.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1991_32x129_2004.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 . 9 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 113 patterns found. (out of a total of 129 sites) . 25 sites without polymorphism (19.38%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6154.7776] [Alpha ][ 0.500960] . ( 1 sec) [ -6013.0901] [ 1018] [depth= 4] . ( 1 sec) [ -5823.6980] [ 981] [depth= 6] . ( 1 sec) [ -5661.3130] [ 971] [depth= 1] . ( 1 sec) [ -5658.5184] [ 969] [depth= 5] . ( 1 sec) [ -5658.2593] [ 956] [depth= 1] . ( 2 sec) [ -5596.2397] [ 952] [depth= 3] . ( 2 sec) [ -5537.5155] [ 950] [depth= 3] . ( 2 sec) [ -5480.6118] [ 950] [depth= 5] . ( 2 sec) [ -5341.5870] [ 913] [depth= 16] . ( 2 sec) [ -5274.6224] [ 912] [depth= 1] . ( 2 sec) [ -5261.4832] [ 906] [depth= 9] . ( 3 sec) [ -5105.9656] [ 877] [depth= 6] . ( 3 sec) [ -5076.4103] [ 877] [depth= 1] . ( 3 sec) [ -4993.1200] [ 870] [depth= 9] . ( 3 sec) [ -4593.4784] [ 815] [depth= 8] . ( 3 sec) [ -4548.4180] [ 773] [depth= 8] . ( 3 sec) [ -4479.0564] [ 755] [depth= 12] . ( 4 sec) [ -4132.4064] [ 701] [depth= 14] . ( 4 sec) [ -4044.0406] [ 704] [depth= 2] . ( 4 sec) [ -4019.6032] [ 699] [depth= 6] . ( 4 sec) [ -3991.4953] [ 668] [depth= 12] . ( 4 sec) [ -3987.0578] [ 667] [depth= 1] . ( 5 sec) [ -3969.8273] [ 665] [depth= 7] . ( 5 sec) [ -3965.5623] [ 666] [depth= 4] . ( 5 sec) [ -3949.8772] [ 668] [depth= 13] . ( 5 sec) [ -3736.3386] [ 656] [depth= 2] . ( 6 sec) [ -3728.5597] [ 656] [depth= 1] . ( 6 sec) [ -3716.1228] [ 655] [depth= 2] . ( 6 sec) [ -3693.8609] [ 654] [depth= 1] . ( 6 sec) [ -3682.2189] [ 653] [depth= 4] . ( 6 sec) [ -3536.9534] [ 652] [depth= 1] . ( 6 sec) [ -3485.5603] [ 651] [depth= 2] . ( 6 sec) [ -3477.0474] [ 644] [depth= 1] . ( 7 sec) [ -3331.7829] [ 601] [depth= 9] . ( 7 sec) [ -3331.2853] [ 601] [depth= 1] . ( 7 sec) [ -3292.1222] [ 601] [depth= 2] . ( 7 sec) [ -3281.3173] [ 600] [depth= 1] . ( 7 sec) [ -3257.2883] [ 602] [depth= 3] . ( 7 sec) [ -3246.7742] [ 599] [depth= 2] . ( 8 sec) [ -3218.8118] [ 591] [depth= 5] . ( 8 sec) [ -3170.4889] [ 584] [depth= 2] . ( 8 sec) [ -3006.2007] [ 554] [depth= 2] . ( 8 sec) [ -2981.2965] [ 549] [depth= 1] . ( 8 sec) [ -2954.8087] [ 542] [depth= 3] . ( 9 sec) [ -2943.1100] [ 545] [depth= 3] . ( 9 sec) [ -2919.5983] [ 544] [depth= 2] . ( 9 sec) [ -2876.7893] [ 506] [depth= 7] . ( 9 sec) [ -2789.4313] [ 500] [depth= 1] . ( 9 sec) [ -2759.1415] [ 498] [depth= 4] . ( 11 sec) [ -2756.2357] [ 495] [depth= 2] . ( 11 sec) [ -2754.3576] [ 494] [depth= 7] . ( 11 sec) [ -2753.3435] [ 493] [depth= 1] . ( 11 sec) [ -2721.2595] [ 488] [depth= 3] . ( 11 sec) [ -2717.3206] [ 502] [depth= 2] . ( 11 sec) [ -2679.0694] [ 502] [depth= 1] . ( 11 sec) [ -2672.6339] [ 496] [depth= 3] . ( 12 sec) [ -2665.8568] [ 495] [depth= 1] . ( 12 sec) [ -2663.3813] [ 496] [depth= 1] . ( 12 sec) [ -2658.6435] [ 494] [depth= 1] . ( 12 sec) [ -2658.0662] [ 493] [depth= 1] . ( 13 sec) [ -2644.2586] [ 492] [depth= 4] . ( 13 sec) [ -2643.8466] [ 493] [depth= 1] . ( 13 sec) [ -2642.0322] [ 492] [depth= 1] . ( 13 sec) [ -2640.6377] [ 492] [depth= 1] . ( 14 sec) [ -2633.1760] [ 493] [depth= 2] . ( 14 sec) [ -2603.0947] [ 486] [depth= 4] . ( 15 sec) [ -2599.1523] [ 481] [depth= 6] . ( 15 sec) [ -2598.0274] [ 480] [depth= 1] . ( 15 sec) [ -2553.3832] [Branch lengths ] . ( 15 sec) [ -2543.0759] [Alpha ][ 0.983564] . ( 16 sec) [ -2542.9776] [ 477] [depth= 6] . ( 16 sec) [ -2542.9273] [ 478] [depth= 1] . ( 16 sec) [ -2539.1014] [ 478] [depth= 5] . ( 16 sec) [ -2538.8365] [ 479] [depth= 2] . ( 18 sec) [ -2538.7901] [ 471] [depth= 2] . ( 18 sec) [ -2538.7217] [ 471] [depth= 1] . ( 18 sec) [ -2538.5248] [ 471] [depth= 1] . ( 18 sec) [ -2537.6043] [ 470] [depth= 2] . ( 20 sec) [ -2537.4443] [ 470] [depth= 1] . ( 23 sec) [ -2537.2239] [ 471] [depth= 1] . ( 23 sec) [ -2430.3751] [ 433] [depth= 9] . ( 24 sec) [ -2429.3852] [ 434] [depth= 1] . ( 24 sec) [ -2409.0113] [ 433] [depth= 1] . ( 26 sec) [ -2407.5916] [ 428] [depth= 5] . ( 29 sec) [ -2407.3672] [ 428] [depth= 2] . ( 30 sec) [ -2407.3062] [ 428] [depth= 2] . ( 33 sec) [ -2407.0626] [ 428] [depth= 2] . ( 37 sec) [ -2404.8966] [ 428] [depth= 1] . ( 41 sec) [ -2401.2812] [ 422] [depth= 10] . ( 41 sec) [ -2400.1534] [ 423] [depth= 1] . ( 42 sec) [ -2393.9788] [ 422] [depth= 2] . ( 42 sec) [ -2393.8147] [ 422] [depth= 1] . ( 47 sec) [ -2391.3114] [ 422] [depth= 1] . ( 47 sec) [ -2390.5577] [ 420] [depth= 1] . ( 50 sec) [ -2390.0145] [ 420] [depth= 1] . ( 50 sec) [ -2386.0502] [Branch lengths ] . ( 51 sec) [ -2385.2626] [Alpha ][ 1.240091] . ( 51 sec) [ -2385.2513] [ 419] [depth= 1] . ( 93 sec) [ -2385.0266] [Branch lengths ] . ( 93 sec) [ -2385.0220] [Alpha ][ 1.263520] . ( 93 sec) [ -2385.0220] [Topology ] . ( 94 sec) [ -2384.9949] [Topology ] . ( 95 sec) [ -2384.9857] [Topology ] . ( 96 sec) [ -2384.9813] [Topology ] . ( 97 sec) [ -2384.9789] [Topology ] . ( 98 sec) [ -2384.9774] [Topology ] . ( 99 sec) [ -2384.9765] [Topology ] . ( 99 sec) [ -2384.9764] [Alpha ][ 1.265834] . ( 99 sec) [ -2384.9764] [Topology ] . ( 100 sec) [ -2384.9757] [Topology ] . ( 101 sec) [ -2384.9757] [Alpha ][ 1.265834] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2384.975718. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5587.0898] [Alpha ][ 0.500960] . ( 0 sec) [ -5497.4130] [ 893] [depth= 6] . ( 0 sec) [ -5365.9153] [ 884] [depth= 2] . ( 1 sec) [ -5258.5060] [ 852] [depth= 4] . ( 1 sec) [ -5251.7953] [ 851] [depth= 1] . ( 1 sec) [ -5192.6262] [ 849] [depth= 5] . ( 1 sec) [ -5160.1770] [ 842] [depth= 1] . ( 1 sec) [ -5117.5605] [ 835] [depth= 6] . ( 1 sec) [ -4920.9718] [ 833] [depth= 1] . ( 2 sec) [ -4703.3292] [ 790] [depth= 7] . ( 2 sec) [ -4606.3214] [ 785] [depth= 1] . ( 2 sec) [ -4437.5967] [ 779] [depth= 10] . ( 2 sec) [ -4437.1034] [ 772] [depth= 1] . ( 2 sec) [ -4413.1166] [ 764] [depth= 1] . ( 2 sec) [ -4360.3268] [ 741] [depth= 3] . ( 2 sec) [ -4300.8626] [ 732] [depth= 6] . ( 3 sec) [ -4285.9863] [ 733] [depth= 1] . ( 3 sec) [ -4203.3687] [ 726] [depth= 1] . ( 3 sec) [ -4195.9051] [ 726] [depth= 1] . ( 3 sec) [ -4186.5898] [ 724] [depth= 1] . ( 3 sec) [ -3918.8574] [ 678] [depth= 16] . ( 3 sec) [ -3872.1410] [ 671] [depth= 4] . ( 4 sec) [ -3859.4166] [ 672] [depth= 1] . ( 4 sec) [ -3795.1475] [ 655] [depth= 5] . ( 4 sec) [ -3721.4083] [ 650] [depth= 3] . ( 4 sec) [ -3720.8896] [ 652] [depth= 1] . ( 4 sec) [ -3701.2714] [ 652] [depth= 1] . ( 5 sec) [ -3661.9667] [ 645] [depth= 7] . ( 5 sec) [ -3651.9394] [ 638] [depth= 1] . ( 5 sec) [ -3631.9111] [ 636] [depth= 2] . ( 5 sec) [ -3601.8664] [ 637] [depth= 1] . ( 5 sec) [ -3601.0557] [ 635] [depth= 1] . ( 5 sec) [ -3595.5565] [ 636] [depth= 1] . ( 5 sec) [ -3509.2791] [ 631] [depth= 7] . ( 6 sec) [ -3366.0628] [ 611] [depth= 2] . ( 6 sec) [ -3227.8874] [ 581] [depth= 7] . ( 6 sec) [ -3222.9602] [ 580] [depth= 1] . ( 6 sec) [ -3124.4416] [ 563] [depth= 7] . ( 6 sec) [ -3083.5597] [ 553] [depth= 4] . ( 6 sec) [ -3076.1030] [ 549] [depth= 4] . ( 7 sec) [ -3008.6067] [ 552] [depth= 3] . ( 7 sec) [ -2858.2178] [ 500] [depth= 7] . ( 7 sec) [ -2839.8857] [ 498] [depth= 2] . ( 7 sec) [ -2823.9709] [ 500] [depth= 1] . ( 8 sec) [ -2740.1530] [ 499] [depth= 3] . ( 8 sec) [ -2735.3320] [ 499] [depth= 5] . ( 8 sec) [ -2731.1574] [ 499] [depth= 1] . ( 8 sec) [ -2712.9390] [ 496] [depth= 4] . ( 8 sec) [ -2695.2017] [ 490] [depth= 4] . ( 8 sec) [ -2693.8994] [ 491] [depth= 1] . ( 9 sec) [ -2692.2319] [ 492] [depth= 3] . ( 9 sec) [ -2683.2368] [ 491] [depth= 1] . ( 11 sec) [ -2653.6907] [ 489] [depth= 7] . ( 11 sec) [ -2650.4609] [ 488] [depth= 1] . ( 12 sec) [ -2643.4654] [ 487] [depth= 2] . ( 12 sec) [ -2639.6600] [ 486] [depth= 1] . ( 12 sec) [ -2602.8668] [ 486] [depth= 6] . ( 12 sec) [ -2499.5277] [ 446] [depth= 11] . ( 12 sec) [ -2496.2027] [ 444] [depth= 1] . ( 12 sec) [ -2490.4850] [ 443] [depth= 1] . ( 13 sec) [ -2488.7878] [ 443] [depth= 1] . ( 13 sec) [ -2475.3751] [ 438] [depth= 4] . ( 13 sec) [ -2474.5771] [ 442] [depth= 2] . ( 13 sec) [ -2474.4340] [ 443] [depth= 1] . ( 13 sec) [ -2463.2486] [ 441] [depth= 4] . ( 13 sec) [ -2461.1294] [ 441] [depth= 1] . ( 14 sec) [ -2458.9681] [ 436] [depth= 4] . ( 16 sec) [ -2458.6323] [ 436] [depth= 2] . ( 16 sec) [ -2457.9576] [ 435] [depth= 1] . ( 16 sec) [ -2456.6263] [ 435] [depth= 2] . ( 16 sec) [ -2451.1466] [ 434] [depth= 3] . ( 16 sec) [ -2440.3800] [ 434] [depth= 1] . ( 17 sec) [ -2438.8474] [ 433] [depth= 2] . ( 17 sec) [ -2425.1962] [Branch lengths ] . ( 17 sec) [ -2412.5792] [Alpha ][ 1.000357] . ( 17 sec) [ -2412.5341] [ 428] [depth= 6] . ( 18 sec) [ -2412.5173] [ 428] [depth= 1] . ( 19 sec) [ -2412.5064] [ 428] [depth= 1] . ( 21 sec) [ -2412.3422] [ 427] [depth= 2] . ( 21 sec) [ -2412.2188] [ 426] [depth= 1] . ( 21 sec) [ -2409.5326] [ 424] [depth= 1] . ( 22 sec) [ -2409.0329] [ 425] [depth= 1] . ( 22 sec) [ -2408.5208] [ 424] [depth= 1] . ( 23 sec) [ -2399.5133] [ 421] [depth= 2] . ( 24 sec) [ -2399.5018] [ 422] [depth= 1] . ( 31 sec) [ -2399.4571] [ 426] [depth= 9] . ( 31 sec) [ -2398.1927] [ 425] [depth= 2] . ( 32 sec) [ -2396.1742] [ 425] [depth= 1] . ( 44 sec) [ -2396.1617] [ 425] [depth= 1] . ( 49 sec) [ -2396.1306] [ 426] [depth= 1] . ( 55 sec) [ -2396.0085] [ 426] [depth= 1] . ( 55 sec) [ -2395.2835] [ 426] [depth= 1] . ( 58 sec) [ -2391.2718] [Branch lengths ] . ( 58 sec) [ -2390.2038] [Alpha ][ 1.318991] . ( 109 sec) [ -2389.8610] [Branch lengths ] . ( 109 sec) [ -2389.8610] [Topology ] . ( 110 sec) [ -2389.7905] [Topology ] . ( 111 sec) [ -2389.7461] [Topology ] . ( 112 sec) [ -2389.7114] [Topology ] . ( 113 sec) [ -2389.6829] [Topology ] . ( 114 sec) [ -2389.6584] [Topology ] . ( 115 sec) [ -2389.6373] [Topology ] . ( 115 sec) [ -2389.6316] [Alpha ][ 1.346237] . ( 115 sec) [ -2389.6316] [Topology ] . ( 116 sec) [ -2389.6131] [Topology ] . ( 117 sec) [ -2389.5974] [Topology ] . ( 118 sec) [ -2389.5837] [Topology ] . ( 119 sec) [ -2389.5718] [Topology ] . ( 120 sec) [ -2389.5616] [Topology ] . ( 121 sec) [ -2389.5526] [Topology ] . ( 121 sec) [ -2389.5526] [Alpha ][ 1.347583] . ( 121 sec) [ -2389.5526] [Topology ] . ( 122 sec) [ -2389.5448] [Topology ] . ( 123 sec) [ -2389.5378] [Topology ] . ( 124 sec) [ -2389.5317] [Topology ] . ( 125 sec) [ -2389.5263] [Topology ] . ( 126 sec) [ -2389.5216] [Topology ] . ( 127 sec) [ -2389.5174] [Topology ] . ( 127 sec) [ -2389.5174] [Alpha ][ 1.345139] . ( 127 sec) [ -2389.5174] [Topology ] . ( 128 sec) [ -2389.5136] [Topology ] . ( 129 sec) [ -2389.5103] [Topology ] . ( 130 sec) [ -2389.5082] [Topology ] . ( 131 sec) [ -2389.5075] [Topology ] . ( 131 sec) [ -2389.5075] [Alpha ][ 1.345139] . ( 131 sec) [ -2389.5075] [Topology ] . ( 132 sec) [ -2389.5072] [Topology ] . ( 132 sec) [ -2389.5072] [Alpha ][ 1.345139] . Checking for NNIs, optimizing five branches... . ( 139 sec) [ -2389.5069] [Topology ] . Checking for NNIs, optimizing five branches... . ( 146 sec) [ -2389.5067] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2389.506705. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5287.1890] [Alpha ][ 0.500960] . ( 0 sec) [ -5110.7983] [ 886] [depth= 9] . ( 0 sec) [ -4872.1897] [ 848] [depth= 8] . ( 1 sec) [ -4707.0948] [ 794] [depth= 4] . ( 1 sec) [ -4673.2630] [ 785] [depth= 1] . ( 1 sec) [ -4642.2159] [ 778] [depth= 7] . ( 1 sec) [ -4497.9970] [ 773] [depth= 3] . ( 1 sec) [ -4313.1496] [ 725] [depth= 5] . ( 1 sec) [ -4279.0093] [ 721] [depth= 1] . ( 1 sec) [ -4066.8738] [ 674] [depth= 2] . ( 2 sec) [ -3920.3363] [ 658] [depth= 5] . ( 2 sec) [ -3904.4150] [ 654] [depth= 1] . ( 2 sec) [ -3879.0741] [ 649] [depth= 4] . ( 2 sec) [ -3869.3769] [ 652] [depth= 2] . ( 2 sec) [ -3845.2760] [ 648] [depth= 3] . ( 2 sec) [ -3706.4399] [ 596] [depth= 7] . ( 3 sec) [ -3614.2200] [ 594] [depth= 5] . ( 3 sec) [ -3584.3646] [ 593] [depth= 3] . ( 3 sec) [ -3568.8082] [ 592] [depth= 1] . ( 3 sec) [ -3566.0018] [ 590] [depth= 6] . ( 3 sec) [ -3563.5000] [ 589] [depth= 1] . ( 3 sec) [ -3563.3368] [ 590] [depth= 1] . ( 4 sec) [ -3532.8206] [ 584] [depth= 4] . ( 4 sec) [ -3510.2779] [ 584] [depth= 1] . ( 4 sec) [ -3178.9849] [ 548] [depth= 4] . ( 4 sec) [ -3168.6257] [ 541] [depth= 4] . ( 4 sec) [ -3090.6519] [ 537] [depth= 1] . ( 4 sec) [ -3067.0561] [ 539] [depth= 1] . ( 5 sec) [ -3009.9126] [ 539] [depth= 2] . ( 5 sec) [ -2983.4255] [ 537] [depth= 7] . ( 5 sec) [ -2865.3274] [ 507] [depth= 2] . ( 5 sec) [ -2860.9540] [ 506] [depth= 1] . ( 5 sec) [ -2792.8981] [ 496] [depth= 9] . ( 5 sec) [ -2752.8322] [ 492] [depth= 6] . ( 5 sec) [ -2724.0870] [ 490] [depth= 8] . ( 6 sec) [ -2703.0788] [ 487] [depth= 2] . ( 6 sec) [ -2702.2245] [ 489] [depth= 1] . ( 6 sec) [ -2699.4157] [ 487] [depth= 1] . ( 6 sec) [ -2674.6299] [ 479] [depth= 2] . ( 6 sec) [ -2670.8347] [ 479] [depth= 1] . ( 6 sec) [ -2662.5513] [ 477] [depth= 1] . ( 7 sec) [ -2653.5697] [ 477] [depth= 1] . ( 7 sec) [ -2641.0355] [ 476] [depth= 3] . ( 7 sec) [ -2636.6427] [ 473] [depth= 2] . ( 7 sec) [ -2625.5992] [ 471] [depth= 1] . ( 7 sec) [ -2624.0923] [ 472] [depth= 1] . ( 8 sec) [ -2621.2165] [ 471] [depth= 1] . ( 8 sec) [ -2620.7553] [ 473] [depth= 1] . ( 9 sec) [ -2615.7667] [ 472] [depth= 1] . ( 9 sec) [ -2614.6626] [ 470] [depth= 4] . ( 11 sec) [ -2509.6012] [ 435] [depth= 5] . ( 14 sec) [ -2503.3974] [ 435] [depth= 1] . ( 14 sec) [ -2503.1561] [ 435] [depth= 1] . ( 16 sec) [ -2492.9729] [ 436] [depth= 1] . ( 16 sec) [ -2485.4751] [ 436] [depth= 1] . ( 16 sec) [ -2476.8922] [ 437] [depth= 1] . ( 16 sec) [ -2470.5680] [ 438] [depth= 2] . ( 16 sec) [ -2468.0435] [ 437] [depth= 2] . ( 17 sec) [ -2464.2938] [ 436] [depth= 1] . ( 18 sec) [ -2462.5120] [ 436] [depth= 1] . ( 19 sec) [ -2460.4138] [ 437] [depth= 1] . ( 19 sec) [ -2410.5169] [Branch lengths ] . ( 19 sec) [ -2399.0220] [Alpha ][ 1.000317] . ( 20 sec) [ -2398.9183] [ 433] [depth= 3] . ( 20 sec) [ -2397.8334] [ 432] [depth= 5] . ( 20 sec) [ -2395.8443] [ 428] [depth= 5] . ( 21 sec) [ -2395.6842] [ 429] [depth= 2] . ( 22 sec) [ -2395.6535] [ 429] [depth= 1] . ( 24 sec) [ -2394.8893] [ 427] [depth= 1] . ( 24 sec) [ -2394.7765] [ 427] [depth= 1] . ( 27 sec) [ -2394.7638] [ 427] [depth= 1] . ( 27 sec) [ -2394.5297] [ 426] [depth= 1] . ( 29 sec) [ -2393.9262] [ 425] [depth= 2] . ( 33 sec) [ -2393.4736] [ 425] [depth= 1] . ( 35 sec) [ -2393.1738] [ 425] [depth= 1] . ( 36 sec) [ -2392.7043] [ 425] [depth= 1] . ( 36 sec) [ -2391.3895] [ 425] [depth= 1] . ( 36 sec) [ -2390.9928] [ 425] [depth= 1] . ( 39 sec) [ -2390.7372] [ 425] [depth= 2] . ( 44 sec) [ -2390.6842] [ 425] [depth= 1] . ( 44 sec) [ -2390.6008] [ 426] [depth= 1] . ( 44 sec) [ -2390.4977] [ 426] [depth= 1] . ( 46 sec) [ -2390.2513] [ 426] [depth= 1] . ( 49 sec) [ -2390.1862] [ 426] [depth= 1] . ( 51 sec) [ -2390.1152] [ 426] [depth= 1] . ( 51 sec) [ -2390.1024] [ 426] [depth= 1] . ( 52 sec) [ -2386.3119] [Branch lengths ] . ( 52 sec) [ -2385.7435] [Alpha ][ 1.221981] . ( 53 sec) [ -2385.7270] [ 419] [depth= 6] . ( 53 sec) [ -2385.7084] [ 424] [depth= 8] . ( 78 sec) [ -2385.6408] [ 428] [depth= 1] . ( 85 sec) [ -2385.6209] [ 428] [depth= 1] . ( 98 sec) [ -2384.9652] [Branch lengths ] . ( 98 sec) [ -2384.8483] [Alpha ][ 1.341671] . ( 98 sec) [ -2384.8483] [Topology ] . ( 99 sec) [ -2384.7562] [Topology ] . ( 100 sec) [ -2384.7051] [Topology ] . ( 101 sec) [ -2384.6663] [Topology ] . ( 102 sec) [ -2384.6356] [Topology ] . ( 103 sec) [ -2384.6098] [Topology ] . ( 104 sec) [ -2384.5879] [Topology ] . ( 104 sec) [ -2384.5877] [Alpha ][ 1.346003] . ( 104 sec) [ -2384.5877] [Topology ] . ( 105 sec) [ -2384.5689] [Topology ] . ( 106 sec) [ -2384.5526] [Topology ] . ( 107 sec) [ -2384.5384] [Topology ] . ( 108 sec) [ -2384.5261] [Topology ] . ( 109 sec) [ -2384.5154] [Topology ] . ( 110 sec) [ -2384.5060] [Topology ] . ( 110 sec) [ -2384.5060] [Alpha ][ 1.344199] . ( 110 sec) [ -2384.5060] [Topology ] . ( 111 sec) [ -2384.4977] [Topology ] . ( 112 sec) [ -2384.4904] [Topology ] . ( 113 sec) [ -2384.4839] [Topology ] . ( 114 sec) [ -2384.4782] [Topology ] . ( 115 sec) [ -2384.4732] [Topology ] . ( 116 sec) [ -2384.4687] [Topology ] . ( 116 sec) [ -2384.4686] [Alpha ][ 1.342257] . ( 116 sec) [ -2384.4686] [Topology ] . ( 117 sec) [ -2384.4647] [Topology ] . ( 118 sec) [ -2384.4628] [Topology ] . ( 119 sec) [ -2384.4621] [Topology ] . ( 119 sec) [ -2384.4621] [Alpha ][ 1.342257] . ( 119 sec) [ -2384.4621] [Topology ] . ( 120 sec) [ -2384.4619] [Topology ] . ( 121 sec) [ -2384.4619] [Alpha ][ 1.342257] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2384.461915. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5717.7283] [Alpha ][ 0.500960] . ( 0 sec) [ -5678.1926] [ 969] [depth= 10] . ( 1 sec) [ -5484.4751] [ 921] [depth= 7] . ( 1 sec) [ -5334.7990] [ 915] [depth= 5] . ( 1 sec) [ -5214.5057] [ 882] [depth= 1] . ( 1 sec) [ -5138.5315] [ 873] [depth= 6] . ( 1 sec) [ -5059.0227] [ 871] [depth= 2] . ( 1 sec) [ -4840.0603] [ 829] [depth= 1] . ( 2 sec) [ -4794.1770] [ 828] [depth= 5] . ( 2 sec) [ -4760.5196] [ 822] [depth= 2] . ( 2 sec) [ -4603.5696] [ 819] [depth= 3] . ( 2 sec) [ -4545.1798] [ 807] [depth= 1] . ( 2 sec) [ -4541.4764] [ 805] [depth= 3] . ( 2 sec) [ -4480.4206] [ 804] [depth= 4] . ( 2 sec) [ -4454.1069] [ 803] [depth= 1] . ( 2 sec) [ -4438.0322] [ 800] [depth= 3] . ( 3 sec) [ -4423.2907] [ 803] [depth= 1] . ( 3 sec) [ -4360.6734] [ 790] [depth= 3] . ( 3 sec) [ -4332.0838] [ 786] [depth= 1] . ( 3 sec) [ -4323.7592] [ 784] [depth= 6] . ( 3 sec) [ -4320.2624] [ 783] [depth= 1] . ( 4 sec) [ -4168.8093] [ 752] [depth= 8] . ( 4 sec) [ -4150.6100] [ 751] [depth= 2] . ( 4 sec) [ -4111.3097] [ 713] [depth= 1] . ( 4 sec) [ -4100.3991] [ 711] [depth= 4] . ( 4 sec) [ -4017.2240] [ 710] [depth= 4] . ( 4 sec) [ -3933.3787] [ 693] [depth= 9] . ( 4 sec) [ -3830.1482] [ 668] [depth= 8] . ( 5 sec) [ -3509.2753] [ 613] [depth= 7] . ( 5 sec) [ -3486.7613] [ 611] [depth= 1] . ( 5 sec) [ -3482.9223] [ 611] [depth= 1] . ( 5 sec) [ -3440.5800] [ 606] [depth= 5] . ( 5 sec) [ -3431.7469] [ 605] [depth= 1] . ( 6 sec) [ -3416.1841] [ 608] [depth= 5] . ( 6 sec) [ -3404.5679] [ 607] [depth= 1] . ( 6 sec) [ -3404.1785] [ 607] [depth= 1] . ( 6 sec) [ -3380.9635] [ 602] [depth= 3] . ( 6 sec) [ -3374.1541] [ 600] [depth= 2] . ( 7 sec) [ -3315.0495] [ 570] [depth= 10] . ( 7 sec) [ -3314.1275] [ 571] [depth= 1] . ( 7 sec) [ -3305.4114] [ 562] [depth= 2] . ( 7 sec) [ -3301.7280] [ 562] [depth= 8] . ( 7 sec) [ -3238.2811] [ 555] [depth= 10] . ( 8 sec) [ -3207.2039] [ 555] [depth= 1] . ( 8 sec) [ -3203.5855] [ 557] [depth= 2] . ( 8 sec) [ -3201.4828] [ 557] [depth= 1] . ( 9 sec) [ -3035.2964] [ 544] [depth= 9] . ( 9 sec) [ -2997.8393] [ 538] [depth= 3] . ( 9 sec) [ -2996.3467] [ 538] [depth= 1] . ( 9 sec) [ -2954.9172] [ 541] [depth= 1] . ( 10 sec) [ -2944.0288] [ 538] [depth= 1] . ( 10 sec) [ -2939.1554] [ 537] [depth= 7] . ( 10 sec) [ -2901.2745] [ 536] [depth= 2] . ( 10 sec) [ -2883.8126] [ 536] [depth= 3] . ( 10 sec) [ -2783.0817] [ 498] [depth= 10] . ( 12 sec) [ -2757.2563] [ 500] [depth= 2] . ( 12 sec) [ -2756.1737] [ 500] [depth= 2] . ( 12 sec) [ -2751.4802] [ 499] [depth= 1] . ( 12 sec) [ -2728.8786] [ 494] [depth= 5] . ( 13 sec) [ -2723.4894] [ 495] [depth= 1] . ( 13 sec) [ -2706.3264] [ 491] [depth= 3] . ( 13 sec) [ -2682.7633] [ 484] [depth= 9] . ( 13 sec) [ -2675.4221] [ 485] [depth= 4] . ( 13 sec) [ -2675.1092] [ 485] [depth= 1] . ( 15 sec) [ -2636.9863] [ 485] [depth= 2] . ( 15 sec) [ -2586.4282] [ 449] [depth= 6] . ( 15 sec) [ -2505.0782] [Branch lengths ] . ( 15 sec) [ -2496.0437] [Alpha ][ 0.955508] . ( 16 sec) [ -2494.8820] [ 446] [depth= 8] . ( 16 sec) [ -2492.0885] [ 445] [depth= 1] . ( 17 sec) [ -2482.5077] [ 449] [depth= 1] . ( 17 sec) [ -2482.2645] [ 448] [depth= 1] . ( 17 sec) [ -2482.2351] [ 449] [depth= 1] . ( 18 sec) [ -2459.3390] [ 445] [depth= 1] . ( 18 sec) [ -2440.6534] [ 443] [depth= 2] . ( 21 sec) [ -2440.6343] [ 443] [depth= 1] . ( 26 sec) [ -2418.8221] [ 429] [depth= 5] . ( 26 sec) [ -2410.7367] [ 428] [depth= 5] . ( 27 sec) [ -2408.7050] [ 430] [depth= 1] . ( 27 sec) [ -2407.0971] [ 431] [depth= 4] . ( 27 sec) [ -2404.8924] [ 432] [depth= 7] . ( 28 sec) [ -2403.0435] [ 432] [depth= 1] . ( 29 sec) [ -2402.8918] [ 432] [depth= 1] . ( 29 sec) [ -2402.5801] [ 432] [depth= 1] . ( 30 sec) [ -2402.5585] [ 432] [depth= 1] . ( 30 sec) [ -2402.2164] [ 431] [depth= 3] . ( 31 sec) [ -2402.1710] [ 432] [depth= 2] . ( 34 sec) [ -2402.0756] [ 431] [depth= 2] . ( 35 sec) [ -2402.0497] [ 431] [depth= 1] . ( 43 sec) [ -2399.6618] [ 431] [depth= 1] . ( 46 sec) [ -2399.0758] [ 431] [depth= 1] . ( 46 sec) [ -2399.0657] [ 431] [depth= 1] . ( 46 sec) [ -2398.9442] [ 432] [depth= 1] . ( 52 sec) [ -2398.8110] [ 432] [depth= 1] . ( 55 sec) [ -2396.0724] [Branch lengths ] . ( 55 sec) [ -2395.0838] [Alpha ][ 1.234244] . ( 55 sec) [ -2395.0690] [ 429] [depth= 5] . ( 58 sec) [ -2395.0173] [ 430] [depth= 1] . ( 64 sec) [ -2394.5853] [ 431] [depth= 3] . ( 64 sec) [ -2391.2502] [ 430] [depth= 3] . ( 68 sec) [ -2391.0977] [ 429] [depth= 1] . ( 68 sec) [ -2391.0222] [ 429] [depth= 1] . ( 76 sec) [ -2390.9769] [ 429] [depth= 1] . ( 94 sec) [ -2390.9461] [ 429] [depth= 1] . ( 105 sec) [ -2390.0895] [Branch lengths ] . ( 105 sec) [ -2389.9880] [Alpha ][ 1.346827] . ( 106 sec) [ -2389.9638] [ 428] [depth= 4] . ( 122 sec) [ -2389.9438] [ 428] [depth= 1] . ( 159 sec) [ -2389.8468] [Branch lengths ] . ( 159 sec) [ -2389.8465] [Alpha ][ 1.352634] . ( 159 sec) [ -2389.8465] [Topology ] . ( 160 sec) [ -2389.8171] [Topology ] . ( 161 sec) [ -2389.7979] [Topology ] . ( 162 sec) [ -2389.7876] [Topology ] . ( 163 sec) [ -2389.7960] [Topology ] . Moving backward . ( 163 sec) [ -2389.7357] [Topology ] . ( 164 sec) [ -2389.7204] [Topology ] . ( 165 sec) [ -2389.7081] [Topology ] . ( 166 sec) [ -2389.6983] [Topology ] . ( 166 sec) [ -2389.6982] [Alpha ][ 1.348988] . ( 166 sec) [ -2389.6982] [Topology ] . ( 167 sec) [ -2389.6899] [Topology ] . ( 168 sec) [ -2389.6835] [Topology ] . ( 169 sec) [ -2389.6786] [Topology ] . ( 170 sec) [ -2389.6752] [Topology ] . ( 171 sec) [ -2389.6715] [Topology ] . ( 172 sec) [ -2389.6691] [Topology ] . ( 172 sec) [ -2389.6690] [Alpha ][ 1.346935] . ( 173 sec) [ -2389.6690] [Topology ] . ( 174 sec) [ -2389.6659] [Topology ] . ( 175 sec) [ -2389.6636] [Topology ] . ( 175 sec) [ -2389.6630] [Topology ] . ( 176 sec) [ -2389.6630] [Alpha ][ 1.345588] . ( 176 sec) [ -2389.6630] [Topology ] . ( 177 sec) [ -2389.6627] [Topology ] . ( 177 sec) [ -2389.6627] [Alpha ][ 1.346934] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2389.662679. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5127.3510] [Alpha ][ 0.500960] . ( 0 sec) [ -5043.6468] [ 836] [depth= 10] . ( 0 sec) [ -4801.9567] [ 809] [depth= 7] . ( 0 sec) [ -4699.7402] [ 800] [depth= 11] . ( 1 sec) [ -4688.2715] [ 796] [depth= 7] . ( 1 sec) [ -4643.0223] [ 797] [depth= 1] . ( 1 sec) [ -4552.1578] [ 781] [depth= 7] . ( 1 sec) [ -4544.5812] [ 769] [depth= 2] . ( 1 sec) [ -4500.6792] [ 766] [depth= 8] . ( 1 sec) [ -4430.8770] [ 764] [depth= 6] . ( 2 sec) [ -4389.7123] [ 759] [depth= 1] . ( 2 sec) [ -4254.9659] [ 742] [depth= 5] . ( 2 sec) [ -3878.0741] [ 700] [depth= 5] . ( 2 sec) [ -3870.1643] [ 699] [depth= 3] . ( 2 sec) [ -3823.7023] [ 699] [depth= 3] . ( 2 sec) [ -3660.2657] [ 695] [depth= 2] . ( 2 sec) [ -3654.3798] [ 693] [depth= 4] . ( 2 sec) [ -3570.4032] [ 655] [depth= 4] . ( 3 sec) [ -3523.6910] [ 650] [depth= 5] . ( 3 sec) [ -3486.1852] [ 650] [depth= 1] . ( 3 sec) [ -3448.9530] [ 638] [depth= 2] . ( 3 sec) [ -3446.7633] [ 639] [depth= 1] . ( 3 sec) [ -3345.8354] [ 636] [depth= 6] . ( 3 sec) [ -3336.4516] [ 637] [depth= 1] . ( 3 sec) [ -3295.5297] [ 629] [depth= 5] . ( 4 sec) [ -3285.1722] [ 629] [depth= 1] . ( 4 sec) [ -3160.7885] [ 593] [depth= 8] . ( 5 sec) [ -3159.7300] [ 594] [depth= 1] . ( 5 sec) [ -3111.2065] [ 547] [depth= 4] . ( 5 sec) [ -3108.5952] [ 546] [depth= 1] . ( 5 sec) [ -3100.3369] [ 542] [depth= 2] . ( 5 sec) [ -3098.6417] [ 540] [depth= 2] . ( 5 sec) [ -3095.0092] [ 539] [depth= 5] . ( 6 sec) [ -3081.0194] [ 539] [depth= 1] . ( 7 sec) [ -2916.0546] [ 487] [depth= 5] . ( 7 sec) [ -2915.2421] [ 487] [depth= 1] . ( 7 sec) [ -2910.0576] [ 483] [depth= 5] . ( 7 sec) [ -2907.6733] [ 483] [depth= 1] . ( 7 sec) [ -2907.3102] [ 483] [depth= 2] . ( 9 sec) [ -2902.0255] [ 488] [depth= 2] . ( 9 sec) [ -2871.0506] [ 487] [depth= 2] . ( 9 sec) [ -2827.5309] [ 487] [depth= 2] . ( 10 sec) [ -2794.2196] [ 482] [depth= 2] . ( 10 sec) [ -2790.6250] [ 482] [depth= 1] . ( 11 sec) [ -2790.4628] [ 482] [depth= 1] . ( 11 sec) [ -2758.0759] [ 480] [depth= 1] . ( 11 sec) [ -2757.4514] [ 480] [depth= 1] . ( 11 sec) [ -2756.8416] [ 479] [depth= 1] . ( 11 sec) [ -2755.1024] [ 480] [depth= 1] . ( 12 sec) [ -2754.8795] [ 482] [depth= 1] . ( 12 sec) [ -2754.0876] [ 483] [depth= 1] . ( 12 sec) [ -2709.0499] [ 454] [depth= 5] . ( 12 sec) [ -2648.3263] [ 454] [depth= 7] . ( 12 sec) [ -2571.8117] [ 454] [depth= 1] . ( 14 sec) [ -2563.9909] [ 457] [depth= 4] . ( 14 sec) [ -2563.5340] [ 457] [depth= 2] . ( 14 sec) [ -2553.7590] [ 456] [depth= 7] . ( 14 sec) [ -2550.9217] [ 455] [depth= 1] . ( 15 sec) [ -2550.6521] [ 455] [depth= 2] . ( 15 sec) [ -2519.5033] [ 436] [depth= 9] . ( 15 sec) [ -2509.2702] [ 435] [depth= 1] . ( 15 sec) [ -2492.9596] [ 435] [depth= 3] . ( 16 sec) [ -2488.6713] [ 435] [depth= 1] . ( 17 sec) [ -2476.0313] [ 436] [depth= 2] . ( 18 sec) [ -2472.7874] [ 435] [depth= 4] . ( 20 sec) [ -2434.7216] [Branch lengths ] . ( 20 sec) [ -2423.5010] [Alpha ][ 1.000142] . ( 20 sec) [ -2423.1986] [ 433] [depth= 3] . ( 20 sec) [ -2421.6093] [ 430] [depth= 2] . ( 20 sec) [ -2420.4448] [ 429] [depth= 5] . ( 21 sec) [ -2420.2555] [ 429] [depth= 1] . ( 23 sec) [ -2410.9979] [ 428] [depth= 4] . ( 23 sec) [ -2410.9876] [ 428] [depth= 1] . ( 25 sec) [ -2410.1370] [ 428] [depth= 1] . ( 26 sec) [ -2408.2669] [ 426] [depth= 1] . ( 26 sec) [ -2401.2847] [ 424] [depth= 7] . ( 27 sec) [ -2401.2518] [ 424] [depth= 1] . ( 32 sec) [ -2401.0510] [ 424] [depth= 1] . ( 35 sec) [ -2400.9899] [ 424] [depth= 1] . ( 35 sec) [ -2400.8456] [ 424] [depth= 1] . ( 35 sec) [ -2400.6524] [ 424] [depth= 1] . ( 38 sec) [ -2399.9122] [ 424] [depth= 1] . ( 46 sec) [ -2397.5583] [ 429] [depth= 2] . ( 46 sec) [ -2397.3755] [ 429] [depth= 1] . ( 50 sec) [ -2397.2054] [ 429] [depth= 1] . ( 51 sec) [ -2397.0746] [ 431] [depth= 1] . ( 54 sec) [ -2394.3617] [ 430] [depth= 2] . ( 54 sec) [ -2393.9911] [ 430] [depth= 1] . ( 54 sec) [ -2393.1184] [ 430] [depth= 1] . ( 55 sec) [ -2392.3681] [ 430] [depth= 3] . ( 56 sec) [ -2388.6571] [Branch lengths ] . ( 56 sec) [ -2388.0647] [Alpha ][ 1.220717] . ( 56 sec) [ -2388.0409] [ 423] [depth= 7] . ( 56 sec) [ -2387.8919] [ 425] [depth= 9] . ( 56 sec) [ -2385.3241] [ 425] [depth= 2] . ( 98 sec) [ -2385.3081] [ 425] [depth= 1] . ( 99 sec) [ -2384.7773] [Branch lengths ] . ( 99 sec) [ -2384.6617] [Alpha ][ 1.339385] . ( 99 sec) [ -2384.6430] [ 424] [depth= 8] . ( 119 sec) [ -2384.4512] [ 427] [depth= 1] . ( 148 sec) [ -2384.3757] [Branch lengths ] . ( 148 sec) [ -2384.3753] [Alpha ][ 1.346378] . ( 148 sec) [ -2384.3753] [Topology ] . ( 149 sec) [ -2384.3606] [Topology ] . ( 150 sec) [ -2384.3513] [Topology ] . ( 151 sec) [ -2384.3447] [Topology ] . ( 152 sec) [ -2384.3403] [Topology ] . ( 153 sec) [ -2384.3361] [Topology ] . ( 154 sec) [ -2384.3325] [Topology ] . ( 154 sec) [ -2384.3324] [Alpha ][ 1.342666] . ( 154 sec) [ -2384.3324] [Topology ] . ( 155 sec) [ -2384.3313] [Topology ] . ( 156 sec) [ -2384.3308] [Topology ] . ( 156 sec) [ -2384.3308] [Alpha ][ 1.342666] . ( 156 sec) [ -2384.3308] [Topology ] . ( 157 sec) [ -2384.3306] [Topology ] . ( 158 sec) [ -2384.3306] [Alpha ][ 1.342666] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2384.330594. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 0 sec) [ -2496.1543] [Topology ] . ( 1 sec) [ -2426.2101] [Topology ] . ( 2 sec) [ -2408.7866] [Topology ] . ( 3 sec) [ -2399.9867] [Topology ] . ( 4 sec) [ -2397.8601] [Topology ] . ( 5 sec) [ -2397.4479] [Topology ] . ( 6 sec) [ -2397.3036] [Topology ] . ( 7 sec) [ -2397.2430] [Topology ] . ( 8 sec) [ -2397.2138] [Topology ] . ( 9 sec) [ -2397.1983] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -2395.8503] [Topology ] . ( 17 sec) [ -2394.5012] [Alpha ][ 1.313066] . ( 17 sec) [ -2394.5012] [Topology ] . ( 18 sec) [ -2394.4118] [Topology ] . ( 19 sec) [ -2394.3864] [Topology ] . ( 20 sec) [ -2394.3757] [Topology ] . ( 21 sec) [ -2394.3709] [Topology ] . ( 22 sec) [ -2394.3686] [Topology ] . ( 23 sec) [ -2394.3674] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -2394.1201] [Topology ] . ( 30 sec) [ -2394.1162] [Alpha ][ 1.291508] . ( 30 sec) [ -2394.1162] [Topology ] . ( 31 sec) [ -2394.1143] [Topology ] . ( 32 sec) [ -2394.1136] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -2394.1136] [Alpha ][ 1.289494] . ( 39 sec) [ -2394.1136] [Topology ] . ( 40 sec) [ -2394.1132] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 53 sec) [ -2494.7867] [ 428] [depth= 1] . ( 53 sec) [ -2494.7532] [ 428] [depth= 1] . ( 53 sec) [ -2494.6570] [ 428] [depth= 1] . ( 54 sec) [ -2492.7817] [ 428] [depth= 1] . ( 54 sec) [ -2478.1770] [ 425] [depth= 2] . ( 55 sec) [ -2478.0286] [ 425] [depth= 1] . ( 55 sec) [ -2472.2849] [ 424] [depth= 1] . ( 56 sec) [ -2467.8608] [ 423] [depth= 1] . ( 58 sec) [ -2467.8396] [ 424] [depth= 1] . ( 58 sec) [ -2466.6043] [ 424] [depth= 1] . ( 58 sec) [ -2466.5595] [ 423] [depth= 1] . ( 59 sec) [ -2466.0622] [ 423] [depth= 2] . ( 59 sec) [ -2464.9704] [ 424] [depth= 1] . ( 59 sec) [ -2464.9498] [ 424] [depth= 1] . ( 60 sec) [ -2461.7771] [ 421] [depth= 1] . ( 61 sec) [ -2418.2926] [ 422] [depth= 1] . ( 63 sec) [ -2418.0150] [ 421] [depth= 1] . ( 65 sec) [ -2416.6167] [ 425] [depth= 1] . ( 67 sec) [ -2415.7755] [ 425] [depth= 1] . ( 67 sec) [ -2415.4146] [ 422] [depth= 2] . ( 67 sec) [ -2412.8793] [ 427] [depth= 5] . ( 67 sec) [ -2412.5181] [ 430] [depth= 1] . ( 67 sec) [ -2410.3918] [ 428] [depth= 1] . ( 69 sec) [ -2408.9820] [ 431] [depth= 2] . ( 69 sec) [ -2408.0823] [ 428] [depth= 2] . ( 69 sec) [ -2407.4660] [ 429] [depth= 1] . ( 71 sec) [ -2405.1994] [ 428] [depth= 2] . ( 72 sec) [ -2405.1753] [ 427] [depth= 1] . ( 72 sec) [ -2402.6960] [ 425] [depth= 1] . ( 74 sec) [ -2402.1954] [ 424] [depth= 1] . ( 75 sec) [ -2401.8737] [ 424] [depth= 1] . ( 76 sec) [ -2399.8426] [ 424] [depth= 2] . ( 76 sec) [ -2399.6347] [ 424] [depth= 1] . ( 79 sec) [ -2399.3996] [ 424] [depth= 2] . ( 81 sec) [ -2390.3633] [Branch lengths ] . ( 82 sec) [ -2389.3200] [Alpha ][ 1.355713] . ( 98 sec) [ -2389.2749] [ 425] [depth= 1] . ( 100 sec) [ -2389.2330] [ 421] [depth= 2] . ( 100 sec) [ -2388.0985] [ 425] [depth= 2] . ( 112 sec) [ -2387.9053] [ 423] [depth= 4] . ( 116 sec) [ -2387.5581] [ 424] [depth= 1] . ( 119 sec) [ -2386.4682] [ 424] [depth= 2] . ( 120 sec) [ -2385.9907] [ 424] [depth= 2] . ( 121 sec) [ -2385.6290] [ 424] [depth= 2] . ( 122 sec) [ -2385.3606] [ 424] [depth= 2] . ( 122 sec) [ -2384.6288] [Branch lengths ] . ( 122 sec) [ -2384.6282] [Alpha ][ 1.346040] . ( 141 sec) [ -2384.6100] [ 427] [depth= 1] . ( 141 sec) [ -2384.5969] [ 424] [depth= 1] . ( 171 sec) [ -2384.4898] [Branch lengths ] . ( 171 sec) [ -2384.4898] [Alpha ][ 1.346040] . ( 171 sec) [ -2384.4898] [Topology ] . ( 172 sec) [ -2384.4753] [Topology ] . ( 173 sec) [ -2384.4686] [Topology ] . ( 174 sec) [ -2384.4652] [Topology ] . ( 175 sec) [ -2384.4635] [Topology ] . ( 176 sec) [ -2384.4626] [Topology ] . ( 177 sec) [ -2384.4625] [Alpha ][ 1.342407] . ( 177 sec) [ -2384.4625] [Topology ] . ( 178 sec) [ -2384.4620] [Topology ] . ( 178 sec) [ -2384.4620] [Alpha ][ 1.342407] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -2384.4617] [Topology ] . Checking for NNIs, optimizing five branches... . ( 191 sec) [ -2384.4616] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2394.113150 . Log likelihood obtained after SPR moves : -2384.461583 . Log likelihood of the current tree: -2384.461583. . Printing the most likely tree in file 'proteic_M1991_32x129_2004.phy_phyml_tree.txt'... . Best log likelihood : -2384.330594 . Time used 0h3m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 930.25user 0.00system 15:36.03elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps