.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2707_115x1677_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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 759 patterns found. (out of a total of 1677 sites) . 924 sites without polymorphism (55.10%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 46Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -11652.5156] [GTR parameters ] . ( 6 sec) [ -11452.6188] [Alpha ][ 0.500960] . ( 7 sec) [ -11452.0929] [ 1804] [depth= 1] . ( 7 sec) [ -11450.2527] [ 1804] [depth= 1] . ( 7 sec) [ -11449.6563] [ 1804] [depth= 1] . ( 8 sec) [ -11449.6408] [ 1804] [depth= 1] . ( 8 sec) [ -11449.1939] [ 1804] [depth= 2] . ( 9 sec) [ -11448.9557] [ 1804] [depth= 2] . ( 10 sec) [ -11444.7108] [ 1803] [depth= 2] . ( 11 sec) [ -11443.9941] [ 1803] [depth= 1] . ( 11 sec) [ -11443.6221] [ 1803] [depth= 1] . ( 12 sec) [ -11442.0931] [ 1803] [depth= 3] . ( 13 sec) [ -11439.9495] [ 1818] [depth= 1] . ( 14 sec) [ -11431.1045] [ 1815] [depth= 1] . ( 18 sec) [ -11430.6152] [ 1815] [depth= 1] . ( 19 sec) [ -11430.4390] [ 1815] [depth= 1] . ( 20 sec) [ -11430.2673] [ 1815] [depth= 1] . ( 23 sec) [ -11428.1390] [ 1817] [depth= 1] . ( 25 sec) [ -11409.9023] [ 1814] [depth= 2] . ( 25 sec) [ -11351.0470] [ 1815] [depth= 1] . ( 25 sec) [ -11219.8702] [ 1820] [depth= 1] . ( 26 sec) [ -11042.4463] [ 1815] [depth= 1] . ( 26 sec) [ -11039.1229] [ 1817] [depth= 1] . ( 27 sec) [ -11029.1819] [ 1803] [depth= 9] . ( 27 sec) [ -11028.6471] [ 1803] [depth= 1] . ( 28 sec) [ -11025.1252] [ 1803] [depth= 2] . ( 28 sec) [ -11023.4149] [ 1803] [depth= 2] . ( 28 sec) [ -11023.2196] [ 1803] [depth= 2] . ( 29 sec) [ -11022.7907] [ 1803] [depth= 2] . ( 30 sec) [ -10828.0909] [ 1798] [depth= 6] . ( 30 sec) [ -10827.2230] [ 1798] [depth= 1] . ( 31 sec) [ -10826.0826] [ 1798] [depth= 1] . ( 31 sec) [ -10825.7921] [ 1798] [depth= 1] . ( 32 sec) [ -10825.0248] [ 1798] [depth= 1] . ( 32 sec) [ -10825.0023] [ 1798] [depth= 3] . ( 33 sec) [ -10824.8504] [ 1798] [depth= 1] . ( 33 sec) [ -10824.4036] [ 1798] [depth= 2] . ( 33 sec) [ -10824.3740] [ 1798] [depth= 1] . ( 34 sec) [ -10824.3609] [ 1798] [depth= 3] . ( 35 sec) [ -10824.2134] [ 1798] [depth= 1] . ( 35 sec) [ -10824.1720] [ 1798] [depth= 1] . ( 36 sec) [ -10650.4439] [ 1798] [depth= 1] . ( 36 sec) [ -10435.1391] [ 1798] [depth= 2] . ( 37 sec) [ -10435.0388] [ 1798] [depth= 1] . ( 38 sec) [ -10434.9969] [ 1798] [depth= 1] . ( 38 sec) [ -10434.9145] [ 1798] [depth= 2] . ( 39 sec) [ -10434.8560] [ 1798] [depth= 3] . ( 39 sec) [ -10434.7906] [ 1798] [depth= 1] . ( 41 sec) [ -10434.7669] [ 1798] [depth= 1] . ( 41 sec) [ -10433.1648] [ 1799] [depth= 1] . ( 41 sec) [ -10433.1466] [ 1799] [depth= 2] . ( 42 sec) [ -10433.1290] [ 1799] [depth= 1] . ( 43 sec) [ -10433.1059] [ 1799] [depth= 2] . ( 43 sec) [ -10432.7326] [ 1799] [depth= 2] . ( 44 sec) [ -10432.2983] [ 1799] [depth= 1] . ( 45 sec) [ -10431.7210] [ 1799] [depth= 2] . ( 46 sec) [ -10427.2431] [ 1799] [depth= 2] . ( 46 sec) [ -10427.2310] [ 1799] [depth= 1] . ( 48 sec) [ -10376.9645] [ 1795] [depth= 3] . ( 48 sec) [ -10376.8623] [ 1795] [depth= 2] . ( 49 sec) [ -10376.8184] [ 1795] [depth= 2] . ( 49 sec) [ -10375.9879] [ 1795] [depth= 2] . ( 49 sec) [ -10375.8222] [ 1795] [depth= 3] . ( 51 sec) [ -10366.3897] [ 1798] [depth= 1] . ( 52 sec) [ -10362.6424] [ 1798] [depth= 2] . ( 53 sec) [ -10362.3775] [ 1798] [depth= 3] . ( 53 sec) [ -10361.3281] [ 1798] [depth= 3] . ( 53 sec) [ -10361.2681] [ 1798] [depth= 1] . ( 54 sec) [ -10361.2281] [ 1798] [depth= 2] . ( 55 sec) [ -10359.2596] [ 1796] [depth= 3] . ( 55 sec) [ -10357.0546] [ 1796] [depth= 3] . ( 56 sec) [ -10347.8067] [ 1794] [depth= 1] . ( 56 sec) [ -10346.8731] [ 1794] [depth= 4] . ( 57 sec) [ -10346.4970] [ 1794] [depth= 5] . ( 58 sec) [ -10346.0418] [ 1794] [depth= 1] . ( 59 sec) [ -10345.8869] [ 1794] [depth= 1] . ( 59 sec) [ -10345.8067] [ 1794] [depth= 1] . ( 60 sec) [ -10345.7526] [ 1794] [depth= 2] . ( 62 sec) [ -10335.2221] [ 1794] [depth= 1] . ( 63 sec) [ -10334.0217] [ 1794] [depth= 2] . ( 64 sec) [ -10330.8158] [ 1791] [depth= 2] . ( 64 sec) [ -10329.4364] [ 1789] [depth= 2] . ( 66 sec) [ -10328.8312] [ 1790] [depth= 3] . ( 67 sec) [ -10327.8645] [ 1790] [depth= 2] . ( 67 sec) [ -10326.6783] [ 1791] [depth= 3] . ( 68 sec) [ -10260.9370] [ 1792] [depth= 1] . ( 68 sec) [ -10203.2505] [ 1790] [depth= 2] . ( 69 sec) [ -10195.4381] [ 1787] [depth= 1] . ( 69 sec) [ -10166.1145] [ 1785] [depth= 2] . ( 69 sec) [ -10163.0153] [ 1784] [depth= 2] . ( 70 sec) [ -10162.9705] [ 1784] [depth= 1] . ( 70 sec) [ -10149.8849] [ 1789] [depth= 6] . ( 71 sec) [ -10138.6464] [ 1790] [depth= 1] . ( 72 sec) [ -10135.8407] [ 1790] [depth= 3] . ( 72 sec) [ -10123.6677] [ 1790] [depth= 3] . ( 73 sec) [ -10123.5711] [ 1790] [depth= 1] . ( 73 sec) [ -10122.5382] [ 1790] [depth= 1] . ( 74 sec) [ -10113.5522] [ 1791] [depth= 1] . ( 74 sec) [ -10109.1624] [ 1789] [depth= 2] . ( 75 sec) [ -10108.4039] [ 1789] [depth= 3] . ( 75 sec) [ -10108.2961] [ 1789] [depth= 1] . ( 75 sec) [ -10108.2479] [ 1789] [depth= 1] . ( 76 sec) [ -10108.2048] [ 1789] [depth= 1] . ( 77 sec) [ -10107.4078] [ 1789] [depth= 1] . ( 77 sec) [ -10107.3728] [ 1789] [depth= 1] . ( 79 sec) [ -10107.2358] [ 1789] [depth= 2] . ( 79 sec) [ -10106.9683] [ 1789] [depth= 1] . ( 80 sec) [ -10106.7458] [ 1789] [depth= 1] . ( 80 sec) [ -10106.0910] [ 1789] [depth= 1] . ( 81 sec) [ -10103.6183] [ 1789] [depth= 3] . ( 82 sec) [ -10102.0231] [ 1789] [depth= 3] . ( 83 sec) [ -10101.9326] [ 1789] [depth= 2] . ( 84 sec) [ -10101.6950] [ 1789] [depth= 4] . ( 84 sec) [ -10101.4496] [ 1789] [depth= 2] . ( 85 sec) [ -10100.9194] [ 1789] [depth= 3] . ( 85 sec) [ -10100.8809] [ 1789] [depth= 3] . ( 86 sec) [ -10100.7475] [ 1789] [depth= 2] . ( 87 sec) [ -10100.7107] [ 1789] [depth= 1] . ( 87 sec) [ -10100.6921] [ 1789] [depth= 3] . ( 88 sec) [ -10100.6061] [ 1789] [depth= 2] . ( 89 sec) [ -10100.5671] [ 1789] [depth= 3] . ( 90 sec) [ -10100.2496] [ 1789] [depth= 2] . ( 90 sec) [ -10100.2161] [ 1789] [depth= 1] . ( 91 sec) [ -10100.1469] [ 1789] [depth= 3] . ( 91 sec) [ -10099.7828] [ 1789] [depth= 2] . ( 92 sec) [ -10099.7590] [ 1789] [depth= 2] . ( 93 sec) [ -10099.7471] [ 1789] [depth= 1] . ( 96 sec) [ -10099.6376] [ 1789] [depth= 4] . ( 98 sec) [ -9944.4227] [Branch lengths ] . ( 106 sec) [ -9935.2722] [GTR parameters ] . ( 107 sec) [ -9877.0018] [Alpha ][ 0.271447] . ( 108 sec) [ -9876.9062] [ 1789] [depth= 1] . ( 109 sec) [ -9876.7712] [ 1789] [depth= 1] . ( 110 sec) [ -9876.7495] [ 1789] [depth= 1] . ( 110 sec) [ -9876.5377] [ 1789] [depth= 3] . ( 111 sec) [ -9876.5185] [ 1789] [depth= 3] . ( 114 sec) [ -9876.4111] [ 1789] [depth= 1] . ( 114 sec) [ -9876.3291] [ 1789] [depth= 1] . ( 116 sec) [ -9872.6045] [ 1776] [depth= 1] . ( 116 sec) [ -9865.3771] [ 1789] [depth= 1] . ( 121 sec) [ -9865.1160] [ 1789] [depth= 1] . ( 122 sec) [ -9864.9182] [ 1789] [depth= 1] . ( 125 sec) [ -9864.2155] [ 1790] [depth= 1] . ( 126 sec) [ -9864.0536] [ 1790] [depth= 1] . ( 129 sec) [ -9863.9488] [ 1790] [depth= 3] . ( 130 sec) [ -9863.8763] [ 1790] [depth= 5] . ( 130 sec) [ -9863.8219] [ 1790] [depth= 1] . ( 131 sec) [ -9862.9055] [ 1789] [depth= 1] . ( 133 sec) [ -9862.8314] [ 1789] [depth= 3] . ( 135 sec) [ -9862.7292] [ 1789] [depth= 3] . ( 135 sec) [ -9862.4908] [ 1788] [depth= 1] . ( 136 sec) [ -9862.1687] [ 1788] [depth= 1] . ( 137 sec) [ -9862.1448] [ 1788] [depth= 1] . ( 137 sec) [ -9861.3375] [ 1788] [depth= 1] . ( 138 sec) [ -9861.0859] [ 1788] [depth= 1] . ( 138 sec) [ -9861.0583] [ 1788] [depth= 1] . ( 139 sec) [ -9860.9287] [ 1788] [depth= 1] . ( 139 sec) [ -9860.8872] [ 1788] [depth= 2] . ( 140 sec) [ -9860.8483] [ 1788] [depth= 1] . ( 141 sec) [ -9860.7514] [ 1788] [depth= 2] . ( 142 sec) [ -9860.5679] [ 1788] [depth= 1] . ( 145 sec) [ -9860.4004] [ 1788] [depth= 2] . ( 147 sec) [ -9860.0607] [ 1788] [depth= 3] . ( 148 sec) [ -9860.0164] [ 1788] [depth= 2] . ( 150 sec) [ -9859.9543] [ 1788] [depth= 2] . ( 150 sec) [ -9859.1857] [ 1788] [depth= 3] . ( 151 sec) [ -9859.1482] [ 1788] [depth= 1] . ( 153 sec) [ -9859.0050] [ 1788] [depth= 2] . ( 154 sec) [ -9858.9486] [ 1788] [depth= 3] . ( 155 sec) [ -9858.8871] [ 1788] [depth= 3] . ( 155 sec) [ -9858.6013] [ 1788] [depth= 3] . ( 156 sec) [ -9858.5783] [ 1788] [depth= 1] . ( 160 sec) [ -9858.4644] [ 1788] [depth= 1] . ( 160 sec) [ -9858.3341] [ 1788] [depth= 2] . ( 162 sec) [ -9858.2978] [ 1788] [depth= 2] . ( 173 sec) [ -9857.8745] [ 1788] [depth= 1] . ( 174 sec) [ -9857.0572] [ 1788] [depth= 1] . ( 175 sec) [ -9857.0059] [ 1788] [depth= 4] . ( 175 sec) [ -9856.9936] [ 1788] [depth= 3] . ( 176 sec) [ -9856.9320] [ 1788] [depth= 1] . ( 177 sec) [ -9856.9012] [ 1788] [depth= 1] . ( 181 sec) [ -9851.3450] [ 1787] [depth= 7] . ( 182 sec) [ -9851.2765] [ 1787] [depth= 2] . ( 183 sec) [ -9851.2492] [ 1787] [depth= 5] . ( 184 sec) [ -9851.1471] [ 1787] [depth= 1] . ( 185 sec) [ -9851.1267] [ 1787] [depth= 1] . ( 186 sec) [ -9851.0937] [ 1787] [depth= 1] . ( 192 sec) [ -9851.0642] [ 1787] [depth= 1] . ( 200 sec) [ -9815.1254] [Branch lengths ] . ( 210 sec) [ -9811.3223] [GTR parameters ] . ( 210 sec) [ -9810.5589] [Alpha ][ 0.255479] . ( 212 sec) [ -9810.5179] [ 1787] [depth= 3] . ( 212 sec) [ -9810.5020] [ 1787] [depth= 1] . ( 214 sec) [ -9810.4838] [ 1787] [depth= 2] . ( 215 sec) [ -9810.4722] [ 1787] [depth= 2] . ( 218 sec) [ -9809.7955] [ 1774] [depth= 1] . ( 225 sec) [ -9809.7264] [ 1774] [depth= 1] . ( 228 sec) [ -9809.6553] [ 1774] [depth= 1] . ( 234 sec) [ -9809.4110] [ 1774] [depth= 1] . ( 236 sec) [ -9809.3962] [ 1774] [depth= 3] . ( 242 sec) [ -9809.2722] [ 1774] [depth= 1] . ( 247 sec) [ -9809.2597] [ 1774] [depth= 4] . ( 247 sec) [ -9809.1483] [ 1774] [depth= 1] . ( 251 sec) [ -9809.1172] [ 1774] [depth= 2] . ( 255 sec) [ -9809.1015] [ 1774] [depth= 5] . ( 257 sec) [ -9809.0620] [ 1774] [depth= 2] . ( 258 sec) [ -9809.0261] [ 1774] [depth= 2] . ( 264 sec) [ -9808.8734] [ 1774] [depth= 3] . ( 273 sec) [ -9808.3122] [ 1774] [depth= 7] . ( 284 sec) [ -9808.1910] [ 1774] [depth= 1] . ( 297 sec) [ -9787.8812] [Branch lengths ] . ( 304 sec) [ -9787.0675] [GTR parameters ] . ( 305 sec) [ -9786.7710] [Alpha ][ 0.246535] . ( 306 sec) [ -9786.7497] [ 1774] [depth= 3] . ( 307 sec) [ -9786.7136] [ 1774] [depth= 1] . ( 307 sec) [ -9786.6948] [ 1774] [depth= 1] . ( 308 sec) [ -9786.6329] [ 1774] [depth= 1] . ( 322 sec) [ -9786.5767] [ 1774] [depth= 1] . ( 326 sec) [ -9786.5182] [ 1774] [depth= 1] . ( 328 sec) [ -9786.4775] [ 1774] [depth= 1] . ( 339 sec) [ -9786.3982] [ 1774] [depth= 1] . ( 357 sec) [ -9786.3673] [ 1774] [depth= 3] . ( 394 sec) [ -9786.3388] [ 1774] [depth= 1] . ( 405 sec) [ -9772.7379] [Branch lengths ] . ( 412 sec) [ -9772.4413] [GTR parameters ] . ( 413 sec) [ -9772.0456] [Alpha ][ 0.237090] . ( 415 sec) [ -9772.0108] [ 1774] [depth= 2] . ( 416 sec) [ -9771.9915] [ 1774] [depth= 1] . ( 417 sec) [ -9771.9419] [ 1774] [depth= 2] . ( 418 sec) [ -9771.9047] [ 1774] [depth= 2] . ( 419 sec) [ -9771.8773] [ 1774] [depth= 1] . ( 427 sec) [ -9771.8285] [ 1774] [depth= 1] . ( 430 sec) [ -9771.7989] [ 1774] [depth= 1] . ( 442 sec) [ -9771.7850] [ 1774] [depth= 2] . ( 457 sec) [ -9771.7642] [ 1774] [depth= 3] . ( 491 sec) [ -9760.6972] [Branch lengths ] . ( 497 sec) [ -9760.5250] [GTR parameters ] . ( 498 sec) [ -9759.9012] [Alpha ][ 0.226176] . ( 499 sec) [ -9759.8887] [ 1774] [depth= 1] . ( 500 sec) [ -9759.8755] [ 1774] [depth= 1] . ( 501 sec) [ -9759.7911] [ 1774] [depth= 3] . ( 501 sec) [ -9759.7745] [ 1774] [depth= 1] . ( 502 sec) [ -9759.5712] [ 1774] [depth= 1] . ( 510 sec) [ -9759.5445] [ 1774] [depth= 1] . ( 515 sec) [ -9759.5291] [ 1774] [depth= 1] . ( 539 sec) [ -9759.5115] [ 1774] [depth= 3] . ( 558 sec) [ -9759.4994] [ 1774] [depth= 2] . ( 577 sec) [ -9751.0941] [Branch lengths ] . ( 583 sec) [ -9750.9754] [GTR parameters ] . ( 584 sec) [ -9750.2414] [Alpha ][ 0.215114] . ( 586 sec) [ -9750.2261] [ 1774] [depth= 3] . ( 586 sec) [ -9750.1902] [ 1774] [depth= 2] . ( 588 sec) [ -9750.1657] [ 1774] [depth= 1] . ( 608 sec) [ -9750.1495] [ 1774] [depth= 2] . ( 652 sec) [ -9749.7855] [ 1774] [depth= 11] . ( 656 sec) [ -9749.7720] [ 1774] [depth= 2] . ( 679 sec) [ -9743.7801] [Branch lengths ] . ( 686 sec) [ -9743.6853] [GTR parameters ] . ( 687 sec) [ -9743.0241] [Alpha ][ 0.205252] . ( 689 sec) [ -9743.0080] [ 1774] [depth= 1] . ( 694 sec) [ -9742.9947] [ 1774] [depth= 2] . ( 749 sec) [ -9742.9833] [ 1774] [depth= 2] . ( 767 sec) [ -9738.6340] [Branch lengths ] . ( 771 sec) [ -9738.5689] [GTR parameters ] . ( 772 sec) [ -9738.1181] [Alpha ][ 0.197400] . ( 774 sec) [ -9738.1052] [ 1774] [depth= 2] . ( 806 sec) [ -9738.0888] [ 1774] [depth= 2] . ( 873 sec) [ -9734.6726] [Branch lengths ] . ( 879 sec) [ -9734.6314] [GTR parameters ] . ( 880 sec) [ -9734.4431] [Alpha ][ 0.192450] . ( 968 sec) [ -9733.7422] [Branch lengths ] . ( 1054 sec) [ -9733.6716] [ 1774] [depth= 1] . ( 1143 sec) [ -9732.4967] [ 1776] [depth= 2] . ( 1178 sec) [ -9731.5889] [ 1776] [depth= 1] . ( 1193 sec) [ -9731.1330] [ 1775] [depth= 1] . ( 1207 sec) [ -9730.6958] [ 1776] [depth= 1] . ( 1208 sec) [ -9730.5985] [ 1776] [depth= 1] . ( 1212 sec) [ -9730.5126] [ 1776] [depth= 1] . ( 1218 sec) [ -9730.2038] [ 1777] [depth= 1] . ( 1238 sec) [ -9730.1196] [ 1777] [depth= 1] . ( 1245 sec) [ -9730.0875] [ 1777] [depth= 4] . ( 1247 sec) [ -9730.0733] [ 1777] [depth= 2] . ( 1248 sec) [ -9730.0306] [ 1777] [depth= 1] . ( 1276 sec) [ -9728.1241] [Branch lengths ] . ( 1281 sec) [ -9728.0866] [GTR parameters ] . ( 1281 sec) [ -9727.9373] [Alpha ][ 0.188093] . ( 1385 sec) [ -9726.9079] [ 1775] [depth= 3] . ( 1466 sec) [ -9726.6041] [ 1775] [depth= 4] . ( 1475 sec) [ -9726.0621] [ 1776] [depth= 1] . ( 1487 sec) [ -9724.5205] [ 1776] [depth= 1] . ( 1487 sec) [ -9724.3749] [ 1776] [depth= 2] . ( 1490 sec) [ -9724.2192] [ 1776] [depth= 1] . ( 1491 sec) [ -9724.2089] [ 1776] [depth= 1] . ( 1502 sec) [ -9724.1881] [ 1776] [depth= 1] . ( 1503 sec) [ -9724.1758] [ 1777] [depth= 2] . ( 1506 sec) [ -9724.1428] [ 1777] [depth= 1] . ( 1510 sec) [ -9724.1085] [ 1777] [depth= 1] . ( 1518 sec) [ -9724.0686] [ 1777] [depth= 1] . ( 1518 sec) [ -9723.9315] [ 1776] [depth= 1] . ( 1519 sec) [ -9723.8550] [ 1776] [depth= 1] . ( 1521 sec) [ -9723.8438] [ 1776] [depth= 3] . ( 1522 sec) [ -9723.8323] [ 1776] [depth= 2] . ( 1547 sec) [ -9722.4644] [Branch lengths ] . ( 1552 sec) [ -9722.4014] [GTR parameters ] . ( 1552 sec) [ -9722.3508] [Alpha ][ 0.185603] . ( 1738 sec) [ -9716.8512] [ 1776] [depth= 3] . ( 1750 sec) [ -9716.7702] [ 1776] [depth= 1] . ( 1753 sec) [ -9716.4947] [ 1775] [depth= 1] . ( 1763 sec) [ -9716.0322] [ 1775] [depth= 2] . ( 1766 sec) [ -9716.0123] [ 1776] [depth= 1] . ( 1772 sec) [ -9715.9584] [ 1776] [depth= 8] . ( 1778 sec) [ -9715.9162] [ 1777] [depth= 3] . ( 1786 sec) [ -9715.8882] [ 1777] [depth= 2] . ( 1797 sec) [ -9715.8386] [ 1777] [depth= 1] . ( 1798 sec) [ -9715.6260] [ 1777] [depth= 3] . ( 1801 sec) [ -9715.6117] [ 1776] [depth= 1] . ( 1827 sec) [ -9714.6599] [Branch lengths ] . ( 1833 sec) [ -9714.5855] [GTR parameters ] . ( 1833 sec) [ -9714.5439] [Alpha ][ 0.183409] . ( 2078 sec) [ -9714.0999] [ 1775] [depth= 2] . ( 2084 sec) [ -9714.0779] [ 1775] [depth= 1] . ( 2112 sec) [ -9714.0433] [ 1775] [depth= 1] . ( 2117 sec) [ -9714.0300] [ 1775] [depth= 2] . ( 2140 sec) [ -9713.3934] [Branch lengths ] . ( 2144 sec) [ -9713.3698] [GTR parameters ] . ( 2144 sec) [ -9713.3524] [Alpha ][ 0.182031] . ( 2463 sec) [ -9713.1446] [Branch lengths ] . ( 2463 sec) [ -9713.1446] [Topology ] . ( 2468 sec) [ -9713.1136] [Topology ] . ( 2473 sec) [ -9713.1000] [Topology ] . ( 2478 sec) [ -9713.0914] [Topology ] . ( 2483 sec) [ -9713.0853] [Topology ] . ( 2487 sec) [ -9713.0803] [Topology ] . ( 2492 sec) [ -9713.0761] [Topology ] . ( 2496 sec) [ -9713.0651] [GTR parameters ] . ( 2496 sec) [ -9712.9916] [Alpha ][ 0.179171] . ( 2496 sec) [ -9712.9916] [Topology ] . ( 2501 sec) [ -9712.9592] [Topology ] . ( 2505 sec) [ -9712.9430] [Topology ] . ( 2510 sec) [ -9712.9333] [Topology ] . ( 2515 sec) [ -9712.9268] [Topology ] . ( 2520 sec) [ -9712.9220] [Topology ] . ( 2525 sec) [ -9712.9180] [Topology ] . ( 2528 sec) [ -9712.9142] [GTR parameters ] . ( 2528 sec) [ -9712.8947] [Alpha ][ 0.177719] . ( 2528 sec) [ -9712.8947] [Topology ] . ( 2534 sec) [ -9712.8815] [Topology ] . ( 2538 sec) [ -9712.8739] [Topology ] . ( 2543 sec) [ -9712.8687] [Topology ] . ( 2548 sec) [ -9712.8647] [Topology ] . ( 2553 sec) [ -9712.8613] [Topology ] . ( 2558 sec) [ -9712.8583] [Topology ] . ( 2561 sec) [ -9712.8569] [GTR parameters ] . ( 2561 sec) [ -9712.8500] [Alpha ][ 0.176881] . ( 2561 sec) [ -9712.8500] [Topology ] . ( 2566 sec) [ -9712.8438] [Topology ] . ( 2571 sec) [ -9712.8397] [Topology ] . ( 2576 sec) [ -9712.8365] [Topology ] . ( 2581 sec) [ -9712.8338] [Topology ] . ( 2586 sec) [ -9712.8313] [Topology ] . ( 2591 sec) [ -9712.8291] [Topology ] . ( 2593 sec) [ -9712.8285] [GTR parameters ] . ( 2593 sec) [ -9712.8258] [Alpha ][ 0.176385] . ( 2593 sec) [ -9712.8258] [Topology ] . ( 2598 sec) [ -9712.8225] [Topology ] . ( 2603 sec) [ -9712.8199] [Topology ] . ( 2608 sec) [ -9712.8176] [Topology ] . ( 2613 sec) [ -9712.8156] [Topology ] . ( 2618 sec) [ -9712.8137] [Topology ] . ( 2624 sec) [ -9712.8119] [Topology ] . ( 2626 sec) [ -9712.8117] [GTR parameters ] . ( 2627 sec) [ -9712.8106] [Alpha ][ 0.176093] . ( 2627 sec) [ -9712.8106] [Topology ] . ( 2633 sec) [ -9712.8084] [Topology ] . ( 2638 sec) [ -9712.8065] [Topology ] . ( 2644 sec) [ -9712.8048] [Topology ] . ( 2650 sec) [ -9712.8032] [Topology ] . ( 2656 sec) [ -9712.8016] [Topology ] . ( 2661 sec) [ -9712.8001] [Topology ] . ( 2662 sec) [ -9712.8000] [GTR parameters ] . ( 2663 sec) [ -9712.7995] [Alpha ][ 0.175912] . ( 2663 sec) [ -9712.7995] [Topology ] . ( 2669 sec) [ -9712.7979] [Topology ] . ( 2674 sec) [ -9712.7964] [Topology ] . ( 2680 sec) [ -9712.7957] [Topology ] . ( 2681 sec) [ -9712.7957] [GTR parameters ] . ( 2682 sec) [ -9712.7956] [Alpha ][ 0.175657] . ( 2682 sec) [ -9712.7956] [Topology ] . ( 2688 sec) [ -9712.7950] [Topology ] . ( 2689 sec) [ -9712.7950] [GTR parameters ] . ( 2690 sec) [ -9712.7950] [Alpha ][ 0.175657] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9712.795038. . Printing the most likely tree in file 'nucleic_M2707_115x1677_2006.phy_phyml_tree.txt'... . Time used 0h45m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1694.14user 0.00system 45:37.77elapsed 61%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps