.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2558_27x1060_2005.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... . 746 patterns found. (out of a total of 1060 sites) . 362 sites without polymorphism (34.15%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 47Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -46890.9736] [Alpha ][ 0.500960] . ( 3 sec) [ -46357.2178] [ 8746] [depth= 9] . ( 4 sec) [ -45997.9903] [ 8646] [depth= 7] . ( 4 sec) [ -45972.4069] [ 8638] [depth= 1] . ( 5 sec) [ -45701.3129] [ 8606] [depth= 4] . ( 6 sec) [ -45662.8371] [ 8589] [depth= 1] . ( 6 sec) [ -45010.7116] [ 8496] [depth= 4] . ( 7 sec) [ -44788.4319] [ 8430] [depth= 1] . ( 7 sec) [ -43324.0775] [ 8363] [depth= 5] . ( 8 sec) [ -43037.5837] [ 8292] [depth= 1] . ( 9 sec) [ -42652.4099] [ 8264] [depth= 1] . ( 9 sec) [ -42621.4362] [ 8269] [depth= 1] . ( 10 sec) [ -42138.2983] [ 8197] [depth= 3] . ( 11 sec) [ -42074.0089] [ 8167] [depth= 2] . ( 11 sec) [ -41506.5697] [ 8092] [depth= 5] . ( 12 sec) [ -41328.9264] [ 8110] [depth= 1] . ( 12 sec) [ -40938.4869] [ 8066] [depth= 5] . ( 13 sec) [ -40683.6234] [ 8053] [depth= 2] . ( 14 sec) [ -40591.6708] [ 8043] [depth= 4] . ( 14 sec) [ -40366.7222] [ 7897] [depth= 8] . ( 15 sec) [ -40263.4679] [ 7897] [depth= 1] . ( 16 sec) [ -40086.3105] [ 7889] [depth= 2] . ( 17 sec) [ -40052.7532] [ 7891] [depth= 1] . ( 18 sec) [ -40012.6603] [ 7870] [depth= 1] . ( 18 sec) [ -39957.7006] [ 7844] [depth= 4] . ( 19 sec) [ -39867.3291] [ 7835] [depth= 1] . ( 20 sec) [ -39443.7495] [ 7820] [depth= 1] . ( 20 sec) [ -39395.9866] [ 7817] [depth= 1] . ( 22 sec) [ -39255.0475] [ 7786] [depth= 1] . ( 23 sec) [ -39134.7141] [ 7771] [depth= 2] . ( 23 sec) [ -38789.6493] [ 7770] [depth= 1] . ( 24 sec) [ -38713.0888] [ 7763] [depth= 4] . ( 26 sec) [ -38707.1947] [ 7763] [depth= 1] . ( 26 sec) [ -38695.9414] [ 7755] [depth= 3] . ( 27 sec) [ -38636.5448] [ 7751] [depth= 1] . ( 28 sec) [ -38548.4085] [ 7727] [depth= 2] . ( 29 sec) [ -38415.4463] [ 7720] [depth= 2] . ( 30 sec) [ -38414.6331] [ 7706] [depth= 5] . ( 31 sec) [ -38394.8563] [ 7710] [depth= 3] . ( 31 sec) [ -38370.9296] [ 7693] [depth= 2] . ( 33 sec) [ -38361.4343] [ 7687] [depth= 2] . ( 34 sec) [ -38281.0030] [ 7687] [depth= 3] . ( 35 sec) [ -38107.9437] [ 7685] [depth= 1] . ( 36 sec) [ -37970.1887] [ 7685] [depth= 1] . ( 36 sec) [ -37956.5941] [ 7681] [depth= 1] . ( 37 sec) [ -37937.5319] [ 7679] [depth= 1] . ( 38 sec) [ -37907.4326] [ 7668] [depth= 3] . ( 39 sec) [ -37898.1493] [ 7668] [depth= 1] . ( 39 sec) [ -37888.6879] [ 7666] [depth= 2] . ( 40 sec) [ -37888.2830] [ 7658] [depth= 1] . ( 41 sec) [ -37884.6855] [ 7661] [depth= 1] . ( 42 sec) [ -37883.7737] [ 7658] [depth= 1] . ( 43 sec) [ -37879.6604] [ 7656] [depth= 1] . ( 45 sec) [ -37802.8761] [ 7655] [depth= 1] . ( 45 sec) [ -37779.1744] [ 7659] [depth= 1] . ( 46 sec) [ -37775.6162] [ 7656] [depth= 1] . ( 48 sec) [ -37401.5673] [Branch lengths ] . ( 49 sec) [ -37363.5527] [Alpha ][ 0.679038] . ( 52 sec) [ -37354.4341] [ 7659] [depth= 2] . ( 53 sec) [ -37340.4459] [ 7660] [depth= 1] . ( 54 sec) [ -37321.0540] [ 7652] [depth= 4] . ( 56 sec) [ -37317.1192] [ 7664] [depth= 1] . ( 58 sec) [ -37303.0740] [ 7666] [depth= 2] . ( 59 sec) [ -37295.6160] [ 7675] [depth= 1] . ( 60 sec) [ -37293.7881] [ 7677] [depth= 1] . ( 62 sec) [ -37290.1064] [ 7687] [depth= 1] . ( 64 sec) [ -37289.3554] [ 7690] [depth= 1] . ( 66 sec) [ -37289.3375] [ 7690] [depth= 1] . ( 69 sec) [ -37281.7407] [ 7688] [depth= 2] . ( 72 sec) [ -37278.1059] [ 7673] [depth= 3] . ( 72 sec) [ -37251.7032] [ 7649] [depth= 4] . ( 74 sec) [ -37249.0378] [ 7640] [depth= 1] . ( 80 sec) [ -37248.0291] [ 7645] [depth= 2] . ( 81 sec) [ -37247.8557] [ 7646] [depth= 1] . ( 82 sec) [ -37246.2056] [ 7642] [depth= 3] . ( 98 sec) [ -37209.2381] [Branch lengths ] . ( 99 sec) [ -37207.6109] [Alpha ][ 0.635645] . ( 106 sec) [ -37206.0810] [ 7642] [depth= 1] . ( 122 sec) [ -37205.3087] [ 7640] [depth= 1] . ( 129 sec) [ -37205.0789] [ 7642] [depth= 1] . ( 130 sec) [ -37204.8610] [ 7640] [depth= 2] . ( 136 sec) [ -37204.7084] [ 7642] [depth= 4] . ( 148 sec) [ -37195.3360] [Branch lengths ] . ( 149 sec) [ -37194.5229] [Alpha ][ 0.606641] . ( 173 sec) [ -37193.4971] [ 7646] [depth= 1] . ( 190 sec) [ -37193.1014] [ 7644] [depth= 4] . ( 199 sec) [ -37190.0109] [Branch lengths ] . ( 200 sec) [ -37189.4029] [Alpha ][ 0.582586] . ( 257 sec) [ -37188.1708] [Branch lengths ] . ( 258 sec) [ -37188.1708] [Topology ] . ( 261 sec) [ -37187.9947] [Topology ] . ( 265 sec) [ -37187.9325] [Topology ] . ( 269 sec) [ -37187.9059] [Topology ] . ( 273 sec) [ -37187.8939] [Topology ] . ( 277 sec) [ -37187.8883] [Topology ] . ( 281 sec) [ -37187.8857] [Topology ] . ( 282 sec) [ -37187.2872] [Alpha ][ 0.559609] . ( 282 sec) [ -37187.2872] [Topology ] . ( 286 sec) [ -37187.0342] [Topology ] . ( 290 sec) [ -37186.9476] [Topology ] . ( 294 sec) [ -37186.9112] [Topology ] . ( 298 sec) [ -37186.8952] [Topology ] . ( 302 sec) [ -37186.8881] [Topology ] . ( 306 sec) [ -37186.8848] [Topology ] . ( 306 sec) [ -37186.6682] [Alpha ][ 0.546385] . ( 307 sec) [ -37186.6682] [Topology ] . ( 311 sec) [ -37186.5626] [Topology ] . ( 315 sec) [ -37186.5262] [Topology ] . ( 318 sec) [ -37186.5108] [Topology ] . ( 322 sec) [ -37186.5039] [Topology ] . ( 326 sec) [ -37186.5008] [Topology ] . ( 330 sec) [ -37186.4992] [Topology ] . ( 331 sec) [ -37186.4027] [Alpha ][ 0.537884] . ( 331 sec) [ -37186.4027] [Topology ] . ( 335 sec) [ -37186.3561] [Topology ] . ( 339 sec) [ -37186.3402] [Topology ] . ( 343 sec) [ -37186.3335] [Topology ] . ( 347 sec) [ -37186.3305] [Topology ] . ( 351 sec) [ -37186.3290] [Topology ] . ( 355 sec) [ -37186.3283] [Topology ] . ( 355 sec) [ -37186.2831] [Alpha ][ 0.531756] . ( 356 sec) [ -37186.2831] [Topology ] . ( 360 sec) [ -37186.2583] [Topology ] . ( 364 sec) [ -37186.2499] [Topology ] . ( 367 sec) [ -37186.2464] [Topology ] . ( 371 sec) [ -37186.2449] [Topology ] . ( 375 sec) [ -37186.2441] [Topology ] . ( 376 sec) [ -37186.2233] [Alpha ][ 0.527622] . ( 376 sec) [ -37186.2233] [Topology ] . ( 380 sec) [ -37186.2113] [Topology ] . ( 384 sec) [ -37186.2074] [Topology ] . ( 388 sec) [ -37186.2059] [Topology ] . ( 392 sec) [ -37186.2053] [Topology ] . ( 393 sec) [ -37186.1976] [Alpha ][ 0.525097] . ( 393 sec) [ -37186.1976] [Topology ] . ( 397 sec) [ -37186.1921] [Topology ] . ( 401 sec) [ -37186.1902] [Topology ] . ( 405 sec) [ -37186.1894] [Topology ] . ( 406 sec) [ -37186.1862] [Alpha ][ 0.523442] . ( 406 sec) [ -37186.1862] [Topology ] . ( 410 sec) [ -37186.1832] [Topology ] . ( 414 sec) [ -37186.1821] [Topology ] . ( 417 sec) [ -37186.1817] [Topology ] . ( 418 sec) [ -37186.1802] [Alpha ][ 0.522297] . ( 419 sec) [ -37186.1802] [Topology ] . ( 422 sec) [ -37186.1787] [Topology ] . ( 426 sec) [ -37186.1781] [Topology ] . ( 427 sec) [ -37186.1776] [Alpha ][ 0.521618] . ( 427 sec) [ -37186.1776] [Topology ] . ( 431 sec) [ -37186.1767] [Topology ] . ( 432 sec) [ -37186.1766] [Alpha ][ 0.521096] . ( 432 sec) [ -37186.1766] [Topology ] . ( 436 sec) [ -37186.1757] [Topology ] . ( 437 sec) [ -37186.1757] [Alpha ][ 0.521096] . Checking for NNIs, optimizing five branches... . ( 479 sec) [ -37186.0055] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -37186.005520. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -46228.8378] [Alpha ][ 0.500960] . ( 2 sec) [ -45798.4618] [ 9048] [depth= 8] . ( 3 sec) [ -45578.3777] [ 8973] [depth= 9] . ( 3 sec) [ -45329.0801] [ 8974] [depth= 1] . ( 4 sec) [ -45318.9692] [ 8957] [depth= 2] . ( 4 sec) [ -45200.0157] [ 8944] [depth= 2] . ( 5 sec) [ -44920.2050] [ 8817] [depth= 5] . ( 6 sec) [ -44782.8738] [ 8689] [depth= 4] . ( 6 sec) [ -44654.0917] [ 8646] [depth= 4] . ( 7 sec) [ -44301.4249] [ 8617] [depth= 3] . ( 8 sec) [ -43554.1479] [ 8451] [depth= 4] . ( 8 sec) [ -43224.5325] [ 8429] [depth= 1] . ( 9 sec) [ -43190.8555] [ 8445] [depth= 1] . ( 10 sec) [ -42670.1837] [ 8380] [depth= 2] . ( 12 sec) [ -42584.2550] [ 8367] [depth= 9] . ( 13 sec) [ -42540.2337] [ 8289] [depth= 6] . ( 14 sec) [ -42400.0403] [ 8232] [depth= 1] . ( 14 sec) [ -42078.1459] [ 8212] [depth= 1] . ( 15 sec) [ -42008.3783] [ 8215] [depth= 7] . ( 16 sec) [ -41600.4314] [ 8213] [depth= 1] . ( 17 sec) [ -41408.6178] [ 8213] [depth= 2] . ( 18 sec) [ -40779.6375] [ 8170] [depth= 1] . ( 18 sec) [ -40503.2079] [ 8056] [depth= 7] . ( 19 sec) [ -40499.1694] [ 8052] [depth= 1] . ( 20 sec) [ -40091.8316] [ 7953] [depth= 5] . ( 20 sec) [ -39813.5101] [ 7921] [depth= 3] . ( 21 sec) [ -39596.1144] [ 7908] [depth= 1] . ( 22 sec) [ -39346.6807] [ 7843] [depth= 2] . ( 22 sec) [ -39223.2480] [ 7802] [depth= 2] . ( 23 sec) [ -39096.8475] [ 7769] [depth= 2] . ( 24 sec) [ -39066.9571] [ 7775] [depth= 1] . ( 25 sec) [ -38982.0092] [ 7773] [depth= 2] . ( 25 sec) [ -38891.8342] [ 7776] [depth= 1] . ( 26 sec) [ -38750.2387] [ 7763] [depth= 2] . ( 27 sec) [ -38695.3645] [ 7747] [depth= 1] . ( 27 sec) [ -38664.2341] [ 7735] [depth= 4] . ( 29 sec) [ -38607.5094] [ 7739] [depth= 2] . ( 31 sec) [ -38562.8296] [ 7734] [depth= 1] . ( 31 sec) [ -38449.2316] [ 7734] [depth= 1] . ( 32 sec) [ -38430.1544] [ 7730] [depth= 2] . ( 33 sec) [ -38385.0814] [ 7731] [depth= 1] . ( 34 sec) [ -38380.8030] [ 7730] [depth= 1] . ( 34 sec) [ -38322.2098] [ 7720] [depth= 8] . ( 36 sec) [ -38275.0357] [ 7700] [depth= 3] . ( 37 sec) [ -38261.6391] [ 7698] [depth= 1] . ( 38 sec) [ -38071.4032] [ 7729] [depth= 1] . ( 39 sec) [ -37893.1717] [ 7739] [depth= 5] . ( 40 sec) [ -37858.9893] [ 7709] [depth= 1] . ( 40 sec) [ -37665.1287] [ 7674] [depth= 1] . ( 42 sec) [ -37297.7837] [Branch lengths ] . ( 43 sec) [ -37293.4918] [Alpha ][ 0.556981] . ( 48 sec) [ -37291.9725] [ 7677] [depth= 1] . ( 49 sec) [ -37278.4252] [ 7655] [depth= 2] . ( 51 sec) [ -37264.3501] [ 7644] [depth= 2] . ( 52 sec) [ -37259.7004] [ 7648] [depth= 1] . ( 53 sec) [ -37255.9074] [ 7645] [depth= 3] . ( 54 sec) [ -37251.4505] [ 7647] [depth= 1] . ( 57 sec) [ -37244.9784] [ 7638] [depth= 3] . ( 66 sec) [ -37241.0452] [ 7640] [depth= 1] . ( 68 sec) [ -37229.5752] [ 7644] [depth= 1] . ( 69 sec) [ -37228.8898] [ 7639] [depth= 2] . ( 70 sec) [ -37225.7037] [ 7639] [depth= 1] . ( 71 sec) [ -37222.2972] [ 7643] [depth= 2] . ( 73 sec) [ -37216.1957] [ 7644] [depth= 1] . ( 76 sec) [ -37216.0475] [ 7644] [depth= 1] . ( 77 sec) [ -37214.9191] [ 7638] [depth= 1] . ( 82 sec) [ -37213.0406] [ 7642] [depth= 1] . ( 83 sec) [ -37210.7130] [ 7643] [depth= 1] . ( 84 sec) [ -37193.7057] [Branch lengths ] . ( 85 sec) [ -37193.6493] [Alpha ][ 0.549910] . ( 111 sec) [ -37193.5566] [ 7642] [depth= 1] . ( 121 sec) [ -37192.1507] [ 7644] [depth= 1] . ( 140 sec) [ -37188.8215] [Branch lengths ] . ( 141 sec) [ -37188.7783] [Alpha ][ 0.543785] . ( 152 sec) [ -37188.5209] [ 7645] [depth= 1] . ( 201 sec) [ -37187.7758] [Branch lengths ] . ( 202 sec) [ -37187.7383] [Alpha ][ 0.538135] . ( 261 sec) [ -37187.4945] [Branch lengths ] . ( 262 sec) [ -37187.4945] [Topology ] . ( 265 sec) [ -37187.4519] [Topology ] . ( 269 sec) [ -37187.4313] [Topology ] . ( 273 sec) [ -37187.4179] [Topology ] . ( 277 sec) [ -37187.4086] [Topology ] . ( 281 sec) [ -37187.4018] [Topology ] . ( 284 sec) [ -37187.3967] [Topology ] . ( 285 sec) [ -37187.3343] [Alpha ][ 0.530949] . ( 285 sec) [ -37187.3343] [Topology ] . ( 289 sec) [ -37187.3006] [Topology ] . ( 293 sec) [ -37187.2880] [Topology ] . ( 297 sec) [ -37187.2819] [Topology ] . ( 301 sec) [ -37187.2786] [Topology ] . ( 304 sec) [ -37187.2765] [Topology ] . ( 308 sec) [ -37187.2751] [Topology ] . ( 309 sec) [ -37187.2512] [Alpha ][ 0.526528] . ( 309 sec) [ -37187.2512] [Topology ] . ( 313 sec) [ -37187.2370] [Topology ] . ( 317 sec) [ -37187.2319] [Topology ] . ( 321 sec) [ -37187.2295] [Topology ] . ( 324 sec) [ -37187.2283] [Topology ] . ( 328 sec) [ -37187.2276] [Topology ] . ( 329 sec) [ -37187.2166] [Alpha ][ 0.523540] . ( 329 sec) [ -37187.2166] [Topology ] . ( 333 sec) [ -37187.2099] [Topology ] . ( 337 sec) [ -37187.2076] [Topology ] . ( 341 sec) [ -37187.2066] [Topology ] . ( 345 sec) [ -37187.2061] [Topology ] . ( 345 sec) [ -37187.2019] [Alpha ][ 0.521689] . ( 346 sec) [ -37187.2019] [Topology ] . ( 350 sec) [ -37187.1988] [Topology ] . ( 353 sec) [ -37187.1976] [Topology ] . ( 357 sec) [ -37187.1971] [Topology ] . ( 358 sec) [ -37187.1953] [Alpha ][ 0.520433] . ( 358 sec) [ -37187.1953] [Topology ] . ( 362 sec) [ -37187.1935] [Topology ] . ( 366 sec) [ -37187.1928] [Topology ] . ( 366 sec) [ -37187.1923] [Alpha ][ 0.519724] . ( 367 sec) [ -37187.1923] [Topology ] . ( 371 sec) [ -37187.1912] [Topology ] . ( 374 sec) [ -37187.1908] [Topology ] . ( 375 sec) [ -37187.1905] [Alpha ][ 0.519183] . ( 375 sec) [ -37187.1905] [Topology ] . ( 379 sec) [ -37187.1899] [Topology ] . ( 380 sec) [ -37187.1899] [Alpha ][ 0.518663] . Checking for NNIs, optimizing five branches... . ( 423 sec) [ -37186.7414] [Topology ] . Checking for NNIs, optimizing five branches... . ( 468 sec) [ -37186.3104] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -37186.310410. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -44869.5978] [Alpha ][ 0.500960] . ( 2 sec) [ -44398.6848] [ 8940] [depth= 5] . ( 3 sec) [ -44229.2230] [ 8862] [depth= 8] . ( 3 sec) [ -43858.2602] [ 8762] [depth= 3] . ( 4 sec) [ -43504.0699] [ 8724] [depth= 5] . ( 5 sec) [ -43321.3505] [ 8639] [depth= 1] . ( 6 sec) [ -43165.0600] [ 8600] [depth= 3] . ( 7 sec) [ -42626.0683] [ 8470] [depth= 3] . ( 7 sec) [ -42322.3582] [ 8444] [depth= 1] . ( 8 sec) [ -42089.4770] [ 8318] [depth= 8] . ( 9 sec) [ -42023.5649] [ 8323] [depth= 1] . ( 9 sec) [ -41952.6393] [ 8312] [depth= 9] . ( 11 sec) [ -41943.7504] [ 8316] [depth= 1] . ( 12 sec) [ -41943.5349] [ 8338] [depth= 2] . ( 12 sec) [ -41938.8550] [ 8335] [depth= 5] . ( 13 sec) [ -41889.6565] [ 8325] [depth= 2] . ( 14 sec) [ -41717.4698] [ 8251] [depth= 3] . ( 15 sec) [ -41503.7519] [ 8206] [depth= 4] . ( 15 sec) [ -41206.9183] [ 8173] [depth= 2] . ( 16 sec) [ -40904.2680] [ 8115] [depth= 6] . ( 17 sec) [ -40544.1128] [ 8019] [depth= 8] . ( 17 sec) [ -40336.6380] [ 8025] [depth= 1] . ( 18 sec) [ -40086.9015] [ 8025] [depth= 1] . ( 19 sec) [ -39785.9899] [ 7978] [depth= 2] . ( 19 sec) [ -39755.3228] [ 7972] [depth= 1] . ( 20 sec) [ -39688.4116] [ 7988] [depth= 3] . ( 21 sec) [ -39617.4181] [ 7968] [depth= 1] . ( 22 sec) [ -39592.0360] [ 7966] [depth= 2] . ( 22 sec) [ -39524.1310] [ 7929] [depth= 3] . ( 23 sec) [ -39500.5699] [ 7928] [depth= 10] . ( 24 sec) [ -39445.5155] [ 7924] [depth= 1] . ( 24 sec) [ -39219.5440] [ 7902] [depth= 3] . ( 25 sec) [ -38729.8453] [ 7846] [depth= 3] . ( 26 sec) [ -38718.3486] [ 7851] [depth= 1] . ( 27 sec) [ -38705.1562] [ 7818] [depth= 3] . ( 28 sec) [ -38615.7197] [ 7790] [depth= 2] . ( 28 sec) [ -38471.5488] [ 7754] [depth= 2] . ( 29 sec) [ -38307.0275] [ 7768] [depth= 1] . ( 30 sec) [ -38275.3442] [ 7768] [depth= 1] . ( 31 sec) [ -38270.2027] [ 7741] [depth= 1] . ( 32 sec) [ -38223.4234] [ 7751] [depth= 1] . ( 33 sec) [ -38205.6293] [ 7741] [depth= 1] . ( 33 sec) [ -38178.8385] [ 7724] [depth= 1] . ( 34 sec) [ -38117.1848] [ 7716] [depth= 1] . ( 35 sec) [ -38102.8044] [ 7718] [depth= 1] . ( 35 sec) [ -38096.4288] [ 7715] [depth= 1] . ( 36 sec) [ -38024.5390] [ 7718] [depth= 1] . ( 37 sec) [ -38018.3920] [ 7718] [depth= 1] . ( 38 sec) [ -38008.0524] [ 7712] [depth= 1] . ( 38 sec) [ -38000.6309] [ 7702] [depth= 2] . ( 40 sec) [ -37964.4761] [ 7698] [depth= 3] . ( 40 sec) [ -37945.5086] [ 7699] [depth= 1] . ( 41 sec) [ -37890.6592] [ 7697] [depth= 2] . ( 42 sec) [ -37883.7627] [ 7695] [depth= 7] . ( 43 sec) [ -37872.6475] [ 7703] [depth= 1] . ( 43 sec) [ -37762.4114] [ 7707] [depth= 4] . ( 44 sec) [ -37731.6554] [ 7697] [depth= 5] . ( 46 sec) [ -37415.1537] [Branch lengths ] . ( 47 sec) [ -37414.5440] [Alpha ][ 0.521673] . ( 49 sec) [ -37404.2183] [ 7687] [depth= 2] . ( 49 sec) [ -37396.0362] [ 7674] [depth= 1] . ( 50 sec) [ -37350.3406] [ 7655] [depth= 1] . ( 51 sec) [ -37342.2381] [ 7652] [depth= 1] . ( 52 sec) [ -37305.7641] [ 7642] [depth= 4] . ( 55 sec) [ -37304.8327] [ 7643] [depth= 2] . ( 61 sec) [ -37304.4903] [ 7647] [depth= 1] . ( 65 sec) [ -37300.9981] [ 7646] [depth= 1] . ( 68 sec) [ -37295.2505] [ 7636] [depth= 1] . ( 70 sec) [ -37293.6187] [ 7632] [depth= 1] . ( 72 sec) [ -37291.5206] [ 7636] [depth= 1] . ( 73 sec) [ -37286.9203] [ 7642] [depth= 1] . ( 74 sec) [ -37283.8843] [ 7645] [depth= 1] . ( 75 sec) [ -37279.5941] [ 7642] [depth= 1] . ( 76 sec) [ -37274.1803] [ 7645] [depth= 1] . ( 78 sec) [ -37273.6471] [ 7642] [depth= 1] . ( 80 sec) [ -37273.3291] [ 7645] [depth= 1] . ( 81 sec) [ -37273.3167] [ 7644] [depth= 1] . ( 86 sec) [ -37272.8187] [ 7640] [depth= 1] . ( 88 sec) [ -37270.1100] [ 7639] [depth= 5] . ( 89 sec) [ -37256.8947] [ 7641] [depth= 1] . ( 91 sec) [ -37215.6925] [Branch lengths ] . ( 92 sec) [ -37215.6564] [Alpha ][ 0.516335] . ( 98 sec) [ -37214.3592] [ 7639] [depth= 1] . ( 111 sec) [ -37214.1930] [ 7643] [depth= 1] . ( 118 sec) [ -37211.5830] [ 7634] [depth= 1] . ( 125 sec) [ -37208.2187] [ 7637] [depth= 1] . ( 135 sec) [ -37207.2128] [ 7640] [depth= 2] . ( 135 sec) [ -37198.6533] [ 7646] [depth= 1] . ( 142 sec) [ -37197.5988] [ 7647] [depth= 1] . ( 144 sec) [ -37188.2533] [Branch lengths ] . ( 145 sec) [ -37188.2223] [Alpha ][ 0.521153] . ( 210 sec) [ -37186.7645] [Branch lengths ] . ( 210 sec) [ -37186.7645] [Topology ] . ( 214 sec) [ -37186.6607] [Topology ] . ( 217 sec) [ -37186.6330] [Topology ] . ( 221 sec) [ -37186.6209] [Topology ] . ( 225 sec) [ -37186.6150] [Topology ] . ( 229 sec) [ -37186.6120] [Topology ] . ( 233 sec) [ -37186.6103] [Topology ] . ( 233 sec) [ -37186.6101] [Alpha ][ 0.520632] . ( 234 sec) [ -37186.6101] [Topology ] . ( 238 sec) [ -37186.6089] [Topology ] . ( 241 sec) [ -37186.6083] [Topology ] . ( 242 sec) [ -37186.6083] [Alpha ][ 0.520632] . ( 242 sec) [ -37186.6083] [Topology ] . ( 246 sec) [ -37186.6080] [Topology ] . ( 247 sec) [ -37186.6080] [Alpha ][ 0.520632] . Checking for NNIs, optimizing five branches... . ( 287 sec) [ -37186.4667] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -37186.466740. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -44995.7341] [Alpha ][ 0.500960] . ( 3 sec) [ -44387.6249] [ 8898] [depth= 9] . ( 3 sec) [ -44227.9225] [ 8841] [depth= 10] . ( 4 sec) [ -44127.4376] [ 8814] [depth= 1] . ( 5 sec) [ -43812.6601] [ 8822] [depth= 6] . ( 5 sec) [ -43326.3215] [ 8627] [depth= 2] . ( 6 sec) [ -43025.5805] [ 8551] [depth= 5] . ( 6 sec) [ -42862.6949] [ 8501] [depth= 2] . ( 7 sec) [ -41861.9633] [ 8487] [depth= 1] . ( 8 sec) [ -41468.3688] [ 8445] [depth= 4] . ( 8 sec) [ -41190.7477] [ 8384] [depth= 2] . ( 9 sec) [ -40765.0212] [ 8316] [depth= 4] . ( 11 sec) [ -40688.2546] [ 8316] [depth= 1] . ( 11 sec) [ -40567.3505] [ 8307] [depth= 3] . ( 12 sec) [ -40316.7710] [ 8232] [depth= 2] . ( 13 sec) [ -40003.4796] [ 8128] [depth= 4] . ( 13 sec) [ -39871.9877] [ 8124] [depth= 1] . ( 14 sec) [ -39815.5644] [ 8106] [depth= 11] . ( 15 sec) [ -39736.7395] [ 8092] [depth= 2] . ( 16 sec) [ -39633.6723] [ 8065] [depth= 3] . ( 16 sec) [ -39426.3025] [ 7942] [depth= 3] . ( 17 sec) [ -39371.4230] [ 7930] [depth= 1] . ( 18 sec) [ -39269.1560] [ 7907] [depth= 3] . ( 19 sec) [ -39259.1549] [ 7889] [depth= 3] . ( 20 sec) [ -39245.3471] [ 7894] [depth= 1] . ( 22 sec) [ -39244.2849] [ 7888] [depth= 1] . ( 22 sec) [ -39117.3845] [ 7880] [depth= 1] . ( 23 sec) [ -39084.4920] [ 7873] [depth= 1] . ( 24 sec) [ -38948.8718] [ 7866] [depth= 1] . ( 25 sec) [ -38920.2940] [ 7865] [depth= 1] . ( 26 sec) [ -38915.6424] [ 7863] [depth= 1] . ( 26 sec) [ -38914.4417] [ 7865] [depth= 1] . ( 27 sec) [ -38910.6395] [ 7865] [depth= 1] . ( 29 sec) [ -38902.2938] [ 7839] [depth= 3] . ( 30 sec) [ -38654.3814] [ 7829] [depth= 5] . ( 31 sec) [ -38584.6030] [ 7810] [depth= 1] . ( 31 sec) [ -38566.5385] [ 7811] [depth= 1] . ( 32 sec) [ -38544.4834] [ 7800] [depth= 2] . ( 33 sec) [ -38539.5811] [ 7805] [depth= 1] . ( 34 sec) [ -38532.7093] [ 7805] [depth= 2] . ( 35 sec) [ -38517.5045] [ 7809] [depth= 1] . ( 36 sec) [ -38509.2100] [ 7810] [depth= 4] . ( 37 sec) [ -38505.9227] [ 7805] [depth= 1] . ( 38 sec) [ -38179.4546] [ 7799] [depth= 2] . ( 39 sec) [ -38178.1636] [ 7792] [depth= 1] . ( 39 sec) [ -37846.4032] [ 7688] [depth= 2] . ( 40 sec) [ -37797.9308] [ 7675] [depth= 2] . ( 41 sec) [ -37788.6175] [ 7679] [depth= 1] . ( 42 sec) [ -37784.6948] [ 7685] [depth= 1] . ( 42 sec) [ -37779.2065] [ 7682] [depth= 1] . ( 43 sec) [ -37748.3696] [ 7698] [depth= 1] . ( 44 sec) [ -37743.9485] [ 7688] [depth= 2] . ( 45 sec) [ -37686.1345] [ 7674] [depth= 1] . ( 45 sec) [ -37683.6354] [ 7666] [depth= 1] . ( 47 sec) [ -37402.6302] [Branch lengths ] . ( 48 sec) [ -37400.0155] [Alpha ][ 0.544478] . ( 49 sec) [ -37399.0699] [ 7662] [depth= 1] . ( 57 sec) [ -37393.1107] [ 7659] [depth= 1] . ( 58 sec) [ -37369.6820] [ 7637] [depth= 3] . ( 59 sec) [ -37366.5769] [ 7651] [depth= 1] . ( 60 sec) [ -37365.5321] [ 7655] [depth= 1] . ( 61 sec) [ -37363.0514] [ 7648] [depth= 1] . ( 68 sec) [ -37362.9296] [ 7649] [depth= 1] . ( 68 sec) [ -37361.8847] [ 7645] [depth= 2] . ( 70 sec) [ -37359.2195] [ 7648] [depth= 1] . ( 72 sec) [ -37355.2672] [ 7647] [depth= 2] . ( 76 sec) [ -37335.7142] [ 7634] [depth= 1] . ( 79 sec) [ -37309.5643] [ 7630] [depth= 1] . ( 80 sec) [ -37287.8046] [ 7639] [depth= 1] . ( 81 sec) [ -37280.7796] [ 7622] [depth= 2] . ( 84 sec) [ -37268.7981] [ 7631] [depth= 1] . ( 87 sec) [ -37222.1898] [Branch lengths ] . ( 87 sec) [ -37222.1660] [Alpha ][ 0.539948] . ( 90 sec) [ -37216.4757] [ 7631] [depth= 2] . ( 92 sec) [ -37216.1104] [ 7633] [depth= 1] . ( 96 sec) [ -37214.1727] [ 7635] [depth= 1] . ( 97 sec) [ -37213.0488] [ 7637] [depth= 1] . ( 118 sec) [ -37210.2987] [ 7650] [depth= 1] . ( 121 sec) [ -37210.2050] [ 7653] [depth= 1] . ( 122 sec) [ -37203.9883] [ 7643] [depth= 2] . ( 131 sec) [ -37189.8616] [Branch lengths ] . ( 132 sec) [ -37189.8583] [Alpha ][ 0.541535] . ( 144 sec) [ -37189.7083] [ 7644] [depth= 1] . ( 189 sec) [ -37186.8462] [Branch lengths ] . ( 190 sec) [ -37186.8298] [Alpha ][ 0.537793] . ( 247 sec) [ -37186.4111] [Branch lengths ] . ( 247 sec) [ -37186.4111] [Topology ] . ( 251 sec) [ -37186.3612] [Topology ] . ( 255 sec) [ -37186.3439] [Topology ] . ( 259 sec) [ -37186.3360] [Topology ] . ( 263 sec) [ -37186.3319] [Topology ] . ( 267 sec) [ -37186.3296] [Topology ] . ( 270 sec) [ -37186.3282] [Topology ] . ( 271 sec) [ -37186.2785] [Alpha ][ 0.531370] . ( 272 sec) [ -37186.2785] [Topology ] . ( 275 sec) [ -37186.2534] [Topology ] . ( 279 sec) [ -37186.2453] [Topology ] . ( 283 sec) [ -37186.2420] [Topology ] . ( 287 sec) [ -37186.2405] [Topology ] . ( 291 sec) [ -37186.2398] [Topology ] . ( 292 sec) [ -37186.2202] [Alpha ][ 0.527358] . ( 292 sec) [ -37186.2202] [Topology ] . ( 296 sec) [ -37186.2089] [Topology ] . ( 300 sec) [ -37186.2053] [Topology ] . ( 304 sec) [ -37186.2039] [Topology ] . ( 308 sec) [ -37186.2033] [Topology ] . ( 308 sec) [ -37186.1961] [Alpha ][ 0.524913] . ( 309 sec) [ -37186.1961] [Topology ] . ( 313 sec) [ -37186.1909] [Topology ] . ( 317 sec) [ -37186.1892] [Topology ] . ( 320 sec) [ -37186.1885] [Topology ] . ( 321 sec) [ -37186.1854] [Alpha ][ 0.523299] . ( 321 sec) [ -37186.1854] [Topology ] . ( 325 sec) [ -37186.1825] [Topology ] . ( 329 sec) [ -37186.1816] [Topology ] . ( 330 sec) [ -37186.1806] [Alpha ][ 0.522384] . ( 330 sec) [ -37186.1806] [Topology ] . ( 334 sec) [ -37186.1790] [Topology ] . ( 338 sec) [ -37186.1784] [Topology ] . ( 339 sec) [ -37186.1779] [Alpha ][ 0.521690] . ( 339 sec) [ -37186.1779] [Topology ] . ( 343 sec) [ -37186.1769] [Topology ] . ( 344 sec) [ -37186.1768] [Alpha ][ 0.521168] . ( 344 sec) [ -37186.1768] [Topology ] . ( 348 sec) [ -37186.1759] [Topology ] . ( 348 sec) [ -37186.1759] [Alpha ][ 0.521168] . Checking for NNIs, optimizing five branches... . ( 389 sec) [ -37186.0052] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -37186.005234. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -46140.3565] [Alpha ][ 0.500960] . ( 3 sec) [ -45244.4505] [ 9073] [depth= 10] . ( 3 sec) [ -44930.4676] [ 9027] [depth= 4] . ( 4 sec) [ -44431.8535] [ 9037] [depth= 6] . ( 4 sec) [ -44301.3709] [ 8897] [depth= 1] . ( 5 sec) [ -43441.6050] [ 8776] [depth= 5] . ( 6 sec) [ -43150.9149] [ 8768] [depth= 1] . ( 6 sec) [ -42872.1296] [ 8670] [depth= 1] . ( 7 sec) [ -42824.8259] [ 8669] [depth= 2] . ( 8 sec) [ -42718.5305] [ 8636] [depth= 1] . ( 9 sec) [ -42652.7770] [ 8582] [depth= 2] . ( 9 sec) [ -42590.5917] [ 8567] [depth= 1] . ( 10 sec) [ -42548.5555] [ 8577] [depth= 1] . ( 11 sec) [ -42201.7859] [ 8496] [depth= 2] . ( 11 sec) [ -42053.8707] [ 8435] [depth= 2] . ( 12 sec) [ -42043.2363] [ 8421] [depth= 11] . ( 13 sec) [ -41561.7615] [ 8391] [depth= 8] . ( 13 sec) [ -41304.0540] [ 8387] [depth= 1] . ( 14 sec) [ -41196.6456] [ 8380] [depth= 2] . ( 15 sec) [ -41136.4783] [ 8376] [depth= 1] . ( 16 sec) [ -41052.2385] [ 8381] [depth= 2] . ( 16 sec) [ -41026.2743] [ 8375] [depth= 1] . ( 17 sec) [ -40951.2850] [ 8357] [depth= 10] . ( 18 sec) [ -40805.3516] [ 8251] [depth= 9] . ( 19 sec) [ -40643.3861] [ 8177] [depth= 2] . ( 20 sec) [ -40508.6876] [ 8137] [depth= 5] . ( 21 sec) [ -39886.1477] [ 8000] [depth= 2] . ( 22 sec) [ -39871.5104] [ 7959] [depth= 2] . ( 23 sec) [ -39743.1461] [ 7922] [depth= 3] . ( 23 sec) [ -39597.1065] [ 7844] [depth= 2] . ( 24 sec) [ -39477.1650] [ 7813] [depth= 1] . ( 25 sec) [ -39124.6786] [ 7775] [depth= 7] . ( 26 sec) [ -39111.0658] [ 7746] [depth= 4] . ( 26 sec) [ -39094.0251] [ 7753] [depth= 1] . ( 28 sec) [ -39060.9987] [ 7757] [depth= 2] . ( 29 sec) [ -38956.1075] [ 7744] [depth= 3] . ( 29 sec) [ -38814.2199] [ 7737] [depth= 1] . ( 30 sec) [ -38779.7021] [ 7733] [depth= 2] . ( 31 sec) [ -38588.0435] [ 7739] [depth= 2] . ( 32 sec) [ -38585.7078] [ 7733] [depth= 1] . ( 33 sec) [ -38402.6583] [ 7742] [depth= 1] . ( 34 sec) [ -38342.7253] [ 7732] [depth= 1] . ( 34 sec) [ -38292.3871] [ 7724] [depth= 2] . ( 35 sec) [ -38237.4038] [ 7728] [depth= 1] . ( 36 sec) [ -38172.5571] [ 7734] [depth= 1] . ( 36 sec) [ -38162.2551] [ 7729] [depth= 2] . ( 37 sec) [ -38083.3521] [ 7730] [depth= 2] . ( 37 sec) [ -38076.0866] [ 7730] [depth= 1] . ( 38 sec) [ -38062.8472] [ 7730] [depth= 1] . ( 39 sec) [ -37806.6325] [ 7660] [depth= 2] . ( 40 sec) [ -37735.1730] [ 7661] [depth= 2] . ( 40 sec) [ -37700.8709] [ 7661] [depth= 1] . ( 41 sec) [ -37698.3257] [ 7654] [depth= 1] . ( 42 sec) [ -37674.8910] [ 7647] [depth= 4] . ( 43 sec) [ -37673.7300] [ 7650] [depth= 2] . ( 43 sec) [ -37642.1469] [ 7649] [depth= 1] . ( 45 sec) [ -37342.9767] [Branch lengths ] . ( 46 sec) [ -37323.4654] [Alpha ][ 0.626600] . ( 48 sec) [ -37319.0623] [ 7654] [depth= 1] . ( 50 sec) [ -37315.0226] [ 7655] [depth= 1] . ( 56 sec) [ -37312.4323] [ 7653] [depth= 4] . ( 61 sec) [ -37309.1991] [ 7640] [depth= 1] . ( 63 sec) [ -37269.1189] [ 7650] [depth= 1] . ( 64 sec) [ -37263.2453] [ 7650] [depth= 1] . ( 69 sec) [ -37259.5544] [ 7647] [depth= 1] . ( 71 sec) [ -37257.2245] [ 7648] [depth= 1] . ( 72 sec) [ -37253.6153] [ 7649] [depth= 1] . ( 74 sec) [ -37231.4339] [ 7635] [depth= 2] . ( 76 sec) [ -37227.3693] [ 7633] [depth= 1] . ( 85 sec) [ -37227.1946] [ 7638] [depth= 1] . ( 89 sec) [ -37202.0187] [Branch lengths ] . ( 90 sec) [ -37200.9982] [Alpha ][ 0.594620] . ( 99 sec) [ -37199.5158] [ 7634] [depth= 5] . ( 113 sec) [ -37199.1254] [ 7638] [depth= 1] . ( 133 sec) [ -37192.4497] [Branch lengths ] . ( 134 sec) [ -37192.1461] [Alpha ][ 0.577981] . ( 160 sec) [ -37191.8634] [ 7641] [depth= 1] . ( 185 sec) [ -37188.6169] [Branch lengths ] . ( 186 sec) [ -37188.5022] [Alpha ][ 0.568170] . ( 237 sec) [ -37187.7728] [Branch lengths ] . ( 237 sec) [ -37187.7728] [Topology ] . ( 241 sec) [ -37187.6920] [Topology ] . ( 245 sec) [ -37187.6659] [Topology ] . ( 248 sec) [ -37187.6552] [Topology ] . ( 252 sec) [ -37187.6504] [Topology ] . ( 256 sec) [ -37187.6480] [Topology ] . ( 260 sec) [ -37187.6468] [Topology ] . ( 261 sec) [ -37187.3592] [Alpha ][ 0.552672] . ( 261 sec) [ -37187.3592] [Topology ] . ( 265 sec) [ -37187.2352] [Topology ] . ( 268 sec) [ -37187.1932] [Topology ] . ( 272 sec) [ -37187.1758] [Topology ] . ( 276 sec) [ -37187.1683] [Topology ] . ( 280 sec) [ -37187.1649] [Topology ] . ( 283 sec) [ -37187.1634] [Topology ] . ( 284 sec) [ -37187.0523] [Alpha ][ 0.543427] . ( 285 sec) [ -37187.0523] [Topology ] . ( 288 sec) [ -37186.9989] [Topology ] . ( 292 sec) [ -37186.9806] [Topology ] . ( 296 sec) [ -37186.9731] [Topology ] . ( 300 sec) [ -37186.9698] [Topology ] . ( 303 sec) [ -37186.9684] [Topology ] . ( 307 sec) [ -37186.9677] [Topology ] . ( 308 sec) [ -37186.9160] [Alpha ][ 0.536822] . ( 308 sec) [ -37186.9160] [Topology ] . ( 312 sec) [ -37186.8880] [Topology ] . ( 316 sec) [ -37186.8785] [Topology ] . ( 320 sec) [ -37186.8746] [Topology ] . ( 323 sec) [ -37186.8730] [Topology ] . ( 327 sec) [ -37186.8723] [Topology ] . ( 328 sec) [ -37186.8503] [Alpha ][ 0.532534] . ( 328 sec) [ -37186.8503] [Topology ] . ( 332 sec) [ -37186.8372] [Topology ] . ( 336 sec) [ -37186.8327] [Topology ] . ( 340 sec) [ -37186.8309] [Topology ] . ( 343 sec) [ -37186.8301] [Topology ] . ( 344 sec) [ -37186.8214] [Alpha ][ 0.529845] . ( 344 sec) [ -37186.8214] [Topology ] . ( 348 sec) [ -37186.8150] [Topology ] . ( 352 sec) [ -37186.8128] [Topology ] . ( 356 sec) [ -37186.8119] [Topology ] . ( 357 sec) [ -37186.8081] [Alpha ][ 0.528049] . ( 357 sec) [ -37186.8081] [Topology ] . ( 361 sec) [ -37186.8045] [Topology ] . ( 364 sec) [ -37186.8033] [Topology ] . ( 368 sec) [ -37186.8027] [Topology ] . ( 369 sec) [ -37186.8009] [Alpha ][ 0.526777] . ( 369 sec) [ -37186.8009] [Topology ] . ( 373 sec) [ -37186.7990] [Topology ] . ( 377 sec) [ -37186.7983] [Topology ] . ( 377 sec) [ -37186.7977] [Alpha ][ 0.526017] . ( 378 sec) [ -37186.7977] [Topology ] . ( 381 sec) [ -37186.7965] [Topology ] . ( 385 sec) [ -37186.7961] [Topology ] . ( 386 sec) [ -37186.7957] [Alpha ][ 0.525424] . ( 386 sec) [ -37186.7957] [Topology ] . ( 390 sec) [ -37186.7950] [Topology ] . ( 391 sec) [ -37186.7949] [Alpha ][ 0.524899] . Checking for NNIs, optimizing five branches... . ( 431 sec) [ -37186.2565] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -37186.256534. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -37472.1429] [Alpha ][ 0.689004] . ( 1 sec) [ -37472.1429] [Topology ] . ( 5 sec) [ -37275.6590] [Topology ] . ( 10 sec) [ -37238.0253] [Topology ] . ( 14 sec) [ -37217.8995] [Topology ] . ( 18 sec) [ -37208.1468] [Topology ] . ( 22 sec) [ -37203.9396] [Topology ] . ( 26 sec) [ -37202.1545] [Topology ] . ( 29 sec) [ -37201.0720] [Topology ] . ( 33 sec) [ -37200.4740] [Topology ] . ( 37 sec) [ -37200.0690] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -37199.5484] [Topology ] . ( 88 sec) [ -37194.7954] [Alpha ][ 0.615575] . ( 88 sec) [ -37194.7954] [Topology ] . ( 92 sec) [ -37193.2255] [Topology ] . ( 96 sec) [ -37192.6086] [Topology ] . ( 99 sec) [ -37192.3151] [Topology ] . ( 103 sec) [ -37192.1739] [Topology ] . ( 107 sec) [ -37192.1057] [Topology ] . ( 110 sec) [ -37192.0724] [Topology ] . Checking for NNIs, optimizing five branches... . ( 157 sec) [ -37190.4841] [Topology ] . ( 158 sec) [ -37189.3523] [Alpha ][ 0.582519] . ( 158 sec) [ -37189.3523] [Topology ] . ( 162 sec) [ -37188.8012] [Topology ] . ( 166 sec) [ -37188.5915] [Topology ] . ( 170 sec) [ -37188.4981] [Topology ] . ( 173 sec) [ -37188.4556] [Topology ] . ( 177 sec) [ -37188.4359] [Topology ] . ( 181 sec) [ -37188.4268] [Topology ] . Checking for NNIs, optimizing five branches... . ( 226 sec) [ -37188.2745] [Topology ] . ( 227 sec) [ -37187.8143] [Alpha ][ 0.562381] . ( 227 sec) [ -37187.8143] [Topology ] . ( 231 sec) [ -37187.5885] [Topology ] . ( 235 sec) [ -37187.5065] [Topology ] . ( 239 sec) [ -37187.4714] [Topology ] . ( 243 sec) [ -37187.4558] [Topology ] . ( 246 sec) [ -37187.4488] [Topology ] . ( 250 sec) [ -37187.4456] [Topology ] . Checking for NNIs, optimizing five branches... . ( 293 sec) [ -37186.8870] [Topology ] . ( 294 sec) [ -37186.6924] [Alpha ][ 0.549816] . ( 294 sec) [ -37186.6924] [Topology ] . ( 298 sec) [ -37186.5943] [Topology ] . ( 302 sec) [ -37186.5621] [Topology ] . ( 305 sec) [ -37186.5489] [Topology ] . ( 309 sec) [ -37186.5432] [Topology ] . ( 313 sec) [ -37186.5406] [Topology ] . ( 317 sec) [ -37186.5394] [Topology ] . Checking for NNIs, optimizing five branches... . ( 359 sec) [ -37186.4530] [Alpha ][ 0.541753] . ( 360 sec) [ -37186.4530] [Topology ] . ( 363 sec) [ -37186.4112] [Topology ] . ( 367 sec) [ -37186.3977] [Topology ] . ( 371 sec) [ -37186.3922] [Topology ] . ( 375 sec) [ -37186.3898] [Topology ] . ( 379 sec) [ -37186.3887] [Topology ] . ( 382 sec) [ -37186.3881] [Topology ] . Checking for NNIs, optimizing five branches... . ( 425 sec) [ -37186.3475] [Alpha ][ 0.535906] . ( 425 sec) [ -37186.3475] [Topology ] . ( 429 sec) [ -37186.3251] [Topology ] . ( 433 sec) [ -37186.3179] [Topology ] . ( 437 sec) [ -37186.3151] [Topology ] . ( 441 sec) [ -37186.3138] [Topology ] . ( 444 sec) [ -37186.3132] [Topology ] . Checking for NNIs, optimizing five branches... . ( 487 sec) [ -37186.2960] [Alpha ][ 0.532112] . ( 487 sec) [ -37186.2960] [Topology ] . ( 491 sec) [ -37186.2855] [Topology ] . ( 495 sec) [ -37186.2821] [Topology ] . ( 499 sec) [ -37186.2808] [Topology ] . ( 502 sec) [ -37186.2802] [Topology ] . Checking for NNIs, optimizing five branches... . ( 545 sec) [ -37186.2733] [Alpha ][ 0.529697] . ( 545 sec) [ -37186.2733] [Topology ] . ( 549 sec) [ -37186.2682] [Topology ] . ( 553 sec) [ -37186.2664] [Topology ] . ( 557 sec) [ -37186.2657] [Topology ] . Checking for NNIs, optimizing five branches... . ( 599 sec) [ -37186.2628] [Alpha ][ 0.528126] . ( 600 sec) [ -37186.2628] [Topology ] . ( 603 sec) [ -37186.2601] [Topology ] . ( 607 sec) [ -37186.2591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 650 sec) [ -37186.2582] [Alpha ][ 0.527204] . ( 650 sec) [ -37186.2582] [Topology ] . ( 654 sec) [ -37186.2565] [Topology ] . ( 658 sec) [ -37186.2559] [Topology ] . Checking for NNIs, optimizing five branches... . ( 700 sec) [ -37186.2554] [Alpha ][ 0.526493] . ( 700 sec) [ -37186.2554] [Topology ] . ( 704 sec) [ -37186.2544] [Topology ] . ( 708 sec) [ -37186.2540] [Topology ] . Checking for NNIs, optimizing five branches... . ( 750 sec) [ -37186.2537] [Alpha ][ 0.525939] . ( 750 sec) [ -37186.2537] [Topology ] . ( 754 sec) [ -37186.2530] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 839 sec) [ -37472.1429] [Alpha ][ 0.689004] . ( 841 sec) [ -37441.7027] [ 7658] [depth= 1] . ( 842 sec) [ -37425.7851] [ 7666] [depth= 1] . ( 845 sec) [ -37424.7015] [ 7669] [depth= 1] . ( 848 sec) [ -37395.6519] [ 7666] [depth= 1] . ( 850 sec) [ -37395.0472] [ 7667] [depth= 2] . ( 852 sec) [ -37390.6364] [ 7666] [depth= 1] . ( 857 sec) [ -37369.2911] [ 7662] [depth= 2] . ( 858 sec) [ -37358.2377] [ 7651] [depth= 1] . ( 859 sec) [ -37357.1536] [ 7644] [depth= 1] . ( 860 sec) [ -37353.8751] [ 7645] [depth= 1] . ( 863 sec) [ -37350.7777] [ 7648] [depth= 1] . ( 865 sec) [ -37344.0683] [ 7652] [depth= 2] . ( 866 sec) [ -37341.7529] [ 7650] [depth= 1] . ( 867 sec) [ -37340.7846] [ 7645] [depth= 2] . ( 868 sec) [ -37329.8233] [ 7640] [depth= 1] . ( 869 sec) [ -37328.9733] [ 7631] [depth= 1] . ( 871 sec) [ -37324.1842] [ 7636] [depth= 1] . ( 872 sec) [ -37312.8221] [ 7631] [depth= 1] . ( 873 sec) [ -37308.1170] [ 7632] [depth= 1] . ( 874 sec) [ -37303.7814] [ 7638] [depth= 1] . ( 880 sec) [ -37234.4286] [Branch lengths ] . ( 881 sec) [ -37233.5684] [Alpha ][ 0.656739] . ( 891 sec) [ -37230.5585] [ 7641] [depth= 1] . ( 899 sec) [ -37227.8388] [ 7637] [depth= 1] . ( 900 sec) [ -37225.8700] [ 7644] [depth= 1] . ( 901 sec) [ -37221.8936] [ 7644] [depth= 2] . ( 906 sec) [ -37220.5523] [ 7649] [depth= 1] . ( 907 sec) [ -37216.6040] [ 7644] [depth= 1] . ( 913 sec) [ -37215.3248] [ 7645] [depth= 5] . ( 921 sec) [ -37214.2668] [ 7646] [depth= 1] . ( 925 sec) [ -37198.6436] [Branch lengths ] . ( 926 sec) [ -37197.7183] [Alpha ][ 0.624943] . ( 986 sec) [ -37193.2540] [Branch lengths ] . ( 986 sec) [ -37193.2540] [Topology ] . ( 990 sec) [ -37192.4330] [Topology ] . ( 994 sec) [ -37192.0789] [Topology ] . ( 998 sec) [ -37191.8886] [Topology ] . ( 1002 sec) [ -37191.7808] [Topology ] . ( 1005 sec) [ -37191.7185] [Topology ] . ( 1009 sec) [ -37191.6814] [Topology ] . ( 1010 sec) [ -37190.1302] [Alpha ][ 0.585852] . ( 1010 sec) [ -37190.1302] [Topology ] . ( 1014 sec) [ -37189.4975] [Topology ] . ( 1018 sec) [ -37189.2439] [Topology ] . ( 1022 sec) [ -37189.1240] [Topology ] . ( 1026 sec) [ -37189.0654] [Topology ] . ( 1029 sec) [ -37189.0356] [Topology ] . ( 1033 sec) [ -37189.0197] [Topology ] . ( 1034 sec) [ -37188.4951] [Alpha ][ 0.564231] . ( 1034 sec) [ -37188.4951] [Topology ] . ( 1038 sec) [ -37188.2354] [Topology ] . ( 1042 sec) [ -37188.1354] [Topology ] . ( 1046 sec) [ -37188.0896] [Topology ] . ( 1050 sec) [ -37188.0677] [Topology ] . ( 1054 sec) [ -37188.0566] [Topology ] . ( 1057 sec) [ -37188.0507] [Topology ] . ( 1058 sec) [ -37187.8241] [Alpha ][ 0.550604] . ( 1058 sec) [ -37187.8241] [Topology ] . ( 1062 sec) [ -37187.7111] [Topology ] . ( 1066 sec) [ -37187.6690] [Topology ] . ( 1070 sec) [ -37187.6501] [Topology ] . ( 1074 sec) [ -37187.6411] [Topology ] . ( 1077 sec) [ -37187.6365] [Topology ] . ( 1081 sec) [ -37187.6340] [Topology ] . ( 1082 sec) [ -37187.5300] [Alpha ][ 0.541711] . ( 1082 sec) [ -37187.5300] [Topology ] . ( 1086 sec) [ -37187.4790] [Topology ] . ( 1090 sec) [ -37187.4603] [Topology ] . ( 1094 sec) [ -37187.4520] [Topology ] . ( 1097 sec) [ -37187.4481] [Topology ] . ( 1101 sec) [ -37187.4460] [Topology ] . ( 1105 sec) [ -37187.4449] [Topology ] . ( 1106 sec) [ -37187.3950] [Alpha ][ 0.535245] . ( 1106 sec) [ -37187.3950] [Topology ] . ( 1110 sec) [ -37187.3675] [Topology ] . ( 1113 sec) [ -37187.3576] [Topology ] . ( 1117 sec) [ -37187.3533] [Topology ] . ( 1121 sec) [ -37187.3512] [Topology ] . ( 1125 sec) [ -37187.3501] [Topology ] . ( 1129 sec) [ -37187.3495] [Topology ] . ( 1129 sec) [ -37187.3269] [Alpha ][ 0.530911] . ( 1130 sec) [ -37187.3269] [Topology ] . ( 1133 sec) [ -37187.3140] [Topology ] . ( 1137 sec) [ -37187.3094] [Topology ] . ( 1141 sec) [ -37187.3073] [Topology ] . ( 1145 sec) [ -37187.3063] [Topology ] . ( 1145 sec) [ -37187.2978] [Alpha ][ 0.528264] . ( 1146 sec) [ -37187.2978] [Topology ] . ( 1150 sec) [ -37187.2913] [Topology ] . ( 1153 sec) [ -37187.2889] [Topology ] . ( 1157 sec) [ -37187.2877] [Topology ] . ( 1161 sec) [ -37187.2872] [Topology ] . ( 1162 sec) [ -37187.2829] [Alpha ][ 0.526362] . ( 1162 sec) [ -37187.2829] [Topology ] . ( 1166 sec) [ -37187.2794] [Topology ] . ( 1169 sec) [ -37187.2781] [Topology ] . ( 1173 sec) [ -37187.2775] [Topology ] . ( 1174 sec) [ -37187.2750] [Alpha ][ 0.524918] . ( 1174 sec) [ -37187.2750] [Topology ] . ( 1178 sec) [ -37187.2729] [Topology ] . ( 1182 sec) [ -37187.2721] [Topology ] . ( 1182 sec) [ -37187.2714] [Alpha ][ 0.524143] . ( 1183 sec) [ -37187.2714] [Topology ] . ( 1186 sec) [ -37187.2702] [Topology ] . ( 1190 sec) [ -37187.2697] [Topology ] . ( 1191 sec) [ -37187.2694] [Alpha ][ 0.523553] . ( 1191 sec) [ -37187.2694] [Topology ] . ( 1195 sec) [ -37187.2687] [Topology ] . ( 1196 sec) [ -37187.2687] [Alpha ][ 0.523553] . Checking for NNIs, optimizing five branches... . ( 1238 sec) [ -37186.8051] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1278 sec) [ -37186.2686] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -37186.253019 . Log likelihood obtained after SPR moves : -37186.268608 . Log likelihood of the current tree: -37186.253019. . Printing the most likely tree in file 'proteic_M2558_27x1060_2005.phy_phyml_tree.txt'... . Best log likelihood : -37186.005234 . Time used 0h21m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3571.39user 0.00system 59:46.78elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps