.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_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 . Compressing sequences... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -29176.8561] [GTR parameters ] . ( 1 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 2 sec) [ -28718.2078] [Topology ] . ( 4 sec) [ -28358.1403] [Topology ] . ( 8 sec) [ -28287.7496] [Topology ] . ( 11 sec) [ -28272.6038] [Topology ] . ( 14 sec) [ -28264.6408] [Topology ] . ( 17 sec) [ -28262.2033] [Topology ] . ( 20 sec) [ -28260.6583] [Topology ] . ( 23 sec) [ -28260.9603] [Topology ] . Moving backward . ( 23 sec) [ -28257.1897] [Topology ] . ( 26 sec) [ -28256.3358] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -28255.2392] [Topology ] . ( 60 sec) [ -27042.7798] [GTR parameters ] . ( 60 sec) [ -26994.3318] [Alpha ][ 0.359977] . ( 60 sec) [ -26994.3318] [Topology ] . ( 64 sec) [ -26978.7021] [Topology ] . ( 67 sec) [ -26973.8576] [Topology ] . ( 70 sec) [ -26970.8549] [Topology ] . ( 73 sec) [ -26965.9230] [Topology ] . ( 76 sec) [ -26964.8842] [Topology ] . ( 80 sec) [ -26964.6376] [Topology ] . ( 83 sec) [ -26964.5529] [Topology ] . ( 86 sec) [ -26964.5265] [Topology ] . ( 89 sec) [ -26964.5174] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -26964.3230] [Topology ] . ( 121 sec) [ -26962.6025] [GTR parameters ] . ( 122 sec) [ -26958.2517] [Alpha ][ 0.325279] . ( 122 sec) [ -26958.2517] [Topology ] . ( 125 sec) [ -26956.9976] [Topology ] . ( 128 sec) [ -26956.5920] [Topology ] . ( 131 sec) [ -26956.4431] [Topology ] . ( 135 sec) [ -26956.3755] [Topology ] . ( 138 sec) [ -26955.4347] [Topology ] . ( 141 sec) [ -26955.3374] [Topology ] . ( 144 sec) [ -26955.3272] [Topology ] . ( 147 sec) [ -26955.3253] [Topology ] . ( 150 sec) [ -26955.3249] [Topology ] . Checking for NNIs, optimizing five branches... . ( 175 sec) [ -26955.2670] [Topology ] . ( 180 sec) [ -26955.1035] [GTR parameters ] . ( 180 sec) [ -26954.1330] [Alpha ][ 0.309800] . ( 180 sec) [ -26954.1330] [Topology ] . ( 183 sec) [ -26953.6506] [Topology ] . ( 186 sec) [ -26953.5250] [Topology ] . ( 190 sec) [ -26953.4835] [Topology ] . ( 193 sec) [ -26953.4690] [Topology ] . ( 196 sec) [ -26953.4637] [Topology ] . ( 199 sec) [ -26953.4617] [Topology ] . Checking for NNIs, optimizing five branches... . ( 227 sec) [ -26953.4424] [GTR parameters ] . ( 227 sec) [ -26953.1895] [Alpha ][ 0.302220] . ( 228 sec) [ -26953.1895] [Topology ] . ( 231 sec) [ -26953.0886] [Topology ] . ( 234 sec) [ -26953.0576] [Topology ] . ( 237 sec) [ -26953.0468] [Topology ] . ( 240 sec) [ -26953.0429] [Topology ] . ( 243 sec) [ -26953.0415] [Topology ] . ( 246 sec) [ -26953.0409] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -26953.0148] [Topology ] . ( 273 sec) [ -26953.0054] [GTR parameters ] . ( 273 sec) [ -26952.9089] [Alpha ][ 0.297401] . ( 273 sec) [ -26952.9089] [Topology ] . ( 276 sec) [ -26952.8427] [Topology ] . ( 280 sec) [ -26952.8242] [Topology ] . ( 283 sec) [ -26952.8180] [Topology ] . ( 286 sec) [ -26952.8158] [Topology ] . ( 289 sec) [ -26952.8150] [Topology ] . Checking for NNIs, optimizing five branches... . ( 317 sec) [ -26952.8136] [GTR parameters ] . ( 317 sec) [ -26952.7720] [Alpha ][ 0.294258] . ( 317 sec) [ -26952.7720] [Topology ] . ( 320 sec) [ -26952.7518] [Topology ] . ( 323 sec) [ -26952.7458] [Topology ] . ( 326 sec) [ -26952.7438] [Topology ] . ( 330 sec) [ -26952.7431] [Topology ] . Checking for NNIs, optimizing five branches... . ( 355 sec) [ -26952.7430] [GTR parameters ] . ( 355 sec) [ -26952.7312] [Alpha ][ 0.292591] . ( 355 sec) [ -26952.7312] [Topology ] . ( 358 sec) [ -26952.7242] [Topology ] . ( 361 sec) [ -26952.7221] [Topology ] . ( 364 sec) [ -26952.7214] [Topology ] . Checking for NNIs, optimizing five branches... . ( 393 sec) [ -26952.7198] [GTR parameters ] . ( 393 sec) [ -26952.7156] [Alpha ][ 0.291594] . ( 393 sec) [ -26952.7156] [Topology ] . ( 396 sec) [ -26952.7128] [Topology ] . ( 399 sec) [ -26952.7119] [Topology ] . Checking for NNIs, optimizing five branches... . ( 424 sec) [ -26952.7119] [GTR parameters ] . ( 424 sec) [ -26952.7109] [Alpha ][ 0.291108] . ( 425 sec) [ -26952.7109] [Topology ] . ( 428 sec) [ -26952.7096] [Topology ] . ( 431 sec) [ -26952.7092] [Topology ] . Checking for NNIs, optimizing five branches... . ( 456 sec) [ -26952.7091] [GTR parameters ] . ( 456 sec) [ -26952.7086] [Alpha ][ 0.290762] . ( 456 sec) [ -26952.7086] [Topology ] . ( 459 sec) [ -26952.7079] [Topology ] . Checking for NNIs, optimizing five branches... . ( 486 sec) [ -26952.7078] [GTR parameters ] . ( 486 sec) [ -26952.7078] [Alpha ][ 0.290471] . ( 486 sec) [ -26952.7078] [Topology ] . ( 489 sec) [ -26952.7072] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 539 sec) [ -29176.8561] [GTR parameters ] . ( 539 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 540 sec) [ -28715.8595] [ 5819] [depth= 1] . ( 541 sec) [ -28709.8159] [ 5824] [depth= 1] . ( 542 sec) [ -28697.5201] [ 5819] [depth= 1] . ( 543 sec) [ -28696.6045] [ 5823] [depth= 1] . ( 543 sec) [ -28683.6351] [ 5819] [depth= 1] . ( 543 sec) [ -28681.3289] [ 5822] [depth= 1] . ( 543 sec) [ -28679.2730] [ 5819] [depth= 1] . ( 544 sec) [ -28672.1645] [ 5820] [depth= 1] . ( 545 sec) [ -28670.8541] [ 5822] [depth= 1] . ( 545 sec) [ -28669.3735] [ 5824] [depth= 1] . ( 546 sec) [ -28667.7191] [ 5823] [depth= 1] . ( 546 sec) [ -28664.6733] [ 5818] [depth= 1] . ( 546 sec) [ -28658.0320] [ 5822] [depth= 1] . ( 547 sec) [ -28635.3083] [ 5811] [depth= 4] . ( 547 sec) [ -28627.6068] [ 5812] [depth= 1] . ( 547 sec) [ -28627.4745] [ 5811] [depth= 1] . ( 547 sec) [ -28624.7292] [ 5812] [depth= 1] . ( 548 sec) [ -28618.7177] [ 5809] [depth= 1] . ( 548 sec) [ -28618.1073] [ 5811] [depth= 1] . ( 549 sec) [ -28616.9607] [ 5809] [depth= 1] . ( 549 sec) [ -28608.6871] [ 5800] [depth= 1] . ( 549 sec) [ -28605.2953] [ 5801] [depth= 1] . ( 550 sec) [ -28603.7189] [ 5806] [depth= 1] . ( 550 sec) [ -28603.2967] [ 5805] [depth= 1] . ( 550 sec) [ -28596.6809] [ 5802] [depth= 1] . ( 551 sec) [ -28581.8849] [ 5812] [depth= 1] . ( 551 sec) [ -28556.9955] [ 5802] [depth= 1] . ( 552 sec) [ -28553.6707] [ 5805] [depth= 1] . ( 552 sec) [ -28550.7503] [ 5805] [depth= 1] . ( 553 sec) [ -28532.9785] [ 5811] [depth= 2] . ( 553 sec) [ -28505.2161] [ 5801] [depth= 2] . ( 553 sec) [ -28494.7125] [ 5801] [depth= 1] . ( 553 sec) [ -28493.8834] [ 5801] [depth= 1] . ( 553 sec) [ -28484.6717] [ 5800] [depth= 1] . ( 554 sec) [ -28481.3638] [ 5802] [depth= 1] . ( 554 sec) [ -28479.5954] [ 5800] [depth= 1] . ( 554 sec) [ -28475.0670] [ 5797] [depth= 2] . ( 555 sec) [ -28471.8349] [ 5798] [depth= 1] . ( 555 sec) [ -28471.0611] [ 5799] [depth= 2] . ( 555 sec) [ -28470.1203] [ 5801] [depth= 1] . ( 555 sec) [ -28465.6616] [ 5796] [depth= 1] . ( 555 sec) [ -28456.6326] [ 5803] [depth= 1] . ( 556 sec) [ -28454.4766] [ 5803] [depth= 1] . ( 556 sec) [ -28452.0039] [ 5805] [depth= 2] . ( 556 sec) [ -28450.9616] [ 5805] [depth= 1] . ( 556 sec) [ -28449.4810] [ 5805] [depth= 1] . ( 557 sec) [ -28448.4225] [ 5805] [depth= 1] . ( 557 sec) [ -28442.1678] [ 5798] [depth= 1] . ( 558 sec) [ -28441.6328] [ 5799] [depth= 1] . ( 559 sec) [ -28439.7610] [ 5797] [depth= 1] . ( 559 sec) [ -28436.0051] [ 5799] [depth= 1] . ( 559 sec) [ -28421.7718] [ 5791] [depth= 3] . ( 560 sec) [ -28418.4526] [ 5794] [depth= 1] . ( 560 sec) [ -28415.5810] [ 5791] [depth= 1] . ( 560 sec) [ -28414.3279] [ 5792] [depth= 1] . ( 560 sec) [ -28411.2934] [ 5791] [depth= 1] . ( 561 sec) [ -28408.9258] [ 5788] [depth= 2] . ( 561 sec) [ -28408.0051] [ 5790] [depth= 1] . ( 561 sec) [ -28405.2591] [ 5791] [depth= 1] . ( 561 sec) [ -28404.9784] [ 5791] [depth= 1] . ( 562 sec) [ -28404.3581] [ 5790] [depth= 2] . ( 562 sec) [ -28401.9181] [ 5788] [depth= 1] . ( 564 sec) [ -28401.4738] [ 5788] [depth= 1] . ( 564 sec) [ -28398.8514] [ 5786] [depth= 1] . ( 566 sec) [ -28395.7868] [ 5785] [depth= 1] . ( 569 sec) [ -28393.1605] [ 5784] [depth= 1] . ( 569 sec) [ -28391.5912] [ 5784] [depth= 1] . ( 571 sec) [ -28389.0516] [ 5784] [depth= 4] . ( 573 sec) [ -28385.4871] [ 5783] [depth= 1] . ( 584 sec) [ -28286.9092] [Branch lengths ] . ( 591 sec) [ -27076.2807] [GTR parameters ] . ( 592 sec) [ -27006.2899] [Alpha ][ 0.332427] . ( 595 sec) [ -27005.0990] [ 5785] [depth= 1] . ( 595 sec) [ -27004.5914] [ 5790] [depth= 1] . ( 598 sec) [ -27004.3819] [ 5788] [depth= 1] . ( 598 sec) [ -27003.5448] [ 5785] [depth= 1] . ( 599 sec) [ -26996.9663] [ 5784] [depth= 2] . ( 600 sec) [ -26996.4399] [ 5787] [depth= 1] . ( 601 sec) [ -26994.6504] [ 5788] [depth= 1] . ( 601 sec) [ -26992.4700] [ 5788] [depth= 1] . ( 604 sec) [ -26981.6455] [ 5790] [depth= 1] . ( 604 sec) [ -26981.0775] [ 5792] [depth= 1] . ( 605 sec) [ -26981.0141] [ 5790] [depth= 1] . ( 605 sec) [ -26980.5630] [ 5791] [depth= 1] . ( 605 sec) [ -26977.0447] [ 5793] [depth= 1] . ( 606 sec) [ -26976.5660] [ 5795] [depth= 1] . ( 609 sec) [ -26974.1025] [ 5798] [depth= 1] . ( 637 sec) [ -26954.7785] [Branch lengths ] . ( 642 sec) [ -26952.1491] [GTR parameters ] . ( 642 sec) [ -26951.4636] [Alpha ][ 0.319341] . ( 652 sec) [ -26948.4777] [ 5802] [depth= 3] . ( 687 sec) [ -26946.4044] [Branch lengths ] . ( 692 sec) [ -26946.3229] [GTR parameters ] . ( 692 sec) [ -26946.1128] [Alpha ][ 0.312384] . ( 737 sec) [ -26945.7659] [Branch lengths ] . ( 873 sec) [ -26945.7305] [Branch lengths ] . ( 873 sec) [ -26945.7305] [Topology ] . ( 876 sec) [ -26945.7283] [Topology ] . ( 879 sec) [ -26945.7277] [Topology ] . ( 883 sec) [ -26945.7225] [GTR parameters ] . ( 883 sec) [ -26945.5805] [Alpha ][ 0.306476] . ( 883 sec) [ -26945.5805] [Topology ] . ( 887 sec) [ -26945.5235] [Topology ] . ( 890 sec) [ -26945.5055] [Topology ] . ( 893 sec) [ -26945.4991] [Topology ] . ( 896 sec) [ -26945.4967] [Topology ] . ( 900 sec) [ -26945.4959] [Topology ] . ( 903 sec) [ -26945.4921] [GTR parameters ] . ( 903 sec) [ -26945.4538] [Alpha ][ 0.303429] . ( 903 sec) [ -26945.4538] [Topology ] . ( 907 sec) [ -26945.4361] [Topology ] . ( 910 sec) [ -26945.4305] [Topology ] . ( 913 sec) [ -26945.4285] [Topology ] . ( 916 sec) [ -26945.4277] [Topology ] . ( 920 sec) [ -26945.4266] [GTR parameters ] . ( 920 sec) [ -26945.4159] [Alpha ][ 0.301819] . ( 920 sec) [ -26945.4159] [Topology ] . ( 924 sec) [ -26945.4099] [Topology ] . ( 927 sec) [ -26945.4079] [Topology ] . ( 930 sec) [ -26945.4072] [Topology ] . ( 937 sec) [ -26945.4070] [GTR parameters ] . ( 937 sec) [ -26945.4041] [Alpha ][ 0.300970] . ( 937 sec) [ -26945.4041] [Topology ] . ( 940 sec) [ -26945.4018] [Topology ] . ( 944 sec) [ -26945.4011] [Topology ] . ( 945 sec) [ -26945.4010] [GTR parameters ] . ( 945 sec) [ -26945.4003] [Alpha ][ 0.300543] . ( 945 sec) [ -26945.4003] [Topology ] . ( 948 sec) [ -26945.3992] [Topology ] . ( 952 sec) [ -26945.3989] [Topology ] . ( 955 sec) [ -26945.3988] [GTR parameters ] . ( 955 sec) [ -26945.3985] [Alpha ][ 0.300242] . ( 955 sec) [ -26945.3985] [Topology ] . ( 959 sec) [ -26945.3980] [Topology ] . ( 961 sec) [ -26945.3978] [GTR parameters ] . ( 961 sec) [ -26945.3978] [Alpha ][ 0.300242] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -26952.707180 . Log likelihood obtained after SPR moves : -26945.397843 . Log likelihood of the current tree: -26945.397843. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 0h16m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 979.92user 0.00system 16:27.21elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps