth= 2] . ( 19 sec) [ -11590.7636] [ 1759] [depth= 17] . ( 20 sec) [ -11590.7466] [ 1759] [depth= 1] . ( 20 sec) [ -11485.9161] [ 1732] [depth= 14] . ( 20 sec) [ -11340.2456] [ 1701] [depth= 9] . ( 20 sec) [ -11340.1603] [ 1701] [depth= 2] . ( 20 sec) [ -11322.9420] [ 1699] [depth= 4] . ( 20 sec) [ -11322.1776] [ 1699] [depth= 1] . ( 20 sec) [ -11321.9940] [ 1699] [depth= 3] . ( 20 sec) [ -11321.7155] [ 1699] [depth= 2] . ( 20 sec) [ -11307.2587] [ 1694] [depth= 1] . ( 21 sec) [ -11209.7780] [ 1681] [depth= 12] . ( 21 sec) [ -11203.1983] [ 1680] [depth= 3] . ( 21 sec) [ -11171.6406] [ 1676] [depth= 3] . ( 21 sec) [ -11160.0308] [ 1676] [depth= 1] . ( 21 sec) [ -10933.9341] [ 1607] [depth= 18] . ( 22 sec) [ -10933.6525] [ 1607] [depth= 1] . ( 22 sec) [ -10915.1688] [ 1604] [depth= 8] . ( 22 sec) [ -10763.5816] [ 1584] [depth= 2] . ( 22 sec) [ -10694.9152] [ 1577] [depth= 6] . ( 22 sec) [ -10584.6197] [ 1553] [depth= 7] . ( 23 sec) [ -10576.3341] [ 1552] [depth= 3] . ( 23 sec) [ -10539.0203] [ 1545] [depth= 6] . ( 23 sec) [ -10404.9519] [ 1517] [depth= 9] . ( 23 sec) [ -10373.5382] [ 1513] [depth= 11] . ( 23 sec) [ -10358.2605] [ 1510] [depth= 8] . ( 23 sec) [ -10351.0912] [ 1508] [depth= 11] . ( 23 sec) [ -10348.2188] [ 1508] [depth= 1] . ( 23 sec) [ -10342.7474] [ 1507] [depth= 2] . ( 24 sec) [ -10304.6682] [ 1493] [depth= 16] . ( 24 sec) [ -10288.9769] [ 1494] [depth= 1] . ( 24 sec) [ -10253.1415] [ 1476] [depth= 8] . ( 24 sec) [ -10170.9149] [ 1477] [depth= 1] . ( 24 sec) [ -10065.0652] [ 1457] [depth= 10] . ( 24 sec) [ -10053.1024] [ 1458] [depth= 1] . ( 25 sec) [ -10032.1315] [ 1460] [depth= 4] . ( 25 sec) [ -10030.1568] [ 1460] [depth= 2] . ( 25 sec) [ -10018.8706] [ 1457] [depth= 18] . ( 25 sec) [ -9948.6826] [ 1447] [depth= 17] . ( 25 sec) [ -9942.3655] [ 1447] [depth= 1] . ( 25 sec) [ -9941.9409] [ 1447] [depth= 1] . ( 25 sec) [ -9939.7080] [ 1446] [depth= 1] . ( 26 sec) [ -9910.4701] [ 1446] [depth= 1] . ( 26 sec) [ -9893.7283] [ 1444] [depth= 11] . ( 26 sec) [ -9859.3139] [ 1439] [depth= 4] . ( 26 sec) [ -9779.6190] [ 1438] [depth= 3] . ( 26 sec) [ -9673.4832] [ 1422] [depth= 10] . ( 26 sec) [ -9673.4629] [ 1422] [depth= 2] . ( 26 sec) [ -9670.6798] [ 1419] [depth= 1] . ( 26 sec) [ -9652.3324] [ 1424] [depth= 1] . ( 27 sec) [ -9647.1856] [ 1424] [depth= 3] . ( 27 sec) [ -9647.1364] [ 1424] [depth= 5] . ( 27 sec) [ -9614.1611] [ 1416] [depth= 1] . ( 27 sec) [ -9601.6454] [ 1415] [depth= 5] . ( 27 sec) [ -9548.9440] [ 1406] [depth= 11] . ( 27 sec) [ -9546.0613] [ 1406] [depth= 2] . ( 27 sec) [ -9543.9708] [ 1406] [depth= 2] . ( 27 sec) [ -9542.2654] [ 1406] [depth= 1] . ( 28 sec) [ -9491.1215] [ 1390] [depth= 5] . ( 28 sec) [ -9489.6897] [ 1390] [depth= 1] . ( 28 sec) [ -9489.6751] [ 1390] [depth= 2] . ( 28 sec) [ -9483.8899] [ 1388] [depth= 4] . ( 28 sec) [ -9475.2171] [ 1386] [depth= 6] . ( 28 sec) [ -9463.3959] [ 1379] [depth= 4] . ( 29 sec) [ -9462.7660] [ 1379] [depth= 2] . ( 29 sec) [ -9432.9722] [ 1379] [depth= 4] . ( 29 sec) [ -9384.1453] [ 1376] [depth= 8] . ( 29 sec) [ -9381.7836] [ 1376] [depth= 1] . ( 29 sec) [ -9368.9574] [ 1364] [depth= 7] . ( 29 sec) [ -9358.1341] [ 1360] [depth= 3] . ( 29 sec) [ -9270.5646] [ 1339] [depth= 12] . ( 30 sec) [ -9265.7988] [ 1339] [depth= 3] . ( 30 sec) [ -9229.6146] [ 1328] [depth= 12] . ( 30 sec) [ -9218.0405] [ 1328] [depth= 3] . ( 30 sec) [ -9215.9223] [ 1328] [depth= 1] . ( 30 sec) [ -9183.2317] [ 1305] [depth= 7] . ( 30 sec) [ -9183.1623] [ 1305] [depth= 2] . ( 30 sec) [ -9163.5332] [ 1304] [depth= 11] . ( 31 sec) [ -9156.0721] [ 1304] [depth= 1] . ( 31 sec) [ -8933.2854] [ 1250] [depth= 8] . ( 31 sec) [ -8918.1693] [ 1247] [depth= 8] . ( 31 sec) [ -8895.7235] [ 1250] [depth= 2] . ( 31 sec) [ -8895.6756] [ 1250] [depth= 1] . ( 31 sec) [ -8894.8758] [ 1250] [depth= 1] . ( 32 sec) [ -8883.3490] [ 1255] [depth= 1] . ( 32 sec) [ -8883.2284] [ 1255] [depth= 2] . ( 33 sec) [ -8780.8631] [Branch lengths ] . ( 39 sec) [ -8750.8559] [GTR parameters ] . ( 39 sec) [ -8732.7924] [Alpha ][ 0.337328] . ( 39 sec) [ -8731.0904] [ 1249] [depth= 7] . ( 40 sec) [ -8721.0956] [ 1248] [depth= 2] . ( 40 sec) [ -8714.3389] [ 1247] [depth= 2] . ( 40 sec) [ -8713.4664] [ 1247] [depth= 2] . ( 40 sec) [ -8679.2319] [ 1199] [depth= 11] . ( 41 sec) [ -8632.3347] [ 1183] [depth= 10] . ( 42 sec) [ -8546.8167] [ 1183] [depth= 7] . ( 42 sec) [ -8546.6131] [ 1184] [depth= 1] . ( 42 sec) [ -8542.0594] [ 1183] [depth= 1] . ( 42 sec) [ -8528.1349] [ 1178] [depth= 2] . ( 43 sec) [ -8506.0790] [ 1173] [depth= 4] . ( 43 sec) [ -8451.7645] [ 1158] [depth= 5] . ( 44 sec) [ -8449.8390] [ 1155] [depth= 2] . ( 45 sec) [ -8445.4954] [ 1154] [depth= 6] . ( 46 sec) [ -8445.1572] [ 1154] [depth= 3] . ( 46 sec) [ -8418.3343] [ 1129] [depth= 5] . ( 49 sec) [ -8397.8595] [ 1125] [depth= 2] . ( 50 sec) [ -8388.9464] [ 1123] [depth= 1] . ( 50 sec) [ -8341.0442] [ 1113] [depth= 5] . ( 50 sec) [ -8326.2463] [ 1110] [depth= 2] . ( 50 sec) [ -8323.3222] [ 1110] [depth= 2] . ( 50 sec) [ -8300.4756] [ 1106] [depth= 2] . ( 51 sec) [ -8280.4079] [ 1102] [depth= 1] . ( 51 sec) [ -8280.3221] [ 1102] [depth= 1] . ( 51 sec) [ -8278.1095] [ 1101] [depth= 1] . ( 51 sec) [ -8278.0156] [ 1101] [depth= 1] . ( 51 sec) [ -8277.3223] [ 1101] [depth= 2] . ( 51 sec) [ -8276.7460] [ 1101] [depth= 3] . ( 54 sec) [ -8275.1668] [ 1097] [depth= 10] . ( 56 sec) [ -8253.3381] [ 1095] [depth= 4] . ( 56 sec) [ -8242.1646] [ 1092] [depth= 5] . ( 56 sec) [ -8100.8957] [ 1062] [depth= 6] . ( 57 sec) [ -8100.8844] [ 1062] [depth= 1] . ( 57 sec) [ -8091.3221] [ 1060] [depth= 5] . ( 57 sec) [ -8090.4716] [ 1060] [depth= 1] . ( 57 sec) [ -8090.4556] [ 1060] [depth= 1] . ( 57 sec) [ -8081.1854] [ 1058] [depth= 1] . ( 61 sec) [ -8076.6123] [ 1056] [depth= 6] . ( 61 sec) [ -8075.6232] [ 1056] [depth= 2] . ( 62 sec) [ -8075.5830] [ 1056] [depth= 2] . ( 64 sec) [ -8075.5717] [ 1056] [depth= 2] . ( 65 sec) [ -8075.0299] [ 1058] [depth= 1] . ( 65 sec) [ -8068.5708] [ 1056] [depth= 1] . ( 66 sec) [ -8060.9233] [ 1054] [depth= 2] . ( 66 sec) [ -8060.8227] [ 1054] [depth= 3] . ( 67 sec) [ -8060.8118] [ 1054] [depth= 3] . ( 73 sec) [ -8060.7859] [ 1054] [depth= 2] . ( 75 sec) [ -8058.2989] [ 1053] [depth= 2] . ( 77 sec) [ -8052.8559] [ 1056] [depth= 4] . ( 79 sec) [ -8052.6763] [ 1056] [depth= 1] . ( 82 sec) [ -8043.4121] [ 1054] [depth= 2] . ( 82 sec) [ -8036.5271] [ 1052] [depth= 1] . ( 86 sec) [ -8036.5050] [ 1052] [depth= 1] . ( 86 sec) [ -8031.6191] [ 1049] [depth= 1] . ( 88 sec) [ -8031.5017] [ 1049] [depth= 3] . ( 88 sec) [ -8031.4784] [ 1049] [depth= 1] . ( 88 sec) [ -8031.1397] [ 1049] [depth= 1] . ( 89 sec) [ -7943.3081] [ 1015] [depth= 1] . ( 91 sec) [ -7912.3407] [Branch lengths ] . ( 96 sec) [ -7909.2704] [GTR parameters ] . ( 97 sec) [ -7901.1352] [Alpha ][ 0.455744] . ( 97 sec) [ -7889.8649] [ 1009] [depth= 2] . ( 97 sec) [ -7887.7795] [ 1008] [depth= 6] . ( 98 sec) [ -7886.9129] [ 1006] [depth= 2] . ( 102 sec) [ -7885.1914] [ 1006] [depth= 1] . ( 105 sec) [ -7884.3285] [ 1006] [depth= 4] . ( 106 sec) [ -7883.5568] [ 1006] [depth= 2] . ( 108 sec) [ -7883.0923] [ 1006] [depth= 1] . ( 109 sec) [ -7882.6328] [ 1006] [depth= 5] . ( 109 sec) [ -7882.3979] [ 1006] [depth= 4] . ( 110 sec) [ -7882.3288] [ 1006] [depth= 2] . ( 111 sec) [ -7877.1860] [ 1003] [depth= 1] . ( 113 sec) [ -7877.1741] [ 1003] [depth= 1] . ( 113 sec) [ -7876.8576] [ 1003] [depth= 1] . ( 114 sec) [ -7876.8403] [ 1003] [depth= 1] . ( 122 sec) [ -7876.8022] [ 1003] [depth= 1] . ( 123 sec) [ -7876.7909] [ 1003] [depth= 1] . ( 140 sec) [ -7876.7790] [ 1003] [depth= 1] . ( 145 sec) [ -7876.3259] [ 1003] [depth= 2] . ( 145 sec) [ -7876.2594] [ 1003] [depth= 2] . ( 147 sec) [ -7876.2349] [ 1003] [depth= 2] . ( 147 sec) [ -7876.0943] [ 1003] [depth= 2] . ( 147 sec) [ -7875.9133] [ 1003] [depth= 1] . ( 151 sec) [ -7870.3302] [Branch lengths ] . ( 151 sec) [ -7870.3284] [GTR parameters ] . ( 151 sec) [ -7870.2579] [Alpha ][ 0.469871] . ( 163 sec) [ -7870.2051] [ 1003] [depth= 1] . ( 209 sec) [ -7869.8515] [Branch lengths ] . ( 213 sec) [ -7869.4243] [GTR parameters ] . ( 213 sec) [ -7869.4213] [Alpha ][ 0.472933] . ( 308 sec) [ -7869.3579] [Branch lengths ] . ( 308 sec) [ -7869.3579] [Topology ] . ( 310 sec) [ -7869.3532] [Topology ] . ( 312 sec) [ -7869.3517] [Topology ] . ( 314 sec) [ -7869.3511] [Topology ] . ( 315 sec) [ -7869.3503] [GTR parameters ] . ( 315 sec) [ -7869.3503] [Alpha ][ 0.472933] . ( 315 sec) [ -7869.3503] [Topology ] . ( 317 sec) [ -7869.3500] [Topology ] . ( 318 sec) [ -7869.3500] [GTR parameters ] . ( 319 sec) [ -7869.3500] [Alpha ][ 0.472933] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7869.349981. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7952.3607] [GTR parameters ] . ( 3 sec) [ -7922.0045] [Alpha ][ 0.500960] . ( 3 sec) [ -7922.0045] [Topology ] . ( 5 sec) [ -7888.2427] [Topology ] . ( 7 sec) [ -7882.0784] [Topology ] . ( 10 sec) [ -7877.5421] [Topology ] . ( 12 sec) [ -7874.9338] [Topology ] . ( 14 sec) [ -7873.6053] [Topology ] . ( 16 sec) [ -7873.2530] [Topology ] . ( 18 sec) [ -7873.0995] [Topology ] . ( 20 sec) [ -7872.9835] [Topology ] . ( 22 sec) [ -7872.9341] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -7872.6117] [GTR parameters ] . ( 38 sec) [ -7872.4034] [Alpha ][ 0.474317] . ( 38 sec) [ -7872.4034] [Topology ] . ( 40 sec) [ -7872.3979] [Topology ] . ( 42 sec) [ -7872.3966] [Topology ] . ( 44 sec) [ -7872.3961] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -7872.3933] [GTR parameters ] . ( 57 sec) [ -7872.3933] [Alpha ][ 0.473843] . ( 57 sec) [ -7872.3933] [Topology ] . ( 59 sec) [ -7872.3931] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -7872.3931] [GTR parameters ] . ( 71 sec) [ -7872.3931] [Alpha ][ 0.473843] . ( 71 sec) [ -7872.3931] [Topology ] . ( 73 sec) [ -7872.3930] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 100 sec) [ -7952.3607] [GTR parameters ] . ( 100 sec) [ -7922.0045] [Alpha ][ 0.500960] . ( 101 sec) [ -7921.9865] [ 1008] [depth= 1] . ( 102 sec) [ -7921.9299] [ 1008] [depth= 3] . ( 102 sec) [ -7921.9117] [ 1008] [depth= 3] . ( 102 sec) [ -7921.4488] [ 1008] [depth= 1] . ( 102 sec) [ -7921.4128] [ 1008] [depth= 1] . ( 102 sec) [ -7921.3866] [ 1008] [depth= 4] . ( 102 sec) [ -7921.3643] [ 1008] [depth= 2] . ( 102 sec) [ -7921.3426] [ 1008] [depth= 3] . ( 103 sec) [ -7921.2586] [ 1008] [depth= 2] . ( 103 sec) [ -7921.2289] [ 1008] [depth= 4] . ( 103 sec) [ -7921.2100] [ 1008] [depth= 4] . ( 104 sec) [ -7921.1496] [ 1008] [depth= 1] . ( 105 sec) [ -7920.5718] [ 1008] [depth= 1] . ( 105 sec) [ -7920.5516] [ 1008] [depth= 1] . ( 108 sec) [ -7920.0296] [ 1008] [depth= 1] . ( 109 sec) [ -7919.9843] [ 1008] [depth= 4] . ( 109 sec) [ -7912.5704] [ 1007] [depth= 4] . ( 109 sec) [ -7912.4582] [ 1007] [depth= 3] . ( 109 sec) [ -7912.0542] [ 1007] [depth= 2] . ( 109 sec) [ -7911.7589] [ 1007] [depth= 2] . ( 109 sec) [ -7911.5610] [ 1007] [depth= 1] . ( 109 sec) [ -7911.5009] [ 1007] [depth= 1] . ( 110 sec) [ -7911.4639] [ 1007] [depth= 2] . ( 110 sec) [ -7911.2940] [ 1007] [depth= 1] . ( 110 sec) [ -7911.2596] [ 1007] [depth= 1] . ( 116 sec) [ -7911.0809] [ 1006] [depth= 1] . ( 117 sec) [ -7910.9846] [ 1007] [depth= 1] . ( 118 sec) [ -7910.8110] [ 1007] [depth= 1] . ( 118 sec) [ -7910.6836] [ 1007] [depth= 1] . ( 118 sec) [ -7909.0155] [ 1006] [depth= 1] . ( 122 sec) [ -7908.9445] [ 1006] [depth= 1] . ( 122 sec) [ -7908.8908] [ 1006] [depth= 1] . ( 124 sec) [ -7908.4862] [ 1006] [depth= 4] . ( 124 sec) [ -7906.0923] [ 1006] [depth= 1] . ( 125 sec) [ -7904.4661] [ 1006] [depth= 2] . ( 125 sec) [ -7904.3943] [ 1006] [depth= 1] . ( 125 sec) [ -7902.9703] [ 1006] [depth= 1] . ( 125 sec) [ -7902.9463] [ 1006] [depth= 1] . ( 126 sec) [ -7902.2082] [ 1006] [depth= 1] . ( 129 sec) [ -7899.3771] [ 1006] [depth= 1] . ( 130 sec) [ -7898.8193] [ 1006] [depth= 1] . ( 131 sec) [ -7898.3429] [ 1006] [depth= 1] . ( 131 sec) [ -7895.5364] [ 1005] [depth= 1] . ( 132 sec) [ -7893.3002] [ 1005] [depth= 1] . ( 134 sec) [ -7892.8554] [ 1005] [depth= 1] . ( 135 sec) [ -7892.8389] [ 1005] [depth= 1] . ( 135 sec) [ -7892.7471] [ 1005] [depth= 1] . ( 137 sec) [ -7892.7226] [ 1005] [depth= 2] . ( 137 sec) [ -7892.6897] [ 1005] [depth= 2] . ( 138 sec) [ -7892.5157] [ 1005] [depth= 1] . ( 139 sec) [ -7891.9373] [ 1005] [depth= 1] . ( 139 sec) [ -7891.8842] [ 1005] [depth= 1] . ( 142 sec) [ -7891.8361] [ 1005] [depth= 1] . ( 143 sec) [ -7891.5740] [ 1004] [depth= 2] . ( 144 sec) [ -7888.9031] [ 1004] [depth= 1] . ( 144 sec) [ -7888.8135] [ 1004] [depth= 1] . ( 145 sec) [ -7888.7653] [ 1004] [depth= 1] . ( 147 sec) [ -7888.6147] [ 1004] [depth= 1] . ( 149 sec) [ -7872.1766] [Branch lengths ] . ( 150 sec) [ -7871.8928] [GTR parameters ] . ( 150 sec) [ -7871.6574] [Alpha ][ 0.472364] . ( 172 sec) [ -7871.4930] [ 1003] [depth= 1] . ( 201 sec) [ -7871.4683] [ 1003] [depth= 1] . ( 209 sec) [ -7869.2208] [Branch lengths ] . ( 211 sec) [ -7869.2074] [GTR parameters ] . ( 211 sec) [ -7869.2072] [Alpha ][ 0.473062] . ( 268 sec) [ -7869.0851] [Branch lengths ] . ( 359 sec) [ -7869.0777] [Branch lengths ] . ( 359 sec) [ -7869.0777] [Topology ] . ( 361 sec) [ -7869.0774] [Topology ] . ( 362 sec) [ -7869.0773] [GTR parameters ] . ( 362 sec) [ -7869.0773] [Alpha ][ 0.473062] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7872.392970 . Log likelihood obtained after SPR moves : -7869.077264 . Log likelihood of the current tree: -7869.077264. . Printing the most likely tree in file 'nucleic_M2752_106x1292_2006.phy_phyml_tree.txt'... . Best log likelihood : -7869.077264 . Time used 0h6m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2124.74user 0.00system 35:35.28elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps