.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1392_57x430_2003.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 389 patterns found. (out of a total of 430 sites) . 150 sites without polymorphism (34.88%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 54Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15053.4371] [Alpha ][ 0.500960] . ( 3 sec) [ -14926.8034] [ 2341] [depth= 7] . ( 4 sec) [ -14753.7932] [ 2312] [depth= 4] . ( 5 sec) [ -14722.6173] [ 2309] [depth= 2] . ( 5 sec) [ -14716.6891] [ 2307] [depth= 2] . ( 6 sec) [ -14608.4208] [ 2279] [depth= 1] . ( 7 sec) [ -14499.8180] [ 2277] [depth= 2] . ( 7 sec) [ -14446.9422] [ 2269] [depth= 4] . ( 8 sec) [ -14416.2989] [ 2268] [depth= 2] . ( 8 sec) [ -14371.7778] [ 2248] [depth= 2] . ( 9 sec) [ -14364.6976] [ 2245] [depth= 1] . ( 10 sec) [ -14258.5021] [ 2226] [depth= 11] . ( 10 sec) [ -14256.6794] [ 2226] [depth= 1] . ( 11 sec) [ -14197.3498] [ 2223] [depth= 9] . ( 11 sec) [ -14062.2844] [ 2215] [depth= 3] . ( 12 sec) [ -14038.9066] [ 2212] [depth= 2] . ( 13 sec) [ -13758.8359] [ 2146] [depth= 16] . ( 13 sec) [ -13756.2007] [ 2146] [depth= 9] . ( 14 sec) [ -13621.5591] [ 2122] [depth= 9] . ( 15 sec) [ -13447.0379] [ 2094] [depth= 15] . ( 16 sec) [ -13417.7971] [ 2088] [depth= 13] . ( 16 sec) [ -13336.3063] [ 2086] [depth= 2] . ( 17 sec) [ -13286.5498] [ 2080] [depth= 14] . ( 17 sec) [ -13278.1931] [ 2078] [depth= 3] . ( 18 sec) [ -13183.3547] [ 2072] [depth= 19] . ( 19 sec) [ -13179.2856] [ 2073] [depth= 11] . ( 20 sec) [ -12983.2549] [ 2044] [depth= 11] . ( 20 sec) [ -12980.6359] [ 2043] [depth= 2] . ( 21 sec) [ -12948.2967] [ 2036] [depth= 8] . ( 22 sec) [ -12931.7368] [ 2038] [depth= 2] . ( 23 sec) [ -12900.2816] [ 2028] [depth= 1] . ( 23 sec) [ -12782.3373] [ 2003] [depth= 6] . ( 24 sec) [ -12773.1963] [ 2003] [depth= 2] . ( 25 sec) [ -12762.7676] [ 2003] [depth= 2] . ( 26 sec) [ -12753.3867] [ 2001] [depth= 2] . ( 26 sec) [ -12615.0252] [ 1973] [depth= 3] . ( 27 sec) [ -12578.6261] [ 1977] [depth= 20] . ( 28 sec) [ -12519.9767] [ 1966] [depth= 14] . ( 28 sec) [ -12512.9843] [ 1965] [depth= 1] . ( 29 sec) [ -12510.8803] [ 1965] [depth= 5] . ( 29 sec) [ -12481.4961] [ 1960] [depth= 11] . ( 30 sec) [ -12343.9841] [ 1908] [depth= 7] . ( 31 sec) [ -12271.0346] [ 1891] [depth= 7] . ( 31 sec) [ -12259.0499] [ 1889] [depth= 1] . ( 32 sec) [ -12201.8558] [ 1885] [depth= 2] . ( 33 sec) [ -12167.3531] [ 1881] [depth= 18] . ( 37 sec) [ -12144.5850] [ 1882] [depth= 1] . ( 38 sec) [ -12084.6199] [ 1881] [depth= 15] . ( 39 sec) [ -12056.7521] [ 1879] [depth= 1] . ( 40 sec) [ -12054.1782] [ 1881] [depth= 3] . ( 40 sec) [ -11952.4116] [ 1857] [depth= 11] . ( 41 sec) [ -11785.1492] [ 1842] [depth= 5] . ( 42 sec) [ -11754.6711] [ 1831] [depth= 6] . ( 43 sec) [ -11745.6102] [ 1830] [depth= 1] . ( 43 sec) [ -11597.3280] [ 1803] [depth= 11] . ( 44 sec) [ -11450.7498] [ 1778] [depth= 3] . ( 44 sec) [ -11450.7132] [ 1778] [depth= 1] . ( 45 sec) [ -11388.8318] [ 1773] [depth= 10] . ( 46 sec) [ -11381.0755] [ 1765] [depth= 3] . ( 47 sec) [ -11378.4753] [ 1764] [depth= 1] . ( 47 sec) [ -11378.2849] [ 1762] [depth= 1] . ( 48 sec) [ -11315.0633] [ 1738] [depth= 9] . ( 48 sec) [ -11272.1012] [ 1731] [depth= 2] . ( 49 sec) [ -11246.7268] [ 1723] [depth= 1] . ( 50 sec) [ -11186.9329] [ 1716] [depth= 1] . ( 51 sec) [ -11186.7887] [ 1718] [depth= 2] . ( 52 sec) [ -11180.2938] [ 1717] [depth= 3] . ( 52 sec) [ -11045.1499] [ 1687] [depth= 5] . ( 54 sec) [ -10827.6170] [ 1655] [depth= 9] . ( 55 sec) [ -10753.8347] [ 1638] [depth= 1] . ( 55 sec) [ -10718.9336] [ 1629] [depth= 12] . ( 56 sec) [ -10713.2063] [ 1627] [depth= 1] . ( 57 sec) [ -10707.4013] [ 1626] [depth= 9] . ( 58 sec) [ -10466.8607] [ 1589] [depth= 11] . ( 58 sec) [ -10456.4003] [ 1582] [depth= 1] . ( 59 sec) [ -10263.6759] [ 1581] [depth= 3] . ( 60 sec) [ -10250.9877] [ 1576] [depth= 3] . ( 60 sec) [ -10208.0566] [ 1572] [depth= 1] . ( 62 sec) [ -10150.8796] [ 1556] [depth= 1] . ( 63 sec) [ -10150.1986] [ 1552] [depth= 3] . ( 63 sec) [ -10146.9255] [ 1552] [depth= 3] . ( 64 sec) [ -10125.3600] [ 1553] [depth= 2] . ( 65 sec) [ -10031.8184] [ 1558] [depth= 4] . ( 66 sec) [ -10026.7413] [ 1562] [depth= 4] . ( 66 sec) [ -10026.6741] [ 1563] [depth= 2] . ( 67 sec) [ -10021.5041] [ 1563] [depth= 1] . ( 67 sec) [ -10020.2724] [ 1563] [depth= 1] . ( 68 sec) [ -10004.8101] [ 1556] [depth= 2] . ( 71 sec) [ -10004.7768] [ 1556] [depth= 2] . ( 71 sec) [ -10000.7003] [ 1556] [depth= 5] . ( 72 sec) [ -9977.4398] [ 1552] [depth= 1] . ( 72 sec) [ -9973.5946] [ 1553] [depth= 9] . ( 73 sec) [ -9959.0761] [ 1546] [depth= 7] . ( 78 sec) [ -9884.7277] [ 1527] [depth= 1] . ( 79 sec) [ -9845.3356] [ 1515] [depth= 7] . ( 79 sec) [ -9724.4689] [ 1517] [depth= 4] . ( 80 sec) [ -9710.6914] [ 1509] [depth= 2] . ( 80 sec) [ -9673.2021] [ 1496] [depth= 5] . ( 81 sec) [ -9659.5830] [ 1491] [depth= 4] . ( 81 sec) [ -9652.5624] [ 1488] [depth= 1] . ( 82 sec) [ -9629.8832] [ 1486] [depth= 2] . ( 83 sec) [ -9572.3176] [ 1478] [depth= 1] . ( 84 sec) [ -9476.3929] [ 1489] [depth= 4] . ( 84 sec) [ -9427.4796] [ 1484] [depth= 4] . ( 85 sec) [ -9343.0195] [ 1480] [depth= 2] . ( 86 sec) [ -9341.8791] [ 1480] [depth= 1] . ( 88 sec) [ -9282.9886] [ 1463] [depth= 1] . ( 89 sec) [ -9231.2006] [ 1455] [depth= 11] . ( 90 sec) [ -9226.0582] [ 1453] [depth= 2] . ( 93 sec) [ -9213.2614] [ 1447] [depth= 3] . ( 94 sec) [ -9208.1321] [ 1446] [depth= 2] . ( 95 sec) [ -9188.6712] [ 1441] [depth= 8] . ( 95 sec) [ -9019.8576] [ 1406] [depth= 2] . ( 96 sec) [ -9017.2600] [ 1405] [depth= 1] . ( 97 sec) [ -8995.8021] [ 1399] [depth= 1] . ( 97 sec) [ -8992.9818] [ 1411] [depth= 1] . ( 98 sec) [ -8892.5823] [ 1384] [depth= 2] . ( 99 sec) [ -8853.7095] [ 1384] [depth= 7] . ( 100 sec) [ -8850.7520] [ 1378] [depth= 8] . ( 101 sec) [ -8824.4397] [ 1358] [depth= 2] . ( 101 sec) [ -8823.9882] [ 1358] [depth= 2] . ( 102 sec) [ -8810.1357] [ 1359] [depth= 1] . ( 103 sec) [ -8773.1537] [ 1359] [depth= 1] . ( 104 sec) [ -8771.5788] [ 1358] [depth= 3] . ( 105 sec) [ -8767.0014] [ 1360] [depth= 1] . ( 107 sec) [ -8652.8414] [Branch lengths ] . ( 108 sec) [ -8652.5938] [Alpha ][ 0.527206] . ( 110 sec) [ -8652.0438] [ 1360] [depth= 1] . ( 110 sec) [ -8647.0609] [ 1357] [depth= 2] . ( 111 sec) [ -8594.5215] [ 1347] [depth= 5] . ( 112 sec) [ -8572.2033] [ 1341] [depth= 1] . ( 113 sec) [ -8571.4939] [ 1339] [depth= 1] . ( 115 sec) [ -8570.9425] [ 1340] [depth= 1] . ( 115 sec) [ -8570.5035] [ 1340] [depth= 1] . ( 116 sec) [ -8535.1777] [ 1326] [depth= 9] . ( 118 sec) [ -8535.1562] [ 1326] [depth= 1] . ( 119 sec) [ -8534.7404] [ 1326] [depth= 1] . ( 120 sec) [ -8363.1518] [ 1290] [depth= 3] . ( 120 sec) [ -8363.1404] [ 1290] [depth= 1] . ( 121 sec) [ -8355.3546] [ 1287] [depth= 1] . ( 126 sec) [ -8355.0784] [ 1287] [depth= 2] . ( 129 sec) [ -8352.7669] [ 1286] [depth= 3] . ( 130 sec) [ -8323.6806] [ 1283] [depth= 5] . ( 131 sec) [ -8323.5685] [ 1283] [depth= 1] . ( 132 sec) [ -8322.9054] [ 1282] [depth= 1] . ( 145 sec) [ -8318.1849] [ 1280] [depth= 2] . ( 149 sec) [ -8317.4808] [ 1279] [depth= 1] . ( 162 sec) [ -8317.1296] [ 1279] [depth= 1] . ( 172 sec) [ -8317.0060] [ 1279] [depth= 1] . ( 176 sec) [ -8306.9087] [ 1276] [depth= 1] . ( 183 sec) [ -8306.8974] [ 1276] [depth= 2] . ( 184 sec) [ -8306.7181] [ 1276] [depth= 1] . ( 207 sec) [ -8306.0723] [ 1276] [depth= 1] . ( 216 sec) [ -8286.8440] [ 1270] [depth= 4] . ( 234 sec) [ -8283.8413] [ 1269] [depth= 1] . ( 235 sec) [ -8223.6515] [ 1242] [depth= 7] . ( 236 sec) [ -8217.5752] [ 1241] [depth= 5] . ( 243 sec) [ -8217.2202] [ 1243] [depth= 1] . ( 244 sec) [ -8214.9166] [ 1241] [depth= 2] . ( 247 sec) [ -8214.6942] [ 1237] [depth= 2] . ( 250 sec) [ -8203.6751] [ 1240] [depth= 1] . ( 250 sec) [ -8200.5888] [ 1240] [depth= 2] . ( 260 sec) [ -8188.6209] [ 1238] [depth= 1] . ( 270 sec) [ -8188.5937] [ 1238] [depth= 1] . ( 273 sec) [ -8179.4851] [Branch lengths ] . ( 274 sec) [ -8179.3717] [Alpha ][ 0.546743] . ( 279 sec) [ -8178.8650] [ 1240] [depth= 3] . ( 286 sec) [ -8178.8031] [ 1240] [depth= 1] . ( 290 sec) [ -8178.7835] [ 1240] [depth= 2] . ( 301 sec) [ -8177.7226] [ 1240] [depth= 1] . ( 302 sec) [ -8177.7031] [ 1240] [depth= 2] . ( 315 sec) [ -8177.0556] [ 1239] [depth= 1] . ( 315 sec) [ -8177.0061] [ 1239] [depth= 3] . ( 316 sec) [ -8175.4518] [ 1238] [depth= 1] . ( 340 sec) [ -8172.1384] [ 1238] [depth= 1] . ( 342 sec) [ -8172.0818] [ 1238] [depth= 1] . ( 348 sec) [ -8172.0540] [ 1238] [depth= 1] . ( 359 sec) [ -8170.6037] [ 1238] [depth= 5] . ( 364 sec) [ -8170.5761] [ 1238] [depth= 1] . ( 371 sec) [ -8170.5429] [ 1238] [depth= 1] . ( 383 sec) [ -8170.1216] [ 1236] [depth= 1] . ( 407 sec) [ -8169.5990] [ 1236] [depth= 3] . ( 438 sec) [ -8166.3535] [Branch lengths ] . ( 439 sec) [ -8166.3534] [Alpha ][ 0.547334] . ( 442 sec) [ -8166.3389] [ 1237] [depth= 2] . ( 638 sec) [ -8165.9851] [Branch lengths ] . ( 639 sec) [ -8165.9827] [Alpha ][ 0.550312] . ( 640 sec) [ -8165.9827] [Topology ] . ( 645 sec) [ -8165.9331] [Topology ] . ( 651 sec) [ -8165.9106] [Topology ] . ( 656 sec) [ -8165.8968] [Topology ] . ( 662 sec) [ -8165.8881] [Topology ] . ( 668 sec) [ -8165.8826] [Topology ] . ( 673 sec) [ -8165.8790] [Topology ] . ( 674 sec) [ -8165.8776] [Alpha ][ 0.552505] . ( 674 sec) [ -8165.8776] [Topology ] . ( 680 sec) [ -8165.8750] [Topology ] . ( 686 sec) [ -8165.8732] [Topology ] . ( 691 sec) [ -8165.8721] [Topology ] . ( 697 sec) [ -8165.8714] [Topology ] . ( 698 sec) [ -8165.8714] [Alpha ][ 0.553057] . ( 698 sec) [ -8165.8714] [Topology ] . ( 703 sec) [ -8165.8709] [Topology ] . ( 704 sec) [ -8165.8709] [Alpha ][ 0.553057] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8165.870856. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15807.8574] [Alpha ][ 0.500960] . ( 3 sec) [ -15665.6662] [ 2338] [depth= 13] . ( 3 sec) [ -15485.0516] [ 2307] [depth= 7] . ( 4 sec) [ -15468.1320] [ 2302] [depth= 1] . ( 5 sec) [ -15395.7361] [ 2299] [depth= 3] . ( 5 sec) [ -15386.0137] [ 2293] [depth= 1] . ( 6 sec) [ -15332.7842] [ 2291] [depth= 3] . ( 6 sec) [ -14987.0662] [ 2286] [depth= 3] . ( 7 sec) [ -14822.8761] [ 2287] [depth= 8] . ( 7 sec) [ -14286.1793] [ 2238] [depth= 7] . ( 8 sec) [ -14142.4617] [ 2206] [depth= 6] . ( 9 sec) [ -14113.4315] [ 2205] [depth= 13] . ( 9 sec) [ -14108.9605] [ 2202] [depth= 2] . ( 10 sec) [ -14102.3468] [ 2202] [depth= 1] . ( 11 sec) [ -14030.3907] [ 2196] [depth= 3] . ( 11 sec) [ -14018.0649] [ 2192] [depth= 4] . ( 12 sec) [ -13983.6930] [ 2186] [depth= 7] . ( 12 sec) [ -13978.0152] [ 2187] [depth= 2] . ( 13 sec) [ -13892.1901] [ 2181] [depth= 5] . ( 14 sec) [ -13809.0818] [ 2168] [depth= 16] . ( 14 sec) [ -13721.7072] [ 2171] [depth= 1] . ( 15 sec) [ -13468.8326] [ 2124] [depth= 2] . ( 15 sec) [ -13437.2913] [ 2105] [depth= 8] . ( 16 sec) [ -13427.4350] [ 2108] [depth= 1] . ( 17 sec) [ -13214.2511] [ 2060] [depth= 7] . ( 18 sec) [ -13081.1250] [ 2021] [depth= 7] . ( 18 sec) [ -12860.4308] [ 1999] [depth= 12] . ( 19 sec) [ -12798.1663] [ 1994] [depth= 4] . ( 20 sec) [ -12619.0382] [ 1981] [depth= 13] . ( 20 sec) [ -12606.6820] [ 1985] [depth= 3] . ( 21 sec) [ -12573.2545] [ 1976] [depth= 15] . ( 22 sec) [ -12557.1165] [ 1969] [depth= 3] . ( 22 sec) [ -12536.5103] [ 1966] [depth= 7] . ( 23 sec) [ -12421.9620] [ 1943] [depth= 3] . ( 24 sec) [ -12416.3178] [ 1942] [depth= 5] . ( 24 sec) [ -12376.1409] [ 1942] [depth= 2] . ( 25 sec) [ -12284.3747] [ 1916] [depth= 5] . ( 25 sec) [ -12200.5879] [ 1916] [depth= 1] . ( 26 sec) [ -12188.6645] [ 1901] [depth= 10] . ( 27 sec) [ -12173.6631] [ 1902] [depth= 1] . ( 27 sec) [ -12024.3552] [ 1874] [depth= 3] . ( 28 sec) [ -11884.2725] [ 1834] [depth= 3] . ( 29 sec) [ -11727.3434] [ 1799] [depth= 16] . ( 30 sec) [ -11659.9173] [ 1794] [depth= 15] . ( 31 sec) [ -11644.0126] [ 1815] [depth= 5] . ( 31 sec) [ -11576.9559] [ 1791] [depth= 1] . ( 32 sec) [ -11514.8297] [ 1784] [depth= 7] . ( 32 sec) [ -11513.2021] [ 1782] [depth= 1] . ( 33 sec) [ -11472.0772] [ 1777] [depth= 6] . ( 34 sec) [ -11448.8155] [ 1762] [depth= 5] . ( 35 sec) [ -11315.9009] [ 1731] [depth= 4] . ( 35 sec) [ -11211.4920] [ 1705] [depth= 3] . ( 36 sec) [ -11209.2337] [ 1705] [depth= 1] . ( 37 sec) [ -11204.9042] [ 1702] [depth= 2] . ( 38 sec) [ -11057.1922] [ 1667] [depth= 5] . ( 38 sec) [ -11016.7020] [ 1663] [depth= 1] . ( 39 sec) [ -10810.8170] [ 1656] [depth= 5] . ( 40 sec) [ -10727.9252] [ 1653] [depth= 2] . ( 40 sec) [ -10513.0272] [ 1629] [depth= 8] . ( 42 sec) [ -10504.5867] [ 1632] [depth= 4] . ( 43 sec) [ -10503.2775] [ 1635] [depth= 1] . ( 43 sec) [ -10475.0001] [ 1632] [depth= 13] . ( 44 sec) [ -10403.0091] [ 1605] [depth= 7] . ( 45 sec) [ -10320.4202] [ 1596] [depth= 6] . ( 45 sec) [ -10315.2211] [ 1594] [depth= 2] . ( 46 sec) [ -10300.4357] [ 1589] [depth= 1] . ( 47 sec) [ -10236.6071] [ 1586] [depth= 11] . ( 47 sec) [ -10180.0525] [ 1573] [depth= 10] . ( 49 sec) [ -10172.1448] [ 1570] [depth= 1] . ( 49 sec) [ -10169.3955] [ 1564] [depth= 4] . ( 50 sec) [ -10048.6231] [ 1560] [depth= 3] . ( 51 sec) [ -10007.6943] [ 1535] [depth= 1] . ( 51 sec) [ -9841.6832] [ 1491] [depth= 5] . ( 52 sec) [ -9773.3867] [ 1475] [depth= 7] . ( 53 sec) [ -9735.0237] [ 1466] [depth= 1] . ( 54 sec) [ -9732.4307] [ 1467] [depth= 1] . ( 54 sec) [ -9589.2971] [ 1437] [depth= 1] . ( 55 sec) [ -9584.3812] [ 1439] [depth= 6] . ( 57 sec) [ -9583.9830] [ 1439] [depth= 4] . ( 58 sec) [ -9579.0819] [ 1439] [depth= 3] . ( 59 sec) [ -9466.7684] [ 1413] [depth= 3] . ( 60 sec) [ -9442.0212] [ 1411] [depth= 1] . ( 60 sec) [ -9436.4560] [ 1405] [depth= 3] . ( 61 sec) [ -9361.9445] [ 1377] [depth= 2] . ( 62 sec) [ -9324.1009] [ 1373] [depth= 13] . ( 62 sec) [ -9211.4865] [ 1363] [depth= 14] . ( 64 sec) [ -9207.8158] [ 1359] [depth= 2] . ( 64 sec) [ -9172.4674] [ 1351] [depth= 2] . ( 66 sec) [ -9159.1544] [ 1354] [depth= 1] . ( 66 sec) [ -9126.6176] [ 1345] [depth= 1] . ( 67 sec) [ -9118.9755] [ 1340] [depth= 1] . ( 68 sec) [ -9108.4334] [ 1337] [depth= 4] . ( 68 sec) [ -8945.7633] [ 1302] [depth= 6] . ( 69 sec) [ -8944.7385] [ 1304] [depth= 1] . ( 69 sec) [ -8669.9560] [ 1305] [depth= 2] . ( 71 sec) [ -8647.2543] [ 1299] [depth= 2] . ( 71 sec) [ -8631.6024] [ 1299] [depth= 1] . ( 73 sec) [ -8631.4390] [ 1299] [depth= 1] . ( 74 sec) [ -8618.9551] [ 1300] [depth= 1] . ( 75 sec) [ -8558.3512] [ 1296] [depth= 2] . ( 75 sec) [ -8535.3911] [ 1291] [depth= 1] . ( 76 sec) [ -8490.3066] [ 1280] [depth= 1] . ( 77 sec) [ -8466.4894] [ 1279] [depth= 4] . ( 77 sec) [ -8463.4996] [ 1283] [depth= 2] . ( 78 sec) [ -8457.4414] [ 1280] [depth= 2] . ( 78 sec) [ -8423.4216] [ 1269] [depth= 4] . ( 79 sec) [ -8419.7897] [ 1267] [depth= 2] . ( 80 sec) [ -8360.0747] [ 1268] [depth= 8] . ( 81 sec) [ -8339.2430] [ 1264] [depth= 5] . ( 82 sec) [ -8337.9335] [ 1266] [depth= 2] . ( 82 sec) [ -8330.9229] [ 1266] [depth= 2] . ( 83 sec) [ -8318.9167] [ 1267] [depth= 10] . ( 84 sec) [ -8316.8196] [ 1267] [depth= 1] . ( 85 sec) [ -8316.6256] [ 1268] [depth= 2] . ( 86 sec) [ -8307.7143] [ 1261] [depth= 7] . ( 88 sec) [ -8305.2724] [ 1258] [depth= 3] . ( 89 sec) [ -8302.9381] [ 1256] [depth= 2] . ( 91 sec) [ -8300.1357] [ 1256] [depth= 2] . ( 93 sec) [ -8300.0168] [ 1256] [depth= 3] . ( 93 sec) [ -8299.9702] [ 1256] [depth= 2] . ( 94 sec) [ -8299.1008] [ 1255] [depth= 1] . ( 96 sec) [ -8240.1124] [Branch lengths ] . ( 97 sec) [ -8239.9438] [Alpha ][ 0.523877] . ( 103 sec) [ -8237.4396] [ 1254] [depth= 1] . ( 109 sec) [ -8236.9436] [ 1255] [depth= 1] . ( 113 sec) [ -8234.9403] [ 1255] [depth= 1] . ( 114 sec) [ -8234.8048] [ 1255] [depth= 2] . ( 115 sec) [ -8215.9322] [ 1250] [depth= 1] . ( 117 sec) [ -8215.4075] [ 1249] [depth= 1] . ( 120 sec) [ -8214.4098] [ 1252] [depth= 1] . ( 121 sec) [ -8213.8130] [ 1256] [depth= 3] . ( 124 sec) [ -8213.6768] [ 1256] [depth= 5] . ( 137 sec) [ -8213.4808] [ 1256] [depth= 1] . ( 139 sec) [ -8213.2278] [ 1256] [depth= 1] . ( 140 sec) [ -8213.0380] [ 1256] [depth= 4] . ( 142 sec) [ -8210.7573] [ 1255] [depth= 2] . ( 142 sec) [ -8209.9538] [ 1255] [depth= 1] . ( 144 sec) [ -8209.8132] [ 1255] [depth= 2] . ( 150 sec) [ -8209.2239] [ 1257] [depth= 7] . ( 154 sec) [ -8208.1701] [ 1254] [depth= 1] . ( 154 sec) [ -8199.2676] [ 1252] [depth= 1] . ( 160 sec) [ -8198.7353] [ 1252] [depth= 1] . ( 162 sec) [ -8197.0946] [ 1249] [depth= 4] . ( 165 sec) [ -8196.1388] [ 1247] [depth= 1] . ( 166 sec) [ -8196.0881] [ 1247] [depth= 3] . ( 176 sec) [ -8196.0359] [ 1247] [depth= 4] . ( 186 sec) [ -8195.5922] [ 1248] [depth= 1] . ( 192 sec) [ -8195.5655] [ 1248] [depth= 1] . ( 195 sec) [ -8194.4326] [ 1250] [depth= 2] . ( 195 sec) [ -8188.9181] [ 1250] [depth= 1] . ( 196 sec) [ -8186.5850] [ 1250] [depth= 1] . ( 201 sec) [ -8185.7566] [ 1248] [depth= 2] . ( 204 sec) [ -8185.6313] [ 1248] [depth= 5] . ( 205 sec) [ -8180.1023] [ 1243] [depth= 4] . ( 213 sec) [ -8179.3664] [ 1241] [depth= 1] . ( 217 sec) [ -8177.0476] [ 1240] [depth= 3] . ( 218 sec) [ -8177.0354] [ 1240] [depth= 1] . ( 219 sec) [ -8177.0171] [ 1240] [depth= 1] . ( 225 sec) [ -8168.8328] [Branch lengths ] . ( 226 sec) [ -8168.7314] [Alpha ][ 0.542312] . ( 267 sec) [ -8167.3724] [ 1240] [depth= 3] . ( 308 sec) [ -8167.3433] [ 1240] [depth= 1] . ( 375 sec) [ -8167.3248] [ 1240] [depth= 1] . ( 423 sec) [ -8166.3996] [Branch lengths ] . ( 424 sec) [ -8166.3929] [Alpha ][ 0.547242] . ( 627 sec) [ -8166.2547] [Branch lengths ] . ( 628 sec) [ -8166.2547] [Topology ] . ( 633 sec) [ -8166.2302] [Topology ] . ( 639 sec) [ -8166.2191] [Topology ] . ( 644 sec) [ -8166.2123] [Topology ] . ( 650 sec) [ -8166.2080] [Topology ] . ( 655 sec) [ -8166.2053] [Topology ] . ( 661 sec) [ -8166.2036] [Topology ] . ( 662 sec) [ -8166.1997] [Alpha ][ 0.550983] . ( 662 sec) [ -8166.1997] [Topology ] . ( 668 sec) [ -8166.1982] [Topology ] . ( 673 sec) [ -8166.1972] [Topology ] . ( 674 sec) [ -8166.1972] [Alpha ][ 0.550983] . ( 674 sec) [ -8166.1972] [Topology ] . ( 680 sec) [ -8166.1966] [Topology ] . ( 681 sec) [ -8166.1966] [Alpha ][ 0.551534] . Checking for NNIs, optimizing five branches... . ( 718 sec) [ -8166.1960] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8166.196043. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15946.3086] [Alpha ][ 0.500960] . ( 3 sec) [ -15865.9094] [ 2329] [depth= 16] . ( 4 sec) [ -15691.9893] [ 2301] [depth= 18] . ( 5 sec) [ -15624.3308] [ 2297] [depth= 7] . ( 5 sec) [ -15550.4995] [ 2268] [depth= 1] . ( 6 sec) [ -15537.3322] [ 2258] [depth= 10] . ( 6 sec) [ -15148.6724] [ 2226] [depth= 4] . ( 7 sec) [ -15146.7610] [ 2223] [depth= 1] . ( 8 sec) [ -14888.3272] [ 2222] [depth= 1] . ( 8 sec) [ -14552.4826] [ 2217] [depth= 3] . ( 9 sec) [ -14527.2431] [ 2216] [depth= 5] . ( 9 sec) [ -14526.3713] [ 2214] [depth= 1] . ( 10 sec) [ -14526.2827] [ 2215] [depth= 1] . ( 11 sec) [ -14515.6729] [ 2217] [depth= 3] . ( 12 sec) [ -14321.7506] [ 2174] [depth= 13] . ( 12 sec) [ -14161.9150] [ 2170] [depth= 3] . ( 13 sec) [ -14000.6826] [ 2160] [depth= 4] . ( 13 sec) [ -13999.1012] [ 2159] [depth= 1] . ( 14 sec) [ -13910.5170] [ 2150] [depth= 2] . ( 15 sec) [ -13862.5624] [ 2148] [depth= 11] . ( 15 sec) [ -13662.6532] [ 2117] [depth= 18] . ( 16 sec) [ -13588.8281] [ 2107] [depth= 10] . ( 17 sec) [ -13563.6320] [ 2102] [depth= 2] . ( 17 sec) [ -13541.0239] [ 2090] [depth= 2] . ( 18 sec) [ -13490.1860] [ 2089] [depth= 2] . ( 18 sec) [ -13479.6736] [ 2088] [depth= 7] . ( 19 sec) [ -13401.9357] [ 2087] [depth= 3] . ( 20 sec) [ -13078.3547] [ 2023] [depth= 16] . ( 20 sec) [ -12970.1449] [ 2009] [depth= 5] . ( 21 sec) [ -12933.2131] [ 2006] [depth= 1] . ( 21 sec) [ -12923.7211] [ 2004] [depth= 13] . ( 22 sec) [ -12783.3579] [ 1998] [depth= 6] . ( 24 sec) [ -12782.6069] [ 1998] [depth= 1] . ( 24 sec) [ -12775.5514] [ 1994] [depth= 2] . ( 25 sec) [ -12573.5135] [ 1949] [depth= 10] . ( 25 sec) [ -12406.8408] [ 1936] [depth= 6] . ( 26 sec) [ -12388.4080] [ 1934] [depth= 12] . ( 26 sec) [ -12353.8301] [ 1905] [depth= 3] . ( 27 sec) [ -12239.8251] [ 1901] [depth= 10] . ( 28 sec) [ -12146.1578] [ 1893] [depth= 3] . ( 28 sec) [ -12105.9167] [ 1895] [depth= 1] . ( 29 sec) [ -11983.1839] [ 1867] [depth= 7] . ( 30 sec) [ -11980.6463] [ 1868] [depth= 1] . ( 30 sec) [ -11895.4069] [ 1856] [depth= 12] . ( 31 sec) [ -11843.0518] [ 1850] [depth= 3] . ( 32 sec) [ -11806.3632] [ 1843] [depth= 4] . ( 33 sec) [ -11793.8486] [ 1842] [depth= 2] . ( 33 sec) [ -11785.5771] [ 1827] [depth= 3] . ( 34 sec) [ -11764.2994] [ 1824] [depth= 1] . ( 34 sec) [ -11754.6046] [ 1816] [depth= 3] . ( 35 sec) [ -11648.4648] [ 1792] [depth= 8] . ( 36 sec) [ -11493.9371] [ 1789] [depth= 1] . ( 36 sec) [ -11453.4571] [ 1782] [depth= 1] . ( 37 sec) [ -11443.2580] [ 1780] [depth= 4] . ( 38 sec) [ -11443.2357] [ 1780] [depth= 1] . ( 38 sec) [ -11432.9540] [ 1780] [depth= 1] . ( 39 sec) [ -11395.7467] [ 1776] [depth= 5] . ( 39 sec) [ -11338.2903] [ 1775] [depth= 4] . ( 40 sec) [ -11129.1040] [ 1731] [depth= 8] . ( 41 sec) [ -11129.0869] [ 1731] [depth= 1] . ( 42 sec) [ -10997.0999] [ 1698] [depth= 16] . ( 42 sec) [ -10877.8765] [ 1706] [depth= 8] . ( 43 sec) [ -10863.8383] [ 1698] [depth= 1] . ( 44 sec) [ -10847.8724] [ 1693] [depth= 1] . ( 44 sec) [ -10736.1116] [ 1665] [depth= 1] . ( 45 sec) [ -10585.2593] [ 1636] [depth= 4] . ( 46 sec) [ -10537.2597] [ 1635] [depth= 1] . ( 47 sec) [ -10480.9786] [ 1624] [depth= 8] . ( 48 sec) [ -10455.3433] [ 1624] [depth= 1] . ( 49 sec) [ -10426.5220] [ 1621] [depth= 2] . ( 49 sec) [ -10366.3772] [ 1621] [depth= 2] . ( 50 sec) [ -10266.5442] [ 1610] [depth= 8] . ( 51 sec) [ -10158.8612] [ 1578] [depth= 6] . ( 51 sec) [ -10148.1760] [ 1576] [depth= 1] . ( 52 sec) [ -10114.6749] [ 1563] [depth= 6] . ( 52 sec) [ -10056.6903] [ 1561] [depth= 1] . ( 54 sec) [ -10023.5626] [ 1549] [depth= 7] . ( 55 sec) [ -9926.6663] [ 1530] [depth= 9] . ( 55 sec) [ -9853.0301] [ 1515] [depth= 5] . ( 56 sec) [ -9844.1339] [ 1512] [depth= 2] . ( 56 sec) [ -9808.8102] [ 1507] [depth= 2] . ( 57 sec) [ -9808.2180] [ 1507] [depth= 1] . ( 58 sec) [ -9808.1229] [ 1507] [depth= 1] . ( 59 sec) [ -9683.7851] [ 1481] [depth= 3] . ( 59 sec) [ -9609.9888] [ 1458] [depth= 1] . ( 61 sec) [ -9584.7112] [ 1448] [depth= 1] . ( 61 sec) [ -9308.8127] [ 1453] [depth= 4] . ( 62 sec) [ -9293.5472] [ 1445] [depth= 7] . ( 62 sec) [ -9204.4029] [ 1439] [depth= 3] . ( 63 sec) [ -9169.8469] [ 1429] [depth= 3] . ( 64 sec) [ -9088.7585] [ 1413] [depth= 9] . ( 64 sec) [ -9070.4433] [ 1424] [depth= 1] . ( 65 sec) [ -8923.5742] [ 1393] [depth= 5] . ( 66 sec) [ -8910.3032] [ 1382] [depth= 1] . ( 66 sec) [ -8856.2547] [ 1370] [depth= 1] . ( 67 sec) [ -8852.7593] [ 1374] [depth= 3] . ( 68 sec) [ -8744.9466] [ 1350] [depth= 5] . ( 68 sec) [ -8739.1471] [ 1349] [depth= 1] . ( 69 sec) [ -8711.3629] [ 1344] [depth= 1] . ( 70 sec) [ -8706.6822] [ 1343] [depth= 1] . ( 70 sec) [ -8699.9925] [ 1340] [depth= 2] . ( 71 sec) [ -8699.1300] [ 1339] [depth= 3] . ( 72 sec) [ -8686.5683] [ 1337] [depth= 1] . ( 77 sec) [ -8645.6824] [ 1339] [depth= 1] . ( 78 sec) [ -8630.6852] [ 1336] [depth= 1] . ( 79 sec) [ -8626.6029] [ 1340] [depth= 2] . ( 80 sec) [ -8620.6296] [ 1343] [depth= 1] . ( 80 sec) [ -8609.8592] [ 1337] [depth= 1] . ( 81 sec) [ -8604.4257] [ 1334] [depth= 1] . ( 82 sec) [ -8579.0442] [ 1329] [depth= 6] . ( 83 sec) [ -8570.4220] [ 1333] [depth= 1] . ( 83 sec) [ -8565.8371] [ 1329] [depth= 1] . ( 84 sec) [ -8564.3790] [ 1331] [depth= 1] . ( 85 sec) [ -8554.9121] [ 1328] [depth= 1] . ( 86 sec) [ -8548.8077] [ 1324] [depth= 1] . ( 87 sec) [ -8541.7298] [ 1323] [depth= 2] . ( 88 sec) [ -8539.7491] [ 1323] [depth= 2] . ( 92 sec) [ -8529.9196] [ 1320] [depth= 1] . ( 93 sec) [ -8522.6335] [ 1314] [depth= 2] . ( 94 sec) [ -8521.5037] [ 1314] [depth= 2] . ( 94 sec) [ -8498.9936] [ 1316] [depth= 1] . ( 95 sec) [ -8495.3332] [ 1318] [depth= 1] . ( 95 sec) [ -8493.1272] [ 1315] [depth= 7] . ( 96 sec) [ -8491.2107] [ 1314] [depth= 1] . ( 99 sec) [ -8475.5944] [ 1312] [depth= 3] . ( 100 sec) [ -8474.8182] [ 1311] [depth= 2] . ( 107 sec) [ -8439.0509] [Branch lengths ] . ( 108 sec) [ -8438.5867] [Alpha ][ 0.538685] . ( 111 sec) [ -8438.5408] [ 1311] [depth= 2] . ( 112 sec) [ -8437.4518] [ 1312] [depth= 2] . ( 113 sec) [ -8433.0373] [ 1310] [depth= 1] . ( 127 sec) [ -8399.4777] [ 1301] [depth= 2] . ( 129 sec) [ -8398.4679] [ 1299] [depth= 1] . ( 132 sec) [ -8377.0153] [ 1291] [depth= 2] . ( 145 sec) [ -8364.0138] [ 1284] [depth= 9] . ( 147 sec) [ -8363.9836] [ 1284] [depth= 2] . ( 152 sec) [ -8360.5448] [ 1283] [depth= 6] . ( 156 sec) [ -8356.7299] [ 1282] [depth= 1] . ( 161 sec) [ -8356.4509] [ 1283] [depth= 2] . ( 164 sec) [ -8356.2203] [ 1283] [depth= 2] . ( 165 sec) [ -8356.1977] [ 1281] [depth= 5] . ( 169 sec) [ -8355.7370] [ 1279] [depth= 2] . ( 170 sec) [ -8350.6633] [ 1278] [depth= 1] . ( 173 sec) [ -8350.6523] [ 1278] [depth= 1] . ( 176 sec) [ -8350.3249] [ 1278] [depth= 1] . ( 177 sec) [ -8349.0791] [ 1277] [depth= 1] . ( 187 sec) [ -8348.3767] [ 1278] [depth= 3] . ( 188 sec) [ -8347.1130] [ 1261] [depth= 2] . ( 189 sec) [ -8345.8258] [ 1262] [depth= 1] . ( 189 sec) [ -8319.2339] [ 1255] [depth= 1] . ( 190 sec) [ -8316.0492] [ 1253] [depth= 1] . ( 191 sec) [ -8304.5151] [ 1256] [depth= 1] . ( 192 sec) [ -8304.2107] [ 1255] [depth= 3] . ( 193 sec) [ -8302.4385] [ 1257] [depth= 1] . ( 194 sec) [ -8302.2000] [ 1256] [depth= 1] . ( 196 sec) [ -8302.1762] [ 1256] [depth= 3] . ( 197 sec) [ -8268.8537] [ 1258] [depth= 1] . ( 198 sec) [ -8254.1159] [ 1257] [depth= 3] . ( 198 sec) [ -8243.6231] [ 1254] [depth= 1] . ( 199 sec) [ -8242.8122] [ 1252] [depth= 1] . ( 204 sec) [ -8242.6693] [ 1251] [depth= 2] . ( 204 sec) [ -8242.0338] [ 1252] [depth= 1] . ( 205 sec) [ -8240.5815] [ 1250] [depth= 1] . ( 207 sec) [ -8236.6628] [ 1249] [depth= 1] . ( 208 sec) [ -8236.4445] [ 1249] [depth= 1] . ( 208 sec) [ -8236.4308] [ 1249] [depth= 1] . ( 209 sec) [ -8235.1588] [ 1251] [depth= 1] . ( 209 sec) [ -8190.4151] [ 1242] [depth= 4] . ( 214 sec) [ -8189.0581] [ 1243] [depth= 1] . ( 216 sec) [ -8188.7839] [ 1239] [depth= 1] . ( 218 sec) [ -8183.2019] [ 1239] [depth= 1] . ( 219 sec) [ -8182.8354] [ 1238] [depth= 3] . ( 220 sec) [ -8182.7485] [ 1239] [depth= 1] . ( 225 sec) [ -8179.9243] [ 1239] [depth= 1] . ( 234 sec) [ -8179.2501] [ 1238] [depth= 1] . ( 236 sec) [ -8179.1253] [ 1239] [depth= 1] . ( 243 sec) [ -8170.8061] [Branch lengths ] . ( 243 sec) [ -8170.7649] [Alpha ][ 0.550480] . ( 245 sec) [ -8170.7472] [ 1240] [depth= 1] . ( 246 sec) [ -8170.4994] [ 1241] [depth= 1] . ( 289 sec) [ -8170.2900] [ 1239] [depth= 2] . ( 369 sec) [ -8169.7195] [ 1239] [depth= 1] . ( 434 sec) [ -8169.0722] [ 1239] [depth= 1] . ( 441 sec) [ -8166.9337] [Branch lengths ] . ( 442 sec) [ -8166.9326] [Alpha ][ 0.552369] . ( 642 sec) [ -8166.6990] [Branch lengths ] . ( 642 sec) [ -8166.6990] [Topology ] . ( 648 sec) [ -8166.6657] [Topology ] . ( 653 sec) [ -8166.6506] [Topology ] . ( 659 sec) [ -8166.6412] [Topology ] . ( 664 sec) [ -8166.6351] [Topology ] . ( 670 sec) [ -8166.6311] [Topology ] . ( 676 sec) [ -8166.6285] [Topology ] . ( 677 sec) [ -8166.6230] [Alpha ][ 0.556849] . ( 677 sec) [ -8166.6230] [Topology ] . ( 683 sec) [ -8166.6205] [Topology ] . ( 689 sec) [ -8166.6189] [Topology ] . ( 694 sec) [ -8166.6178] [Topology ] . ( 700 sec) [ -8166.6170] [Topology ] . ( 701 sec) [ -8166.6170] [Alpha ][ 0.557406] . ( 701 sec) [ -8166.6170] [Topology ] . ( 706 sec) [ -8166.6165] [Topology ] . ( 707 sec) [ -8166.6165] [Alpha ][ 0.557406] . Checking for NNIs, optimizing five branches... . ( 744 sec) [ -8166.4148] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8166.414757. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15154.1234] [Alpha ][ 0.500960] . ( 2 sec) [ -14990.8944] [ 2323] [depth= 12] . ( 3 sec) [ -14809.9185] [ 2291] [depth= 2] . ( 4 sec) [ -14710.6503] [ 2288] [depth= 2] . ( 4 sec) [ -14692.2863] [ 2284] [depth= 3] . ( 5 sec) [ -14589.8259] [ 2256] [depth= 2] . ( 5 sec) [ -14511.7884] [ 2249] [depth= 6] . ( 6 sec) [ -14471.4634] [ 2246] [depth= 1] . ( 7 sec) [ -14402.8241] [ 2232] [depth= 9] . ( 7 sec) [ -14340.4269] [ 2226] [depth= 2] . ( 8 sec) [ -14261.2450] [ 2223] [depth= 9] . ( 8 sec) [ -14128.1019] [ 2216] [depth= 2] . ( 9 sec) [ -14025.2093] [ 2207] [depth= 1] . ( 9 sec) [ -13819.2710] [ 2174] [depth= 4] . ( 10 sec) [ -13741.8116] [ 2164] [depth= 7] . ( 11 sec) [ -13721.9446] [ 2158] [depth= 2] . ( 11 sec) [ -13615.1611] [ 2150] [depth= 4] . ( 12 sec) [ -13594.5733] [ 2146] [depth= 1] . ( 12 sec) [ -13433.4271] [ 2128] [depth= 7] . ( 13 sec) [ -13334.3492] [ 2112] [depth= 9] . ( 14 sec) [ -13258.6933] [ 2110] [depth= 1] . ( 14 sec) [ -13057.4083] [ 2077] [depth= 13] . ( 15 sec) [ -13025.5366] [ 2079] [depth= 1] . ( 16 sec) [ -12971.6172] [ 2071] [depth= 9] . ( 16 sec) [ -12927.5519] [ 2070] [depth= 1] . ( 16 sec) [ -12911.4730] [ 2069] [depth= 1] . ( 17 sec) [ -12907.4403] [ 2069] [depth= 11] . ( 18 sec) [ -12829.1643] [ 2049] [depth= 2] . ( 18 sec) [ -12757.5139] [ 2041] [depth= 11] . ( 19 sec) [ -12568.9601] [ 2000] [depth= 14] . ( 20 sec) [ -12484.5320] [ 1998] [depth= 1] . ( 21 sec) [ -12395.1834] [ 1961] [depth= 13] . ( 21 sec) [ -12349.7002] [ 1963] [depth= 2] . ( 22 sec) [ -12339.7663] [ 1962] [depth= 2] . ( 23 sec) [ -12335.6785] [ 1963] [depth= 2] . ( 24 sec) [ -12330.5310] [ 1963] [depth= 1] . ( 24 sec) [ -12306.6084] [ 1959] [depth= 2] . ( 25 sec) [ -12254.0799] [ 1946] [depth= 11] . ( 26 sec) [ -12076.4870] [ 1919] [depth= 7] . ( 26 sec) [ -11983.9875] [ 1923] [depth= 1] . ( 27 sec) [ -11815.7126] [ 1899] [depth= 2] . ( 27 sec) [ -11791.9254] [ 1893] [depth= 1] . ( 28 sec) [ -11784.9712] [ 1897] [depth= 17] . ( 29 sec) [ -11675.0669] [ 1870] [depth= 8] . ( 30 sec) [ -11271.7420] [ 1802] [depth= 9] . ( 30 sec) [ -11213.2261] [ 1818] [depth= 5] . ( 31 sec) [ -11202.2523] [ 1809] [depth= 16] . ( 32 sec) [ -11199.7221] [ 1809] [depth= 8] . ( 32 sec) [ -11112.3446] [ 1806] [depth= 1] . ( 33 sec) [ -11009.4035] [ 1784] [depth= 5] . ( 34 sec) [ -10948.6562] [ 1782] [depth= 1] . ( 34 sec) [ -10945.2131] [ 1782] [depth= 16] . ( 35 sec) [ -10626.9484] [ 1701] [depth= 17] . ( 36 sec) [ -10622.1380] [ 1700] [depth= 15] . ( 37 sec) [ -10619.9648] [ 1698] [depth= 1] . ( 38 sec) [ -10591.6757] [ 1700] [depth= 1] . ( 38 sec) [ -10524.6626] [ 1681] [depth= 2] . ( 39 sec) [ -10458.4654] [ 1663] [depth= 8] . ( 40 sec) [ -10453.5169] [ 1666] [depth= 1] . ( 40 sec) [ -10443.3882] [ 1662] [depth= 4] . ( 41 sec) [ -10442.0117] [ 1662] [depth= 2] . ( 42 sec) [ -10441.3174] [ 1662] [depth= 1] . ( 42 sec) [ -10435.0630] [ 1661] [depth= 1] . ( 43 sec) [ -10435.0304] [ 1661] [depth= 1] . ( 44 sec) [ -10180.6420] [ 1599] [depth= 4] . ( 44 sec) [ -10178.7691] [ 1604] [depth= 2] . ( 45 sec) [ -10165.6700] [ 1596] [depth= 8] . ( 46 sec) [ -10160.9816] [ 1595] [depth= 1] . ( 50 sec) [ -10147.3105] [ 1598] [depth= 10] . ( 51 sec) [ -10108.1933] [ 1588] [depth= 1] . ( 52 sec) [ -10045.2573] [ 1585] [depth= 5] . ( 52 sec) [ -9997.3974] [ 1577] [depth= 8] . ( 53 sec) [ -9964.9302] [ 1578] [depth= 1] . ( 54 sec) [ -9942.4601] [ 1578] [depth= 2] . ( 54 sec) [ -9820.9023] [ 1543] [depth= 11] . ( 55 sec) [ -9807.1549] [ 1538] [depth= 2] . ( 55 sec) [ -9646.2240] [ 1501] [depth= 6] . ( 56 sec) [ -9644.9474] [ 1501] [depth= 1] . ( 57 sec) [ -9517.4776] [ 1500] [depth= 2] . ( 58 sec) [ -9383.3811] [ 1458] [depth= 17] . ( 59 sec) [ -9365.2524] [ 1458] [depth= 3] . ( 60 sec) [ -9360.9922] [ 1457] [depth= 1] . ( 60 sec) [ -9356.6562] [ 1456] [depth= 3] . ( 61 sec) [ -9303.6503] [ 1447] [depth= 8] . ( 62 sec) [ -9279.2272] [ 1440] [depth= 8] . ( 62 sec) [ -9250.7148] [ 1437] [depth= 1] . ( 63 sec) [ -9247.0204] [ 1434] [depth= 1] . ( 64 sec) [ -9208.1732] [ 1435] [depth= 2] . ( 65 sec) [ -9185.1532] [ 1434] [depth= 4] . ( 65 sec) [ -9080.6968] [ 1431] [depth= 10] . ( 66 sec) [ -9078.2364] [ 1431] [depth= 2] . ( 67 sec) [ -9047.7915] [ 1423] [depth= 12] . ( 68 sec) [ -9003.2363] [ 1417] [depth= 11] . ( 68 sec) [ -8984.3634] [ 1413] [depth= 1] . ( 69 sec) [ -8983.3915] [ 1413] [depth= 1] . ( 70 sec) [ -8983.1290] [ 1412] [depth= 1] . ( 71 sec) [ -8982.5257] [ 1411] [depth= 4] . ( 72 sec) [ -8981.2277] [ 1410] [depth= 7] . ( 73 sec) [ -8981.1869] [ 1410] [depth= 4] . ( 74 sec) [ -8970.8612] [ 1409] [depth= 2] . ( 75 sec) [ -8885.4752] [ 1391] [depth= 3] . ( 76 sec) [ -8860.0298] [ 1392] [depth= 1] . ( 76 sec) [ -8777.9183] [ 1367] [depth= 12] . ( 77 sec) [ -8775.7639] [ 1366] [depth= 2] . ( 78 sec) [ -8763.7669] [ 1360] [depth= 12] . ( 78 sec) [ -8761.0607] [ 1360] [depth= 1] . ( 79 sec) [ -8761.0448] [ 1360] [depth= 3] . ( 80 sec) [ -8759.8048] [ 1360] [depth= 1] . ( 81 sec) [ -8757.7432] [ 1359] [depth= 1] . ( 81 sec) [ -8609.9680] [ 1329] [depth= 2] . ( 82 sec) [ -8568.9411] [ 1317] [depth= 5] . ( 85 sec) [ -8527.2809] [ 1309] [depth= 2] . ( 86 sec) [ -8518.7370] [ 1307] [depth= 6] . ( 87 sec) [ -8518.7221] [ 1307] [depth= 2] . ( 88 sec) [ -8445.7630] [ 1287] [depth= 2] . ( 89 sec) [ -8414.8974] [ 1288] [depth= 1] . ( 89 sec) [ -8411.3639] [ 1292] [depth= 2] . ( 90 sec) [ -8409.2584] [ 1295] [depth= 1] . ( 91 sec) [ -8399.0300] [ 1294] [depth= 3] . ( 92 sec) [ -8398.6363] [ 1295] [depth= 5] . ( 93 sec) [ -8398.2409] [ 1293] [depth= 1] . ( 94 sec) [ -8387.3254] [ 1277] [depth= 3] . ( 94 sec) [ -8355.7229] [ 1277] [depth= 4] . ( 95 sec) [ -8349.2352] [ 1276] [depth= 3] . ( 96 sec) [ -8323.5889] [ 1268] [depth= 3] . ( 98 sec) [ -8301.3954] [ 1264] [depth= 4] . ( 99 sec) [ -8299.9559] [ 1262] [depth= 6] . ( 100 sec) [ -8297.6898] [ 1261] [depth= 1] . ( 106 sec) [ -8240.9499] [Branch lengths ] . ( 106 sec) [ -8240.7446] [Alpha ][ 0.526471] . ( 112 sec) [ -8239.2586] [ 1259] [depth= 5] . ( 116 sec) [ -8236.3467] [ 1259] [depth= 8] . ( 118 sec) [ -8234.5617] [ 1255] [depth= 4] . ( 119 sec) [ -8234.4831] [ 1255] [depth= 4] . ( 122 sec) [ -8198.8490] [ 1249] [depth= 1] . ( 128 sec) [ -8198.4940] [ 1246] [depth= 1] . ( 130 sec) [ -8198.4646] [ 1247] [depth= 3] . ( 134 sec) [ -8195.9487] [ 1247] [depth= 1] . ( 139 sec) [ -8195.9375] [ 1247] [depth= 1] . ( 140 sec) [ -8195.8485] [ 1248] [depth= 1] . ( 207 sec) [ -8195.8376] [ 1248] [depth= 1] . ( 218 sec) [ -8195.4872] [ 1247] [depth= 2] . ( 222 sec) [ -8189.9081] [ 1242] [depth= 3] . ( 238 sec) [ -8189.7048] [ 1242] [depth= 1] . ( 240 sec) [ -8187.1864] [ 1241] [depth= 5] . ( 244 sec) [ -8186.7047] [ 1243] [depth= 1] . ( 246 sec) [ -8184.3684] [ 1242] [depth= 3] . ( 271 sec) [ -8177.9760] [Branch lengths ] . ( 272 sec) [ -8177.8286] [Alpha ][ 0.548970] . ( 274 sec) [ -8177.3568] [ 1240] [depth= 1] . ( 287 sec) [ -8174.5799] [ 1237] [depth= 1] . ( 291 sec) [ -8173.5681] [ 1239] [depth= 2] . ( 298 sec) [ -8172.6178] [ 1240] [depth= 1] . ( 299 sec) [ -8172.1487] [ 1240] [depth= 2] . ( 321 sec) [ -8172.1196] [ 1240] [depth= 1] . ( 325 sec) [ -8172.0879] [ 1240] [depth= 3] . ( 329 sec) [ -8170.6218] [ 1239] [depth= 1] . ( 390 sec) [ -8170.6018] [ 1239] [depth= 2] . ( 403 sec) [ -8170.2625] [ 1239] [depth= 2] . ( 461 sec) [ -8167.7588] [Branch lengths ] . ( 462 sec) [ -8167.7541] [Alpha ][ 0.544679] . ( 478 sec) [ -8167.6786] [ 1239] [depth= 1] . ( 487 sec) [ -8167.5050] [ 1238] [depth= 3] . ( 505 sec) [ -8167.4434] [ 1238] [depth= 2] . ( 515 sec) [ -8167.4165] [ 1238] [depth= 1] . ( 516 sec) [ -8167.3686] [ 1239] [depth= 2] . ( 531 sec) [ -8167.3372] [ 1239] [depth= 3] . ( 579 sec) [ -8166.3734] [ 1239] [depth= 1] . ( 659 sec) [ -8165.5893] [Branch lengths ] . ( 660 sec) [ -8165.5844] [Alpha ][ 0.548917] . ( 664 sec) [ -8165.5190] [ 1238] [depth= 2] . ( 870 sec) [ -8165.3641] [Branch lengths ] . ( 871 sec) [ -8165.3633] [Alpha ][ 0.550631] . ( 872 sec) [ -8165.3633] [Topology ] . ( 877 sec) [ -8165.3457] [Topology ] . ( 883 sec) [ -8165.3375] [Topology ] . ( 888 sec) [ -8165.3325] [Topology ] . ( 894 sec) [ -8165.3293] [Topology ] . ( 900 sec) [ -8165.3272] [Topology ] . ( 905 sec) [ -8165.3259] [Topology ] . ( 906 sec) [ -8165.3255] [Alpha ][ 0.551814] . ( 906 sec) [ -8165.3255] [Topology ] . ( 912 sec) [ -8165.3246] [Topology ] . ( 913 sec) [ -8165.3246] [Alpha ][ 0.551814] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8165.324553. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -14903.1502] [Alpha ][ 0.500960] . ( 3 sec) [ -14627.6540] [ 2264] [depth= 8] . ( 4 sec) [ -14489.3971] [ 2231] [depth= 8] . ( 4 sec) [ -14482.6577] [ 2258] [depth= 3] . ( 5 sec) [ -14308.3624] [ 2211] [depth= 8] . ( 5 sec) [ -14257.9614] [ 2191] [depth= 4] . ( 6 sec) [ -14013.6894] [ 2178] [depth= 14] . ( 7 sec) [ -13867.8347] [ 2143] [depth= 3] . ( 7 sec) [ -13834.7105] [ 2142] [depth= 4] . ( 8 sec) [ -13804.9597] [ 2137] [depth= 3] . ( 8 sec) [ -13793.8181] [ 2136] [depth= 3] . ( 9 sec) [ -13667.9223] [ 2125] [depth= 2] . ( 9 sec) [ -13605.3537] [ 2125] [depth= 1] . ( 10 sec) [ -13586.8587] [ 2112] [depth= 1] . ( 11 sec) [ -13543.8623] [ 2111] [depth= 2] . ( 11 sec) [ -13540.5961] [ 2109] [depth= 2] . ( 12 sec) [ -13481.4942] [ 2100] [depth= 1] . ( 13 sec) [ -13399.8042] [ 2077] [depth= 13] . ( 13 sec) [ -13348.4193] [ 2072] [depth= 4] . ( 14 sec) [ -13199.2302] [ 2041] [depth= 11] . ( 15 sec) [ -13144.8844] [ 2029] [depth= 11] . ( 16 sec) [ -13006.7055] [ 2015] [depth= 7] . ( 16 sec) [ -13005.4874] [ 2014] [depth= 6] . ( 17 sec) [ -12997.2298] [ 2013] [depth= 1] . ( 17 sec) [ -12838.4031] [ 1981] [depth= 1] . ( 18 sec) [ -12836.9753] [ 1982] [depth= 1] . ( 19 sec) [ -12730.3856] [ 1970] [depth= 15] . ( 19 sec) [ -12623.3705] [ 1937] [depth= 10] . ( 20 sec) [ -12593.6820] [ 1934] [depth= 1] . ( 20 sec) [ -12532.8634] [ 1931] [depth= 5] . ( 21 sec) [ -12532.5228] [ 1933] [depth= 1] . ( 22 sec) [ -12446.5926] [ 1898] [depth= 4] . ( 22 sec) [ -12327.5508] [ 1894] [depth= 6] . ( 23 sec) [ -12278.7497] [ 1887] [depth= 9] . ( 24 sec) [ -12270.7542] [ 1886] [depth= 3] . ( 24 sec) [ -12206.4949] [ 1885] [depth= 2] . ( 25 sec) [ -12189.6791] [ 1878] [depth= 1] . ( 26 sec) [ -12147.7949] [ 1877] [depth= 2] . ( 26 sec) [ -12144.3903] [ 1871] [depth= 4] . ( 27 sec) [ -12073.9888] [ 1867] [depth= 4] . ( 27 sec) [ -11953.1156] [ 1854] [depth= 1] . ( 28 sec) [ -11770.7381] [ 1852] [depth= 1] . ( 29 sec) [ -11770.2572] [ 1852] [depth= 6] . ( 29 sec) [ -11751.1004] [ 1851] [depth= 2] . ( 30 sec) [ -11648.4258] [ 1819] [depth= 7] . ( 30 sec) [ -11639.9017] [ 1824] [depth= 1] . ( 31 sec) [ -11553.5071] [ 1798] [depth= 8] . ( 32 sec) [ -11415.2854] [ 1794] [depth= 9] . ( 32 sec) [ -11313.7391] [ 1775] [depth= 12] . ( 33 sec) [ -11302.8619] [ 1769] [depth= 10] . ( 34 sec) [ -11105.3548] [ 1735] [depth= 3] . ( 35 sec) [ -11063.4350] [ 1729] [depth= 15] . ( 36 sec) [ -11014.7597] [ 1713] [depth= 11] . ( 37 sec) [ -10960.6958] [ 1694] [depth= 1] . ( 38 sec) [ -10955.8697] [ 1692] [depth= 13] . ( 38 sec) [ -10749.7005] [ 1666] [depth= 3] . ( 39 sec) [ -10633.5122] [ 1640] [depth= 2] . ( 40 sec) [ -10591.9008] [ 1622] [depth= 15] . ( 41 sec) [ -10253.9178] [ 1554] [depth= 17] . ( 42 sec) [ -10246.2297] [ 1565] [depth= 3] . ( 43 sec) [ -10212.3015] [ 1561] [depth= 3] . ( 44 sec) [ -10032.1250] [ 1530] [depth= 6] . ( 44 sec) [ -9992.1429] [ 1526] [depth= 5] . ( 45 sec) [ -9989.5726] [ 1523] [depth= 1] . ( 46 sec) [ -9982.6584] [ 1523] [depth= 1] . ( 46 sec) [ -9965.7368] [ 1513] [depth= 1] . ( 47 sec) [ -9941.4023] [ 1503] [depth= 3] . ( 48 sec) [ -9871.8454] [ 1497] [depth= 6] . ( 49 sec) [ -9820.2721] [ 1498] [depth= 3] . ( 49 sec) [ -9820.2086] [ 1498] [depth= 2] . ( 50 sec) [ -9723.4358] [ 1492] [depth= 2] . ( 50 sec) [ -9604.8500] [ 1458] [depth= 10] . ( 51 sec) [ -9602.9373] [ 1458] [depth= 1] . ( 52 sec) [ -9567.4714] [ 1456] [depth= 1] . ( 52 sec) [ -9552.3346] [ 1453] [depth= 3] . ( 53 sec) [ -9521.7134] [ 1439] [depth= 8] . ( 54 sec) [ -9480.7675] [ 1419] [depth= 3] . ( 55 sec) [ -9478.1082] [ 1411] [depth= 2] . ( 56 sec) [ -9432.7047] [ 1404] [depth= 1] . ( 57 sec) [ -9424.0029] [ 1399] [depth= 1] . ( 57 sec) [ -9397.2010] [ 1400] [depth= 2] . ( 58 sec) [ -9362.5250] [ 1403] [depth= 4] . ( 60 sec) [ -9351.1676] [ 1408] [depth= 4] . ( 61 sec) [ -9266.0372] [ 1391] [depth= 7] . ( 61 sec) [ -9262.6289] [ 1390] [depth= 1] . ( 62 sec) [ -9260.6095] [ 1391] [depth= 2] . ( 62 sec) [ -9244.5473] [ 1388] [depth= 1] . ( 63 sec) [ -8945.8020] [ 1383] [depth= 7] . ( 64 sec) [ -8939.5241] [ 1380] [depth= 2] . ( 65 sec) [ -8934.1434] [ 1381] [depth= 2] . ( 65 sec) [ -8928.2025] [ 1380] [depth= 11] . ( 66 sec) [ -8829.4190] [ 1373] [depth= 2] . ( 67 sec) [ -8821.5626] [ 1368] [depth= 3] . ( 67 sec) [ -8797.6340] [ 1368] [depth= 1] . ( 68 sec) [ -8758.2646] [ 1365] [depth= 2] . ( 69 sec) [ -8754.2612] [ 1363] [depth= 4] . ( 70 sec) [ -8711.7220] [ 1347] [depth= 1] . ( 70 sec) [ -8704.1319] [ 1342] [depth= 1] . ( 74 sec) [ -8675.1051] [ 1336] [depth= 2] . ( 74 sec) [ -8667.9688] [ 1334] [depth= 1] . ( 75 sec) [ -8664.7825] [ 1334] [depth= 3] . ( 76 sec) [ -8612.3103] [ 1320] [depth= 7] . ( 76 sec) [ -8611.9785] [ 1320] [depth= 1] . ( 77 sec) [ -8611.8080] [ 1320] [depth= 1] . ( 78 sec) [ -8589.0722] [ 1318] [depth= 4] . ( 78 sec) [ -8564.2484] [ 1314] [depth= 1] . ( 79 sec) [ -8564.1340] [ 1314] [depth= 2] . ( 80 sec) [ -8492.9310] [ 1296] [depth= 1] . ( 81 sec) [ -8465.9934] [ 1297] [depth= 1] . ( 81 sec) [ -8433.1601] [ 1290] [depth= 3] . ( 82 sec) [ -8420.5422] [ 1288] [depth= 1] . ( 83 sec) [ -8419.2871] [ 1286] [depth= 2] . ( 87 sec) [ -8418.3663] [ 1286] [depth= 1] . ( 92 sec) [ -8404.3924] [ 1285] [depth= 1] . ( 95 sec) [ -8322.5730] [ 1269] [depth= 2] . ( 96 sec) [ -8316.5465] [ 1270] [depth= 1] . ( 98 sec) [ -8316.0529] [ 1269] [depth= 1] . ( 101 sec) [ -8265.6524] [Branch lengths ] . ( 102 sec) [ -8265.3980] [Alpha ][ 0.528905] . ( 103 sec) [ -8265.2031] [ 1269] [depth= 1] . ( 110 sec) [ -8262.1245] [ 1264] [depth= 4] . ( 112 sec) [ -8212.7196] [ 1250] [depth= 2] . ( 117 sec) [ -8212.5399] [ 1250] [depth= 1] . ( 118 sec) [ -8212.1892] [ 1250] [depth= 1] . ( 129 sec) [ -8212.0535] [ 1250] [depth= 1] . ( 133 sec) [ -8185.8951] [ 1244] [depth= 1] . ( 134 sec) [ -8185.1461] [ 1244] [depth= 1] . ( 135 sec) [ -8185.1247] [ 1244] [depth= 3] . ( 139 sec) [ -8185.1099] [ 1244] [depth= 3] . ( 142 sec) [ -8185.0906] [ 1244] [depth= 1] . ( 142 sec) [ -8185.0749] [ 1244] [depth= 2] . ( 144 sec) [ -8184.8897] [ 1244] [depth= 1] . ( 147 sec) [ -8184.7312] [ 1243] [depth= 2] . ( 155 sec) [ -8184.4866] [ 1243] [depth= 1] . ( 158 sec) [ -8183.7667] [ 1244] [depth= 1] . ( 160 sec) [ -8181.4617] [ 1243] [depth= 1] . ( 168 sec) [ -8181.1832] [ 1246] [depth= 1] . ( 168 sec) [ -8181.1690] [ 1246] [depth= 1] . ( 175 sec) [ -8180.1351] [ 1247] [depth= 1] . ( 178 sec) [ -8180.1138] [ 1246] [depth= 2] . ( 185 sec) [ -8178.3528] [ 1245] [depth= 1] . ( 189 sec) [ -8177.7722] [ 1247] [depth= 1] . ( 195 sec) [ -8177.4267] [ 1247] [depth= 1] . ( 196 sec) [ -8177.1365] [ 1245] [depth= 1] . ( 223 sec) [ -8177.1178] [ 1245] [depth= 1] . ( 246 sec) [ -8175.9643] [ 1245] [depth= 3] . ( 265 sec) [ -8168.8036] [Branch lengths ] . ( 266 sec) [ -8168.7320] [Alpha ][ 0.544378] . ( 336 sec) [ -8168.4296] [ 1247] [depth= 2] . ( 362 sec) [ -8168.3555] [ 1247] [depth= 1] . ( 365 sec) [ -8168.3177] [ 1247] [depth= 3] . ( 403 sec) [ -8168.2251] [ 1247] [depth= 1] . ( 414 sec) [ -8168.1380] [ 1247] [depth= 4] . ( 419 sec) [ -8167.9647] [ 1247] [depth= 2] . ( 433 sec) [ -8167.9046] [ 1246] [depth= 1] . ( 467 sec) [ -8166.5501] [Branch lengths ] . ( 468 sec) [ -8166.5468] [Alpha ][ 0.547795] . ( 669 sec) [ -8166.3594] [Branch lengths ] . ( 669 sec) [ -8166.3594] [Topology ] . ( 675 sec) [ -8166.3294] [Topology ] . ( 680 sec) [ -8166.3155] [Topology ] . ( 686 sec) [ -8166.3068] [Topology ] . ( 691 sec) [ -8166.3012] [Topology ] . ( 697 sec) [ -8166.2975] [Topology ] . ( 703 sec) [ -8166.2950] [Topology ] . ( 704 sec) [ -8166.2916] [Alpha ][ 0.551273] . ( 704 sec) [ -8166.2916] [Topology ] . ( 710 sec) [ -8166.2896] [Topology ] . ( 715 sec) [ -8166.2882] [Topology ] . ( 721 sec) [ -8166.2873] [Topology ] . ( 722 sec) [ -8166.2873] [Alpha ][ 0.551825] . ( 722 sec) [ -8166.2873] [Topology ] . ( 728 sec) [ -8166.2866] [Topology ] . ( 728 sec) [ -8166.2866] [Alpha ][ 0.551825] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8166.286616. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -8287.8174] [Alpha ][ 0.500960] . ( 2 sec) [ -8287.8174] [Topology ] . ( 8 sec) [ -8220.7157] [Topology ] . ( 13 sec) [ -8204.4814] [Topology ] . ( 19 sec) [ -8189.3124] [Topology ] . ( 25 sec) [ -8184.9266] [Topology ] . ( 30 sec) [ -8182.8608] [Topology ] . ( 35 sec) [ -8181.0365] [Topology ] . ( 41 sec) [ -8179.1558] [Topology ] . ( 46 sec) [ -8177.7907] [Topology ] . ( 51 sec) [ -8177.0374] [Topology ] . Checking for NNIs, optimizing five branches... . ( 93 sec) [ -8176.8663] [Topology ] . ( 94 sec) [ -8176.2111] [Alpha ][ 0.546347] . ( 95 sec) [ -8176.2111] [Topology ] . ( 100 sec) [ -8176.0377] [Topology ] . ( 105 sec) [ -8175.9637] [Topology ] . ( 111 sec) [ -8175.9221] [Topology ] . ( 116 sec) [ -8175.8970] [Topology ] . ( 121 sec) [ -8175.8813] [Topology ] . ( 127 sec) [ -8175.8714] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -8174.8298] [Topology ] . ( 166 sec) [ -8174.8237] [Alpha ][ 0.551022] . ( 166 sec) [ -8174.8237] [Topology ] . ( 171 sec) [ -8174.6407] [Topology ] . ( 177 sec) [ -8174.6187] [Topology ] . ( 182 sec) [ -8174.6129] [Topology ] . ( 187 sec) [ -8174.6109] [Topology ] . ( 193 sec) [ -8174.6101] [Topology ] . Checking for NNIs, optimizing five branches... . ( 229 sec) [ -8174.6100] [Alpha ][ 0.551573] . ( 230 sec) [ -8174.6100] [Topology ] . ( 235 sec) [ -8174.6095] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 309 sec) [ -8287.8174] [Alpha ][ 0.500960] . ( 311 sec) [ -8282.0664] [ 1252] [depth= 1] . ( 312 sec) [ -8281.7063] [ 1254] [depth= 1] . ( 313 sec) [ -8276.3109] [ 1251] [depth= 2] . ( 324 sec) [ -8271.1817] [ 1250] [depth= 1] . ( 325 sec) [ -8268.4324] [ 1249] [depth= 1] . ( 327 sec) [ -8258.8412] [ 1248] [depth= 2] . ( 329 sec) [ -8251.3287] [ 1246] [depth= 3] . ( 330 sec) [ -8250.9587] [ 1247] [depth= 1] . ( 335 sec) [ -8250.1630] [ 1247] [depth= 1] . ( 337 sec) [ -8248.6685] [ 1246] [depth= 1] . ( 339 sec) [ -8248.2108] [ 1245] [depth= 1] . ( 340 sec) [ -8247.4062] [ 1246] [depth= 1] . ( 344 sec) [ -8247.1577] [ 1246] [depth= 1] . ( 345 sec) [ -8246.7235] [ 1246] [depth= 1] . ( 350 sec) [ -8241.4009] [ 1246] [depth= 3] . ( 350 sec) [ -8239.6538] [ 1244] [depth= 1] . ( 351 sec) [ -8238.4411] [ 1244] [depth= 1] . ( 353 sec) [ -8238.3013] [ 1245] [depth= 1] . ( 354 sec) [ -8238.2470] [ 1245] [depth= 1] . ( 355 sec) [ -8238.1333] [ 1246] [depth= 2] . ( 359 sec) [ -8236.1099] [ 1245] [depth= 1] . ( 361 sec) [ -8235.1795] [ 1248] [depth= 2] . ( 364 sec) [ -8226.4629] [ 1246] [depth= 2] . ( 370 sec) [ -8226.1371] [ 1244] [depth= 3] . ( 371 sec) [ -8225.9515] [ 1241] [depth= 2] . ( 373 sec) [ -8214.9763] [ 1240] [depth= 3] . ( 374 sec) [ -8213.4369] [ 1237] [depth= 2] . ( 375 sec) [ -8207.3726] [ 1234] [depth= 3] . ( 376 sec) [ -8207.3301] [ 1237] [depth= 1] . ( 377 sec) [ -8207.2706] [ 1238] [depth= 1] . ( 378 sec) [ -8206.5969] [ 1239] [depth= 1] . ( 378 sec) [ -8206.4048] [ 1239] [depth= 1] . ( 390 sec) [ -8205.3166] [ 1241] [depth= 1] . ( 391 sec) [ -8205.0649] [ 1240] [depth= 1] . ( 392 sec) [ -8204.6930] [ 1243] [depth= 2] . ( 411 sec) [ -8204.5696] [ 1243] [depth= 1] . ( 425 sec) [ -8204.5483] [ 1243] [depth= 4] . ( 426 sec) [ -8204.0844] [ 1243] [depth= 3] . ( 427 sec) [ -8204.0652] [ 1243] [depth= 2] . ( 427 sec) [ -8203.9225] [ 1243] [depth= 2] . ( 431 sec) [ -8202.0665] [ 1244] [depth= 1] . ( 432 sec) [ -8202.0396] [ 1244] [depth= 4] . ( 433 sec) [ -8202.0149] [ 1244] [depth= 3] . ( 433 sec) [ -8201.7570] [ 1245] [depth= 4] . ( 437 sec) [ -8201.6044] [ 1245] [depth= 1] . ( 438 sec) [ -8201.5626] [ 1245] [depth= 3] . ( 439 sec) [ -8201.4399] [ 1245] [depth= 2] . ( 439 sec) [ -8201.2941] [ 1245] [depth= 2] . ( 447 sec) [ -8179.0267] [Branch lengths ] . ( 448 sec) [ -8178.6907] [Alpha ][ 0.534282] . ( 495 sec) [ -8178.4620] [ 1247] [depth= 2] . ( 602 sec) [ -8177.1880] [ 1246] [depth= 4] . ( 611 sec) [ -8177.1747] [ 1246] [depth= 3] . ( 615 sec) [ -8177.1141] [ 1246] [depth= 2] . ( 616 sec) [ -8174.7627] [ 1245] [depth= 1] . ( 624 sec) [ -8174.6109] [ 1245] [depth= 2] . ( 649 sec) [ -8171.7796] [Branch lengths ] . ( 650 sec) [ -8171.6991] [Alpha ][ 0.551102] . ( 860 sec) [ -8170.9909] [Branch lengths ] . ( 860 sec) [ -8170.9909] [Topology ] . ( 866 sec) [ -8170.8159] [Topology ] . ( 872 sec) [ -8170.5220] [Topology ] . ( 877 sec) [ -8170.4235] [Topology ] . ( 883 sec) [ -8170.3745] [Topology ] . ( 889 sec) [ -8170.3462] [Topology ] . ( 894 sec) [ -8170.3280] [Topology ] . ( 900 sec) [ -8170.3157] [Topology ] . ( 901 sec) [ -8170.2626] [Alpha ][ 0.564768] . ( 901 sec) [ -8170.2626] [Topology ] . ( 907 sec) [ -8170.2486] [Topology ] . ( 912 sec) [ -8170.2391] [Topology ] . ( 918 sec) [ -8170.2325] [Topology ] . ( 924 sec) [ -8170.2280] [Topology ] . ( 929 sec) [ -8170.2248] [Topology ] . ( 935 sec) [ -8170.2226] [Topology ] . ( 936 sec) [ -8170.2216] [Alpha ][ 0.566652] . ( 936 sec) [ -8170.2216] [Topology ] . ( 942 sec) [ -8170.2198] [Topology ] . ( 947 sec) [ -8170.2186] [Topology ] . ( 953 sec) [ -8170.2177] [Topology ] . ( 954 sec) [ -8170.2177] [Alpha ][ 0.567219] . ( 954 sec) [ -8170.2177] [Topology ] . ( 960 sec) [ -8170.2170] [Topology ] . ( 961 sec) [ -8170.2170] [Alpha ][ 0.567219] . Checking for NNIs, optimizing five branches... . ( 997 sec) [ -8170.2167] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8174.609471 . Log likelihood obtained after SPR moves : -8170.216729 . Log likelihood of the current tree: -8170.216729. . Printing the most likely tree in file 'proteic_M1392_57x430_2003.phy_phyml_tree.txt'... . Best log likelihood : -8165.324553 . Time used 0h17m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 5016.63user 0.00system 1:23:56elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps