.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -16171.4937] [GTR parameters ] . ( 6 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 6 sec) [ -16055.6228] [Topology ] . ( 10 sec) [ -15746.4015] [Topology ] . ( 14 sec) [ -15704.7329] [Topology ] . ( 17 sec) [ -15695.3163] [Topology ] . ( 21 sec) [ -15693.0363] [Topology ] . ( 24 sec) [ -15692.2250] [Topology ] . ( 28 sec) [ -15691.7236] [Topology ] . ( 31 sec) [ -15691.0034] [Topology ] . ( 35 sec) [ -15689.1725] [Topology ] . ( 38 sec) [ -15687.5621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -15687.0077] [Topology ] . ( 72 sec) [ -15674.2751] [GTR parameters ] . ( 72 sec) [ -15673.3524] [Alpha ][ 0.534838] . ( 73 sec) [ -15673.3524] [Topology ] . ( 76 sec) [ -15671.9309] [Topology ] . ( 80 sec) [ -15671.3290] [Topology ] . ( 83 sec) [ -15670.9763] [Topology ] . ( 86 sec) [ -15670.7498] [Topology ] . ( 90 sec) [ -15670.5983] [Topology ] . ( 93 sec) [ -15670.4943] [Topology ] . Checking for NNIs, optimizing five branches... . ( 119 sec) [ -15670.4657] [Topology ] . ( 124 sec) [ -15670.3857] [GTR parameters ] . ( 125 sec) [ -15670.3285] [Alpha ][ 0.543674] . ( 125 sec) [ -15670.3285] [Topology ] . ( 128 sec) [ -15670.1641] [Topology ] . ( 132 sec) [ -15670.0851] [Topology ] . ( 135 sec) [ -15670.0324] [Topology ] . ( 138 sec) [ -15669.9950] [Topology ] . ( 142 sec) [ -15669.9680] [Topology ] . ( 145 sec) [ -15669.9482] [Topology ] . Checking for NNIs, optimizing five branches... . ( 171 sec) [ -15669.9480] [Topology ] . ( 174 sec) [ -15669.9440] [GTR parameters ] . ( 174 sec) [ -15669.9395] [Alpha ][ 0.546104] . ( 174 sec) [ -15669.9395] [Topology ] . ( 178 sec) [ -15669.9214] [Topology ] . ( 181 sec) [ -15669.9081] [Topology ] . ( 184 sec) [ -15669.8982] [Topology ] . ( 188 sec) [ -15669.8909] [Topology ] . ( 191 sec) [ -15669.8854] [Topology ] . ( 195 sec) [ -15669.8813] [Topology ] . Checking for NNIs, optimizing five branches... . ( 222 sec) [ -15669.8803] [GTR parameters ] . ( 222 sec) [ -15669.8797] [Alpha ][ 0.547002] . ( 222 sec) [ -15669.8797] [Topology ] . ( 226 sec) [ -15669.8759] [Topology ] . ( 229 sec) [ -15669.8731] [Topology ] . ( 233 sec) [ -15669.8710] [Topology ] . ( 236 sec) [ -15669.8694] [Topology ] . ( 239 sec) [ -15669.8681] [Topology ] . ( 243 sec) [ -15669.8672] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -15669.8667] [GTR parameters ] . ( 271 sec) [ -15669.8666] [Alpha ][ 0.547549] . ( 271 sec) [ -15669.8666] [Topology ] . ( 275 sec) [ -15669.8657] [Topology ] . Checking for NNIs, optimizing five branches... . ( 301 sec) [ -15669.8657] [GTR parameters ] . ( 301 sec) [ -15669.8657] [Alpha ][ 0.547549] . ( 302 sec) [ -15669.8657] [Topology ] . ( 305 sec) [ -15669.8650] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 362 sec) [ -16171.4937] [GTR parameters ] . ( 362 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 363 sec) [ -16051.9734] [ 3233] [depth= 1] . ( 363 sec) [ -16044.4728] [ 3239] [depth= 1] . ( 363 sec) [ -16041.2101] [ 3233] [depth= 1] . ( 363 sec) [ -16031.8120] [ 3236] [depth= 1] . ( 364 sec) [ -16011.4895] [ 3239] [depth= 2] . ( 364 sec) [ -16011.3510] [ 3251] [depth= 2] . ( 365 sec) [ -16002.2772] [ 3253] [depth= 1] . ( 365 sec) [ -15994.3577] [ 3257] [depth= 2] . ( 365 sec) [ -15992.1697] [ 3252] [depth= 2] . ( 365 sec) [ -15990.1296] [ 3256] [depth= 1] . ( 365 sec) [ -15986.2747] [ 3253] [depth= 1] . ( 366 sec) [ -15977.1070] [ 3251] [depth= 1] . ( 367 sec) [ -15973.2771] [ 3237] [depth= 1] . ( 367 sec) [ -15962.2787] [ 3234] [depth= 1] . ( 367 sec) [ -15961.2844] [ 3238] [depth= 1] . ( 367 sec) [ -15934.6332] [ 3238] [depth= 1] . ( 368 sec) [ -15926.3319] [ 3233] [depth= 1] . ( 368 sec) [ -15926.1471] [ 3237] [depth= 2] . ( 368 sec) [ -15894.8668] [ 3228] [depth= 4] . ( 369 sec) [ -15891.4821] [ 3232] [depth= 1] . ( 369 sec) [ -15890.0526] [ 3234] [depth= 2] . ( 369 sec) [ -15888.1122] [ 3228] [depth= 1] . ( 369 sec) [ -15869.6602] [ 3219] [depth= 1] . ( 370 sec) [ -15868.3150] [ 3222] [depth= 1] . ( 370 sec) [ -15859.4357] [ 3218] [depth= 1] . ( 371 sec) [ -15857.6811] [ 3213] [depth= 1] . ( 371 sec) [ -15856.8559] [ 3212] [depth= 1] . ( 371 sec) [ -15850.7281] [ 3215] [depth= 2] . ( 371 sec) [ -15850.6540] [ 3215] [depth= 1] . ( 372 sec) [ -15848.4548] [ 3213] [depth= 3] . ( 372 sec) [ -15847.6184] [ 3213] [depth= 3] . ( 372 sec) [ -15842.3468] [ 3212] [depth= 3] . ( 373 sec) [ -15840.1403] [ 3211] [depth= 1] . ( 373 sec) [ -15838.9389] [ 3211] [depth= 1] . ( 374 sec) [ -15838.9216] [ 3213] [depth= 1] . ( 374 sec) [ -15837.5423] [ 3211] [depth= 2] . ( 374 sec) [ -15836.2600] [ 3210] [depth= 1] . ( 375 sec) [ -15835.9759] [ 3211] [depth= 1] . ( 377 sec) [ -15832.9401] [ 3210] [depth= 1] . ( 378 sec) [ -15829.5869] [ 3210] [depth= 1] . ( 381 sec) [ -15829.1001] [ 3207] [depth= 1] . ( 382 sec) [ -15828.0095] [ 3209] [depth= 1] . ( 383 sec) [ -15825.9446] [ 3209] [depth= 1] . ( 383 sec) [ -15824.7571] [ 3209] [depth= 1] . ( 384 sec) [ -15819.9096] [ 3210] [depth= 1] . ( 385 sec) [ -15819.3978] [ 3210] [depth= 1] . ( 385 sec) [ -15818.9106] [ 3210] [depth= 1] . ( 385 sec) [ -15810.4986] [ 3210] [depth= 1] . ( 386 sec) [ -15810.0893] [ 3209] [depth= 1] . ( 387 sec) [ -15809.8308] [ 3209] [depth= 1] . ( 387 sec) [ -15809.6352] [ 3211] [depth= 1] . ( 389 sec) [ -15809.1639] [ 3211] [depth= 1] . ( 389 sec) [ -15809.0293] [ 3208] [depth= 1] . ( 389 sec) [ -15808.8563] [ 3207] [depth= 1] . ( 391 sec) [ -15805.7668] [ 3206] [depth= 1] . ( 392 sec) [ -15804.8210] [ 3206] [depth= 1] . ( 392 sec) [ -15804.2174] [ 3206] [depth= 1] . ( 392 sec) [ -15803.8278] [ 3206] [depth= 1] . ( 393 sec) [ -15803.3799] [ 3207] [depth= 3] . ( 393 sec) [ -15802.1832] [ 3207] [depth= 1] . ( 394 sec) [ -15802.0612] [ 3207] [depth= 1] . ( 395 sec) [ -15801.8047] [ 3208] [depth= 1] . ( 396 sec) [ -15801.6389] [ 3207] [depth= 3] . ( 397 sec) [ -15801.0621] [ 3207] [depth= 2] . ( 399 sec) [ -15799.8267] [ 3207] [depth= 1] . ( 399 sec) [ -15796.3603] [ 3208] [depth= 2] . ( 399 sec) [ -15795.9391] [ 3208] [depth= 1] . ( 399 sec) [ -15795.8642] [ 3208] [depth= 1] . ( 400 sec) [ -15795.5001] [ 3208] [depth= 1] . ( 400 sec) [ -15795.4702] [ 3208] [depth= 1] . ( 402 sec) [ -15794.4144] [ 3208] [depth= 1] . ( 404 sec) [ -15793.6256] [ 3208] [depth= 1] . ( 404 sec) [ -15793.4448] [ 3208] [depth= 1] . ( 405 sec) [ -15793.4310] [ 3208] [depth= 1] . ( 405 sec) [ -15793.3560] [ 3208] [depth= 1] . ( 406 sec) [ -15793.2598] [ 3208] [depth= 1] . ( 407 sec) [ -15793.2068] [ 3208] [depth= 1] . ( 408 sec) [ -15701.4518] [Branch lengths ] . ( 416 sec) [ -15691.2786] [GTR parameters ] . ( 416 sec) [ -15690.6608] [Alpha ][ 0.528636] . ( 418 sec) [ -15688.7715] [ 3205] [depth= 1] . ( 418 sec) [ -15688.3912] [ 3205] [depth= 1] . ( 418 sec) [ -15687.6891] [ 3208] [depth= 1] . ( 420 sec) [ -15686.9522] [ 3208] [depth= 1] . ( 420 sec) [ -15685.9380] [ 3206] [depth= 1] . ( 423 sec) [ -15685.3836] [ 3208] [depth= 1] . ( 424 sec) [ -15683.1610] [ 3202] [depth= 2] . ( 425 sec) [ -15682.8318] [ 3203] [depth= 1] . ( 429 sec) [ -15682.6232] [ 3202] [depth= 1] . ( 460 sec) [ -15682.5115] [ 3202] [depth= 1] . ( 471 sec) [ -15668.2499] [Branch lengths ] . ( 475 sec) [ -15668.0859] [GTR parameters ] . ( 475 sec) [ -15668.0175] [Alpha ][ 0.538332] . ( 481 sec) [ -15667.9356] [ 3201] [depth= 1] . ( 532 sec) [ -15665.9925] [Branch lengths ] . ( 536 sec) [ -15665.9523] [GTR parameters ] . ( 536 sec) [ -15665.9522] [Alpha ][ 0.538870] . ( 592 sec) [ -15665.2221] [Branch lengths ] . ( 620 sec) [ -15665.2018] [ 3198] [depth= 1] . ( 737 sec) [ -15665.1883] [ 3198] [depth= 2] . ( 743 sec) [ -15664.4440] [Branch lengths ] . ( 747 sec) [ -15664.4289] [GTR parameters ] . ( 748 sec) [ -15664.4139] [Alpha ][ 0.543379] . ( 748 sec) [ -15664.4139] [Topology ] . ( 751 sec) [ -15664.0797] [Topology ] . ( 755 sec) [ -15662.9541] [Topology ] . ( 758 sec) [ -15660.9366] [Topology ] . ( 762 sec) [ -15660.5195] [Topology ] . ( 765 sec) [ -15660.4558] [Topology ] . ( 769 sec) [ -15660.4338] [Topology ] . ( 772 sec) [ -15660.4330] [GTR parameters ] . ( 772 sec) [ -15660.4301] [Alpha ][ 0.545315] . ( 772 sec) [ -15660.4301] [Topology ] . ( 776 sec) [ -15660.4171] [Topology ] . ( 779 sec) [ -15660.4087] [Topology ] . ( 783 sec) [ -15660.4028] [Topology ] . ( 786 sec) [ -15660.3985] [Topology ] . ( 790 sec) [ -15660.3953] [Topology ] . ( 793 sec) [ -15660.3930] [Topology ] . ( 795 sec) [ -15660.3925] [GTR parameters ] . ( 795 sec) [ -15660.3922] [Alpha ][ 0.545936] . ( 795 sec) [ -15660.3922] [Topology ] . ( 799 sec) [ -15660.3902] [Topology ] . ( 802 sec) [ -15660.3886] [Topology ] . ( 806 sec) [ -15660.3875] [Topology ] . ( 809 sec) [ -15660.3867] [Topology ] . ( 810 sec) [ -15660.3866] [GTR parameters ] . ( 811 sec) [ -15660.3866] [Alpha ][ 0.545936] . ( 811 sec) [ -15660.3866] [Topology ] . ( 814 sec) [ -15660.3859] [Topology ] . ( 815 sec) [ -15660.3858] [GTR parameters ] . ( 816 sec) [ -15660.3858] [Alpha ][ 0.545936] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -15669.865032 . Log likelihood obtained after SPR moves : -15660.385831 . Log likelihood of the current tree: -15660.385831. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 0h14m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 834.55user 0.00system 14:02.58elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps