.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2382_28x162_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... . 129 patterns found. (out of a total of 162 sites) . 75 sites without polymorphism (46.30%). . [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)... . ( 0 sec) [ -3299.9695] [Alpha ][ 0.500960] . ( 0 sec) [ -3269.7660] [ 539] [depth= 10] . ( 0 sec) [ -3249.4422] [ 534] [depth= 8] . ( 1 sec) [ -3242.7399] [ 531] [depth= 5] . ( 1 sec) [ -3183.6877] [ 528] [depth= 1] . ( 1 sec) [ -3156.5511] [ 525] [depth= 5] . ( 1 sec) [ -3152.6422] [ 524] [depth= 2] . ( 2 sec) [ -3149.0406] [ 524] [depth= 1] . ( 2 sec) [ -3140.0737] [ 523] [depth= 7] . ( 2 sec) [ -3127.6165] [ 524] [depth= 1] . ( 2 sec) [ -3117.7627] [ 519] [depth= 4] . ( 2 sec) [ -3117.7009] [ 518] [depth= 1] . ( 2 sec) [ -3115.5111] [ 519] [depth= 1] . ( 2 sec) [ -3109.9904] [ 518] [depth= 3] . ( 2 sec) [ -3094.3945] [ 516] [depth= 5] . ( 3 sec) [ -3080.6852] [ 514] [depth= 9] . ( 3 sec) [ -3071.1106] [ 511] [depth= 4] . ( 3 sec) [ -3057.0988] [ 509] [depth= 2] . ( 3 sec) [ -3040.6758] [ 506] [depth= 3] . ( 3 sec) [ -3019.4349] [ 500] [depth= 1] . ( 3 sec) [ -2979.4582] [ 495] [depth= 7] . ( 4 sec) [ -2968.1868] [ 493] [depth= 6] . ( 4 sec) [ -2966.7737] [ 491] [depth= 2] . ( 4 sec) [ -2945.1718] [ 485] [depth= 10] . ( 4 sec) [ -2913.6724] [ 483] [depth= 1] . ( 4 sec) [ -2910.6645] [ 480] [depth= 1] . ( 4 sec) [ -2910.3412] [ 479] [depth= 1] . ( 5 sec) [ -2909.2464] [ 475] [depth= 5] . ( 5 sec) [ -2889.3475] [ 473] [depth= 1] . ( 5 sec) [ -2886.4284] [ 474] [depth= 9] . ( 5 sec) [ -2869.6670] [ 471] [depth= 3] . ( 5 sec) [ -2853.7761] [ 471] [depth= 1] . ( 5 sec) [ -2840.1289] [ 468] [depth= 10] . ( 6 sec) [ -2839.1563] [ 466] [depth= 3] . ( 6 sec) [ -2838.5834] [ 466] [depth= 2] . ( 6 sec) [ -2822.6621] [ 461] [depth= 1] . ( 6 sec) [ -2821.2854] [ 461] [depth= 2] . ( 7 sec) [ -2819.8625] [ 460] [depth= 3] . ( 7 sec) [ -2812.9054] [ 460] [depth= 1] . ( 7 sec) [ -2812.3883] [ 462] [depth= 4] . ( 8 sec) [ -2777.7862] [ 465] [depth= 3] . ( 9 sec) [ -2777.4373] [ 464] [depth= 1] . ( 9 sec) [ -2774.7844] [ 463] [depth= 1] . ( 9 sec) [ -2773.2188] [ 464] [depth= 2] . ( 9 sec) [ -2769.4267] [ 462] [depth= 1] . ( 11 sec) [ -2764.7686] [ 461] [depth= 3] . ( 11 sec) [ -2758.5127] [ 460] [depth= 1] . ( 11 sec) [ -2758.2018] [ 462] [depth= 3] . ( 11 sec) [ -2749.0932] [ 455] [depth= 5] . ( 12 sec) [ -2746.1324] [ 456] [depth= 1] . ( 14 sec) [ -2743.3677] [ 456] [depth= 1] . ( 14 sec) [ -2736.4410] [ 455] [depth= 8] . ( 22 sec) [ -2735.6711] [ 457] [depth= 1] . ( 22 sec) [ -2735.5501] [ 457] [depth= 4] . ( 22 sec) [ -2720.4504] [Branch lengths ] . ( 23 sec) [ -2716.2523] [Alpha ][ 0.361528] . ( 23 sec) [ -2713.7488] [ 456] [depth= 4] . ( 23 sec) [ -2712.7424] [ 455] [depth= 4] . ( 25 sec) [ -2711.3813] [ 455] [depth= 1] . ( 26 sec) [ -2711.0090] [ 454] [depth= 1] . ( 26 sec) [ -2709.6514] [ 454] [depth= 1] . ( 27 sec) [ -2707.6756] [ 452] [depth= 7] . ( 29 sec) [ -2707.6080] [ 453] [depth= 1] . ( 45 sec) [ -2705.7956] [ 453] [depth= 1] . ( 45 sec) [ -2705.6246] [ 454] [depth= 1] . ( 55 sec) [ -2704.5762] [ 454] [depth= 1] . ( 58 sec) [ -2703.3784] [ 455] [depth= 1] . ( 70 sec) [ -2703.0591] [ 455] [depth= 6] . ( 73 sec) [ -2700.4573] [ 453] [depth= 2] . ( 82 sec) [ -2700.4208] [ 452] [depth= 1] . ( 88 sec) [ -2700.0487] [ 452] [depth= 3] . ( 89 sec) [ -2696.0030] [Branch lengths ] . ( 89 sec) [ -2696.0007] [Alpha ][ 0.358676] . ( 108 sec) [ -2695.9887] [ 452] [depth= 1] . ( 175 sec) [ -2695.7984] [Branch lengths ] . ( 175 sec) [ -2695.7979] [Alpha ][ 0.357292] . ( 175 sec) [ -2695.7979] [Topology ] . ( 176 sec) [ -2695.7791] [Topology ] . ( 177 sec) [ -2695.7725] [Topology ] . ( 178 sec) [ -2695.7695] [Topology ] . ( 179 sec) [ -2695.7681] [Topology ] . ( 180 sec) [ -2695.7675] [Topology ] . ( 180 sec) [ -2695.7672] [Alpha ][ 0.356319] . ( 180 sec) [ -2695.7672] [Topology ] . ( 181 sec) [ -2695.7668] [Topology ] . ( 181 sec) [ -2695.7668] [Alpha ][ 0.356319] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2695.766816. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3442.3553] [Alpha ][ 0.500960] . ( 0 sec) [ -3418.6224] [ 532] [depth= 10] . ( 1 sec) [ -3373.0455] [ 526] [depth= 6] . ( 1 sec) [ -3364.0516] [ 526] [depth= 1] . ( 1 sec) [ -3326.1870] [ 524] [depth= 5] . ( 1 sec) [ -3325.4962] [ 524] [depth= 3] . ( 1 sec) [ -3306.5994] [ 522] [depth= 4] . ( 1 sec) [ -3176.8055] [ 519] [depth= 4] . ( 1 sec) [ -3158.3216] [ 516] [depth= 1] . ( 1 sec) [ -3138.2016] [ 513] [depth= 2] . ( 2 sec) [ -3097.2986] [ 513] [depth= 3] . ( 2 sec) [ -3086.9850] [ 514] [depth= 1] . ( 2 sec) [ -3059.1633] [ 508] [depth= 7] . ( 2 sec) [ -3056.3583] [ 507] [depth= 1] . ( 2 sec) [ -3055.7715] [ 507] [depth= 1] . ( 2 sec) [ -3054.2062] [ 506] [depth= 1] . ( 2 sec) [ -3040.6406] [ 506] [depth= 3] . ( 2 sec) [ -3033.1062] [ 505] [depth= 1] . ( 3 sec) [ -3027.5210] [ 506] [depth= 5] . ( 3 sec) [ -3024.0542] [ 505] [depth= 1] . ( 3 sec) [ -3022.5099] [ 503] [depth= 1] . ( 3 sec) [ -2999.6671] [ 501] [depth= 4] . ( 3 sec) [ -2994.5192] [ 498] [depth= 9] . ( 3 sec) [ -2970.8664] [ 497] [depth= 2] . ( 4 sec) [ -2937.5781] [ 488] [depth= 4] . ( 4 sec) [ -2937.4485] [ 487] [depth= 1] . ( 4 sec) [ -2936.9320] [ 488] [depth= 1] . ( 4 sec) [ -2934.9910] [ 487] [depth= 2] . ( 4 sec) [ -2934.4823] [ 486] [depth= 1] . ( 5 sec) [ -2932.3960] [ 487] [depth= 1] . ( 5 sec) [ -2932.2601] [ 487] [depth= 2] . ( 5 sec) [ -2927.7110] [ 486] [depth= 2] . ( 5 sec) [ -2926.0033] [ 486] [depth= 1] . ( 5 sec) [ -2922.3651] [ 482] [depth= 1] . ( 5 sec) [ -2919.9227] [ 483] [depth= 2] . ( 5 sec) [ -2911.5765] [ 480] [depth= 6] . ( 6 sec) [ -2874.0647] [ 465] [depth= 4] . ( 6 sec) [ -2873.7660] [ 469] [depth= 1] . ( 6 sec) [ -2872.3368] [ 470] [depth= 1] . ( 7 sec) [ -2868.5139] [ 473] [depth= 4] . ( 7 sec) [ -2867.6047] [ 471] [depth= 2] . ( 8 sec) [ -2865.7310] [ 473] [depth= 3] . ( 8 sec) [ -2860.1250] [ 472] [depth= 1] . ( 8 sec) [ -2859.7555] [ 471] [depth= 3] . ( 10 sec) [ -2858.7250] [ 471] [depth= 1] . ( 10 sec) [ -2854.2851] [ 472] [depth= 3] . ( 10 sec) [ -2812.5978] [ 472] [depth= 1] . ( 10 sec) [ -2812.5027] [ 472] [depth= 1] . ( 10 sec) [ -2807.1185] [ 472] [depth= 5] . ( 12 sec) [ -2801.3065] [ 470] [depth= 7] . ( 12 sec) [ -2779.8204] [ 468] [depth= 6] . ( 12 sec) [ -2773.9654] [ 469] [depth= 9] . ( 12 sec) [ -2772.4034] [ 467] [depth= 1] . ( 12 sec) [ -2752.2646] [ 458] [depth= 6] . ( 12 sec) [ -2751.7324] [ 458] [depth= 4] . ( 13 sec) [ -2751.3187] [ 458] [depth= 1] . ( 15 sec) [ -2746.7342] [ 456] [depth= 4] . ( 15 sec) [ -2744.1010] [ 456] [depth= 2] . ( 16 sec) [ -2743.7067] [ 457] [depth= 2] . ( 17 sec) [ -2741.8734] [ 456] [depth= 1] . ( 18 sec) [ -2732.2071] [Branch lengths ] . ( 18 sec) [ -2728.4020] [Alpha ][ 0.365775] . ( 28 sec) [ -2728.3044] [ 456] [depth= 1] . ( 30 sec) [ -2726.3998] [ 457] [depth= 1] . ( 30 sec) [ -2725.7207] [ 455] [depth= 1] . ( 31 sec) [ -2724.8089] [ 455] [depth= 1] . ( 33 sec) [ -2724.6820] [ 453] [depth= 2] . ( 44 sec) [ -2721.9796] [ 453] [depth= 6] . ( 55 sec) [ -2720.6743] [ 452] [depth= 5] . ( 58 sec) [ -2714.5951] [ 451] [depth= 1] . ( 60 sec) [ -2714.5026] [ 451] [depth= 1] . ( 60 sec) [ -2711.6406] [ 450] [depth= 2] . ( 60 sec) [ -2711.3163] [ 450] [depth= 1] . ( 60 sec) [ -2710.6778] [ 450] [depth= 2] . ( 65 sec) [ -2708.4673] [ 451] [depth= 1] . ( 66 sec) [ -2707.5479] [ 454] [depth= 1] . ( 66 sec) [ -2706.9705] [ 451] [depth= 2] . ( 70 sec) [ -2705.6607] [ 451] [depth= 1] . ( 74 sec) [ -2705.6188] [ 451] [depth= 1] . ( 78 sec) [ -2705.0267] [ 451] [depth= 1] . ( 79 sec) [ -2704.8187] [ 451] [depth= 1] . ( 82 sec) [ -2699.9422] [Branch lengths ] . ( 82 sec) [ -2699.8393] [Alpha ][ 0.347038] . ( 92 sec) [ -2699.4127] [ 451] [depth= 1] . ( 141 sec) [ -2699.3001] [ 452] [depth= 1] . ( 141 sec) [ -2698.6509] [ 452] [depth= 8] . ( 151 sec) [ -2698.5819] [ 453] [depth= 1] . ( 159 sec) [ -2697.4529] [Branch lengths ] . ( 159 sec) [ -2697.4528] [Alpha ][ 0.346252] . ( 189 sec) [ -2696.9066] [ 453] [depth= 1] . ( 223 sec) [ -2696.6878] [ 453] [depth= 1] . ( 241 sec) [ -2696.3501] [Branch lengths ] . ( 241 sec) [ -2696.3463] [Alpha ][ 0.342599] . ( 323 sec) [ -2696.2854] [Branch lengths ] . ( 323 sec) [ -2696.2854] [Topology ] . ( 323 sec) [ -2696.2185] [Topology ] . ( 324 sec) [ -2696.1323] [Topology ] . ( 325 sec) [ -2696.1238] [Topology ] . ( 326 sec) [ -2696.1222] [Topology ] . ( 327 sec) [ -2696.1218] [Topology ] . ( 327 sec) [ -2696.1212] [Alpha ][ 0.343979] . ( 327 sec) [ -2696.1212] [Topology ] . ( 328 sec) [ -2696.1208] [Topology ] . ( 328 sec) [ -2696.1208] [Alpha ][ 0.344323] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2696.120821. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3307.7408] [Alpha ][ 0.500960] . ( 1 sec) [ -3298.3595] [ 539] [depth= 6] . ( 1 sec) [ -3280.9920] [ 541] [depth= 1] . ( 1 sec) [ -3257.2925] [ 533] [depth= 7] . ( 1 sec) [ -3235.6688] [ 531] [depth= 2] . ( 1 sec) [ -3221.4797] [ 529] [depth= 5] . ( 2 sec) [ -3219.7982] [ 527] [depth= 1] . ( 2 sec) [ -3204.2223] [ 523] [depth= 6] . ( 2 sec) [ -3174.4879] [ 523] [depth= 1] . ( 2 sec) [ -3162.8521] [ 524] [depth= 1] . ( 2 sec) [ -3154.1256] [ 520] [depth= 3] . ( 2 sec) [ -3152.5105] [ 519] [depth= 3] . ( 3 sec) [ -3137.0811] [ 518] [depth= 3] . ( 3 sec) [ -3136.6667] [ 518] [depth= 1] . ( 3 sec) [ -3135.0173] [ 520] [depth= 14] . ( 3 sec) [ -3104.8070] [ 518] [depth= 14] . ( 4 sec) [ -2967.1482] [ 510] [depth= 6] . ( 4 sec) [ -2953.4757] [ 507] [depth= 1] . ( 4 sec) [ -2945.4142] [ 504] [depth= 7] . ( 4 sec) [ -2944.6961] [ 502] [depth= 4] . ( 4 sec) [ -2922.8068] [ 501] [depth= 2] . ( 4 sec) [ -2921.3706] [ 500] [depth= 1] . ( 4 sec) [ -2909.5522] [ 497] [depth= 6] . ( 5 sec) [ -2898.4872] [ 494] [depth= 4] . ( 5 sec) [ -2890.3606] [ 491] [depth= 7] . ( 5 sec) [ -2874.7329] [ 489] [depth= 2] . ( 5 sec) [ -2867.8436] [ 486] [depth= 7] . ( 5 sec) [ -2864.9639] [ 484] [depth= 2] . ( 5 sec) [ -2859.0505] [ 484] [depth= 7] . ( 5 sec) [ -2857.5583] [ 482] [depth= 10] . ( 6 sec) [ -2847.2313] [ 483] [depth= 4] . ( 6 sec) [ -2845.5614] [ 483] [depth= 1] . ( 6 sec) [ -2832.5597] [ 479] [depth= 5] . ( 6 sec) [ -2829.6807] [ 474] [depth= 5] . ( 9 sec) [ -2823.9204] [ 475] [depth= 1] . ( 9 sec) [ -2823.2160] [ 474] [depth= 1] . ( 9 sec) [ -2823.0208] [ 475] [depth= 1] . ( 9 sec) [ -2809.7399] [ 470] [depth= 5] . ( 10 sec) [ -2808.9975] [ 470] [depth= 4] . ( 10 sec) [ -2805.0662] [ 468] [depth= 3] . ( 10 sec) [ -2803.4220] [ 473] [depth= 15] . ( 11 sec) [ -2803.0043] [ 472] [depth= 1] . ( 11 sec) [ -2796.5998] [ 470] [depth= 8] . ( 12 sec) [ -2784.2825] [ 469] [depth= 1] . ( 12 sec) [ -2784.0176] [ 468] [depth= 1] . ( 12 sec) [ -2781.2210] [ 469] [depth= 1] . ( 12 sec) [ -2778.3329] [ 468] [depth= 4] . ( 13 sec) [ -2776.2793] [ 468] [depth= 1] . ( 13 sec) [ -2776.2058] [ 469] [depth= 1] . ( 13 sec) [ -2774.8530] [ 468] [depth= 1] . ( 14 sec) [ -2773.8643] [ 469] [depth= 1] . ( 14 sec) [ -2772.2022] [ 467] [depth= 5] . ( 14 sec) [ -2769.2767] [ 466] [depth= 2] . ( 14 sec) [ -2746.1460] [ 463] [depth= 1] . ( 14 sec) [ -2733.9616] [ 457] [depth= 12] . ( 16 sec) [ -2732.0038] [ 458] [depth= 1] . ( 18 sec) [ -2727.9957] [ 459] [depth= 5] . ( 18 sec) [ -2719.9619] [Branch lengths ] . ( 19 sec) [ -2715.9311] [Alpha ][ 0.360952] . ( 19 sec) [ -2715.4253] [ 461] [depth= 2] . ( 27 sec) [ -2714.3697] [ 461] [depth= 3] . ( 27 sec) [ -2713.3904] [ 461] [depth= 1] . ( 33 sec) [ -2711.7877] [ 461] [depth= 1] . ( 37 sec) [ -2711.1041] [ 458] [depth= 1] . ( 37 sec) [ -2710.8614] [ 458] [depth= 1] . ( 42 sec) [ -2710.1165] [ 458] [depth= 1] . ( 48 sec) [ -2709.0419] [ 457] [depth= 1] . ( 53 sec) [ -2708.2234] [ 458] [depth= 2] . ( 65 sec) [ -2707.6136] [ 458] [depth= 1] . ( 66 sec) [ -2707.4596] [ 457] [depth= 1] . ( 71 sec) [ -2706.8637] [ 457] [depth= 2] . ( 83 sec) [ -2702.0340] [ 453] [depth= 1] . ( 86 sec) [ -2702.0121] [ 453] [depth= 1] . ( 88 sec) [ -2700.8284] [ 452] [depth= 1] . ( 92 sec) [ -2697.3640] [Branch lengths ] . ( 93 sec) [ -2697.3428] [Alpha ][ 0.352796] . ( 139 sec) [ -2697.2602] [ 451] [depth= 2] . ( 186 sec) [ -2697.0963] [Branch lengths ] . ( 186 sec) [ -2697.0956] [Alpha ][ 0.354269] . ( 187 sec) [ -2697.0956] [Topology ] . ( 187 sec) [ -2697.0898] [Topology ] . ( 188 sec) [ -2697.0887] [Topology ] . ( 189 sec) [ -2697.0885] [Topology ] . ( 189 sec) [ -2697.0884] [Alpha ][ 0.354758] . ( 189 sec) [ -2697.0884] [Topology ] . ( 190 sec) [ -2697.0882] [Topology ] . ( 191 sec) [ -2697.0882] [Alpha ][ 0.354758] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2697.088238. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3381.5058] [Alpha ][ 0.500960] . ( 1 sec) [ -3326.8678] [ 544] [depth= 8] . ( 1 sec) [ -3297.0084] [ 546] [depth= 2] . ( 1 sec) [ -3258.3183] [ 540] [depth= 8] . ( 1 sec) [ -3230.8463] [ 540] [depth= 1] . ( 1 sec) [ -3208.9088] [ 535] [depth= 7] . ( 1 sec) [ -3163.0920] [ 532] [depth= 2] . ( 2 sec) [ -3141.7969] [ 526] [depth= 1] . ( 2 sec) [ -3123.9787] [ 522] [depth= 5] . ( 2 sec) [ -3062.7185] [ 517] [depth= 5] . ( 2 sec) [ -3049.9179] [ 521] [depth= 1] . ( 2 sec) [ -3032.7995] [ 513] [depth= 2] . ( 2 sec) [ -3015.2078] [ 511] [depth= 10] . ( 2 sec) [ -3008.8073] [ 514] [depth= 1] . ( 3 sec) [ -2998.9610] [ 509] [depth= 7] . ( 3 sec) [ -2997.8677] [ 506] [depth= 2] . ( 3 sec) [ -2989.1252] [ 497] [depth= 13] . ( 3 sec) [ -2970.8653] [ 492] [depth= 3] . ( 3 sec) [ -2968.6704] [ 491] [depth= 2] . ( 3 sec) [ -2953.1737] [ 490] [depth= 5] . ( 3 sec) [ -2949.7031] [ 488] [depth= 1] . ( 3 sec) [ -2941.5528] [ 487] [depth= 1] . ( 4 sec) [ -2927.2813] [ 483] [depth= 2] . ( 4 sec) [ -2926.1045] [ 483] [depth= 3] . ( 4 sec) [ -2918.3677] [ 482] [depth= 2] . ( 4 sec) [ -2891.0726] [ 475] [depth= 14] . ( 5 sec) [ -2862.1533] [ 480] [depth= 6] . ( 5 sec) [ -2846.4546] [ 478] [depth= 6] . ( 5 sec) [ -2840.7558] [ 475] [depth= 4] . ( 5 sec) [ -2839.0190] [ 475] [depth= 1] . ( 6 sec) [ -2833.2360] [ 472] [depth= 5] . ( 6 sec) [ -2831.8864] [ 471] [depth= 1] . ( 7 sec) [ -2829.1183] [ 476] [depth= 10] . ( 7 sec) [ -2826.9152] [ 478] [depth= 2] . ( 10 sec) [ -2816.4034] [ 474] [depth= 4] . ( 10 sec) [ -2809.5892] [ 470] [depth= 6] . ( 10 sec) [ -2805.5626] [ 469] [depth= 2] . ( 10 sec) [ -2804.0179] [ 469] [depth= 1] . ( 10 sec) [ -2803.2898] [ 470] [depth= 1] . ( 11 sec) [ -2800.2156] [ 468] [depth= 5] . ( 11 sec) [ -2800.0277] [ 468] [depth= 1] . ( 12 sec) [ -2796.8766] [ 467] [depth= 1] . ( 12 sec) [ -2792.0955] [ 469] [depth= 3] . ( 12 sec) [ -2779.8252] [ 468] [depth= 3] . ( 13 sec) [ -2779.7143] [ 468] [depth= 1] . ( 14 sec) [ -2779.5744] [ 470] [depth= 1] . ( 14 sec) [ -2778.6653] [ 468] [depth= 1] . ( 14 sec) [ -2776.1492] [ 468] [depth= 1] . ( 14 sec) [ -2774.8185] [ 467] [depth= 3] . ( 14 sec) [ -2772.2020] [ 467] [depth= 1] . ( 16 sec) [ -2771.2048] [ 468] [depth= 2] . ( 20 sec) [ -2767.7451] [ 466] [depth= 1] . ( 23 sec) [ -2767.6658] [ 466] [depth= 1] . ( 23 sec) [ -2767.6167] [ 466] [depth= 1] . ( 23 sec) [ -2767.0750] [ 466] [depth= 1] . ( 24 sec) [ -2761.0443] [ 465] [depth= 7] . ( 24 sec) [ -2760.7903] [ 464] [depth= 1] . ( 25 sec) [ -2760.4167] [ 464] [depth= 1] . ( 27 sec) [ -2759.1458] [ 467] [depth= 2] . ( 29 sec) [ -2746.8019] [Branch lengths ] . ( 29 sec) [ -2743.3648] [Alpha ][ 0.375776] . ( 29 sec) [ -2741.8706] [ 465] [depth= 2] . ( 32 sec) [ -2732.0770] [ 460] [depth= 4] . ( 32 sec) [ -2724.7999] [ 458] [depth= 3] . ( 34 sec) [ -2724.4189] [ 458] [depth= 1] . ( 35 sec) [ -2718.8983] [ 454] [depth= 3] . ( 36 sec) [ -2717.0639] [ 453] [depth= 3] . ( 43 sec) [ -2715.4709] [ 453] [depth= 1] . ( 45 sec) [ -2713.8760] [ 453] [depth= 4] . ( 45 sec) [ -2711.6556] [ 454] [depth= 3] . ( 45 sec) [ -2711.1719] [ 453] [depth= 1] . ( 67 sec) [ -2710.4755] [ 451] [depth= 8] . ( 70 sec) [ -2709.2293] [ 453] [depth= 1] . ( 73 sec) [ -2709.1939] [ 454] [depth= 1] . ( 80 sec) [ -2707.5371] [ 453] [depth= 5] . ( 80 sec) [ -2703.1176] [Branch lengths ] . ( 80 sec) [ -2702.7149] [Alpha ][ 0.338529] . ( 99 sec) [ -2701.6608] [ 451] [depth= 2] . ( 100 sec) [ -2701.5617] [ 452] [depth= 1] . ( 126 sec) [ -2701.1282] [ 452] [depth= 1] . ( 136 sec) [ -2700.2390] [ 452] [depth= 8] . ( 152 sec) [ -2699.9253] [ 451] [depth= 4] . ( 152 sec) [ -2699.1355] [Branch lengths ] . ( 152 sec) [ -2699.1347] [Alpha ][ 0.340131] . ( 221 sec) [ -2698.2249] [ 452] [depth= 2] . ( 222 sec) [ -2697.8635] [Branch lengths ] . ( 222 sec) [ -2697.8635] [Alpha ][ 0.340131] . ( 295 sec) [ -2697.8265] [Branch lengths ] . ( 295 sec) [ -2697.8265] [Topology ] . ( 296 sec) [ -2697.8258] [Topology ] . ( 296 sec) [ -2697.8257] [Alpha ][ 0.339519] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2697.825669. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3539.1311] [Alpha ][ 0.500960] . ( 0 sec) [ -3526.7273] [ 536] [depth= 2] . ( 0 sec) [ -3516.9350] [ 532] [depth= 8] . ( 0 sec) [ -3502.5288] [ 531] [depth= 1] . ( 1 sec) [ -3334.5834] [ 531] [depth= 3] . ( 1 sec) [ -3308.8549] [ 530] [depth= 2] . ( 1 sec) [ -3266.2477] [ 528] [depth= 1] . ( 1 sec) [ -3227.8874] [ 528] [depth= 1] . ( 1 sec) [ -3221.6526] [ 527] [depth= 4] . ( 1 sec) [ -3208.0088] [ 522] [depth= 2] . ( 1 sec) [ -3189.7256] [ 519] [depth= 3] . ( 2 sec) [ -3186.3217] [ 519] [depth= 6] . ( 2 sec) [ -3185.1800] [ 515] [depth= 2] . ( 2 sec) [ -3169.9208] [ 513] [depth= 4] . ( 2 sec) [ -3144.3716] [ 510] [depth= 1] . ( 2 sec) [ -3092.2845] [ 507] [depth= 4] . ( 3 sec) [ -3085.3447] [ 504] [depth= 5] . ( 3 sec) [ -3030.6335] [ 500] [depth= 6] . ( 3 sec) [ -3024.9541] [ 501] [depth= 1] . ( 3 sec) [ -2997.1361] [ 500] [depth= 1] . ( 3 sec) [ -2990.2587] [ 501] [depth= 2] . ( 3 sec) [ -2954.3200] [ 500] [depth= 1] . ( 3 sec) [ -2943.4279] [ 497] [depth= 6] . ( 4 sec) [ -2941.1770] [ 495] [depth= 10] . ( 5 sec) [ -2937.3154] [ 492] [depth= 2] . ( 5 sec) [ -2913.7204] [ 491] [depth= 1] . ( 5 sec) [ -2910.7652] [ 487] [depth= 8] . ( 5 sec) [ -2887.9665] [ 484] [depth= 6] . ( 5 sec) [ -2853.1165] [ 477] [depth= 2] . ( 5 sec) [ -2851.6364] [ 475] [depth= 1] . ( 5 sec) [ -2850.5697] [ 475] [depth= 1] . ( 6 sec) [ -2845.2866] [ 473] [depth= 4] . ( 6 sec) [ -2840.7113] [ 473] [depth= 2] . ( 6 sec) [ -2839.3486] [ 475] [depth= 1] . ( 7 sec) [ -2835.1226] [ 473] [depth= 4] . ( 7 sec) [ -2827.6966] [ 471] [depth= 7] . ( 7 sec) [ -2824.5113] [ 470] [depth= 1] . ( 7 sec) [ -2822.3523] [ 469] [depth= 1] . ( 7 sec) [ -2817.8031] [ 468] [depth= 1] . ( 7 sec) [ -2814.7772] [ 468] [depth= 5] . ( 7 sec) [ -2808.8759] [ 465] [depth= 6] . ( 8 sec) [ -2807.1731] [ 464] [depth= 1] . ( 8 sec) [ -2797.0551] [ 464] [depth= 8] . ( 9 sec) [ -2796.6361] [ 465] [depth= 1] . ( 9 sec) [ -2795.7821] [ 466] [depth= 1] . ( 10 sec) [ -2775.9876] [ 467] [depth= 1] . ( 10 sec) [ -2772.3202] [ 467] [depth= 4] . ( 11 sec) [ -2772.2768] [ 466] [depth= 4] . ( 11 sec) [ -2753.9687] [ 456] [depth= 8] . ( 13 sec) [ -2752.8351] [ 455] [depth= 2] . ( 14 sec) [ -2749.8614] [ 455] [depth= 3] . ( 14 sec) [ -2749.2184] [ 456] [depth= 3] . ( 14 sec) [ -2748.6527] [ 456] [depth= 1] . ( 14 sec) [ -2732.1038] [ 453] [depth= 1] . ( 15 sec) [ -2730.2804] [ 452] [depth= 1] . ( 17 sec) [ -2729.7158] [ 454] [depth= 1] . ( 20 sec) [ -2728.4819] [ 454] [depth= 1] . ( 20 sec) [ -2726.9387] [ 452] [depth= 5] . ( 20 sec) [ -2713.9822] [Branch lengths ] . ( 20 sec) [ -2709.6042] [Alpha ][ 0.351980] . ( 29 sec) [ -2708.8808] [ 453] [depth= 1] . ( 30 sec) [ -2707.1305] [ 453] [depth= 1] . ( 45 sec) [ -2706.5911] [ 455] [depth= 2] . ( 52 sec) [ -2706.1480] [ 454] [depth= 2] . ( 52 sec) [ -2703.8250] [ 454] [depth= 3] . ( 86 sec) [ -2702.7267] [ 455] [depth= 1] . ( 107 sec) [ -2701.5784] [Branch lengths ] . ( 107 sec) [ -2701.5676] [Alpha ][ 0.346315] . ( 201 sec) [ -2701.4972] [Branch lengths ] . ( 201 sec) [ -2701.4972] [Topology ] . ( 201 sec) [ -2701.4950] [Topology ] . ( 202 sec) [ -2701.4946] [Topology ] . ( 203 sec) [ -2701.4946] [Alpha ][ 0.345969] . ( 203 sec) [ -2701.4946] [Topology ] . ( 203 sec) [ -2701.4945] [Topology ] . ( 204 sec) [ -2701.4945] [Alpha ][ 0.345969] . Checking for NNIs, optimizing five branches... . ( 210 sec) [ -2701.4943] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2701.494254. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -2775.6744] [Alpha ][ 0.500960] . ( 1 sec) [ -2775.6744] [Topology ] . ( 2 sec) [ -2730.2341] [Topology ] . ( 2 sec) [ -2719.9969] [Topology ] . ( 3 sec) [ -2718.4262] [Topology ] . ( 4 sec) [ -2717.6659] [Topology ] . ( 5 sec) [ -2717.6758] [Topology ] . Moving backward . ( 5 sec) [ -2717.0282] [Topology ] . ( 6 sec) [ -2716.6701] [Topology ] . ( 7 sec) [ -2716.5370] [Topology ] . ( 8 sec) [ -2716.4326] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -2712.7833] [Alpha ][ 0.369792] . ( 15 sec) [ -2712.7833] [Topology ] . ( 16 sec) [ -2712.6795] [Topology ] . ( 16 sec) [ -2712.6614] [Topology ] . ( 17 sec) [ -2712.6561] [Topology ] . ( 18 sec) [ -2712.6542] [Topology ] . ( 19 sec) [ -2712.6534] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -2712.4946] [Topology ] . ( 25 sec) [ -2712.4788] [Alpha ][ 0.362808] . ( 25 sec) [ -2712.4788] [Topology ] . ( 26 sec) [ -2712.4666] [Topology ] . ( 27 sec) [ -2712.4622] [Topology ] . ( 28 sec) [ -2712.4600] [Topology ] . ( 29 sec) [ -2712.4589] [Topology ] . ( 30 sec) [ -2712.4584] [Topology ] . Checking for NNIs, optimizing five branches... . ( 36 sec) [ -2712.4580] [Alpha ][ 0.363809] . ( 36 sec) [ -2712.4580] [Topology ] . ( 37 sec) [ -2712.4577] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -2775.6744] [Alpha ][ 0.500960] . ( 49 sec) [ -2775.5328] [ 461] [depth= 1] . ( 49 sec) [ -2773.6500] [ 461] [depth= 1] . ( 52 sec) [ -2772.3263] [ 462] [depth= 1] . ( 52 sec) [ -2771.9961] [ 461] [depth= 1] . ( 52 sec) [ -2767.8684] [ 459] [depth= 1] . ( 52 sec) [ -2766.9550] [ 461] [depth= 1] . ( 53 sec) [ -2766.3284] [ 461] [depth= 5] . ( 55 sec) [ -2762.6262] [ 461] [depth= 2] . ( 56 sec) [ -2762.2303] [ 464] [depth= 3] . ( 56 sec) [ -2759.9008] [ 465] [depth= 1] . ( 59 sec) [ -2759.1950] [ 462] [depth= 1] . ( 61 sec) [ -2756.3415] [ 461] [depth= 3] . ( 63 sec) [ -2756.2298] [ 460] [depth= 1] . ( 66 sec) [ -2754.7662] [ 460] [depth= 1] . ( 67 sec) [ -2753.0177] [ 460] [depth= 1] . ( 67 sec) [ -2750.3352] [ 460] [depth= 1] . ( 67 sec) [ -2749.6121] [ 459] [depth= 1] . ( 67 sec) [ -2747.3322] [ 458] [depth= 3] . ( 67 sec) [ -2746.4446] [ 457] [depth= 2] . ( 67 sec) [ -2745.2296] [ 456] [depth= 1] . ( 68 sec) [ -2745.0250] [ 461] [depth= 4] . ( 70 sec) [ -2737.8765] [ 460] [depth= 10] . ( 72 sec) [ -2735.8249] [ 457] [depth= 5] . ( 74 sec) [ -2735.7022] [ 459] [depth= 1] . ( 79 sec) [ -2734.9231] [ 460] [depth= 3] . ( 79 sec) [ -2730.5330] [ 457] [depth= 2] . ( 90 sec) [ -2730.1559] [ 457] [depth= 1] . ( 92 sec) [ -2730.0889] [ 458] [depth= 1] . ( 97 sec) [ -2728.6132] [ 458] [depth= 2] . ( 101 sec) [ -2727.6571] [ 458] [depth= 1] . ( 102 sec) [ -2715.7082] [Branch lengths ] . ( 102 sec) [ -2711.2884] [Alpha ][ 0.350558] . ( 103 sec) [ -2710.3906] [ 459] [depth= 1] . ( 113 sec) [ -2709.5078] [ 459] [depth= 9] . ( 113 sec) [ -2709.0064] [ 460] [depth= 1] . ( 114 sec) [ -2704.5035] [ 455] [depth= 3] . ( 136 sec) [ -2703.9234] [ 455] [depth= 1] . ( 139 sec) [ -2703.7549] [ 456] [depth= 1] . ( 140 sec) [ -2703.6862] [ 455] [depth= 1] . ( 145 sec) [ -2702.5294] [ 454] [depth= 1] . ( 151 sec) [ -2701.9852] [ 454] [depth= 6] . ( 182 sec) [ -2698.6579] [Branch lengths ] . ( 182 sec) [ -2698.6432] [Alpha ][ 0.343831] . ( 212 sec) [ -2698.2040] [ 454] [depth= 5] . ( 214 sec) [ -2698.1853] [ 455] [depth= 1] . ( 266 sec) [ -2697.3130] [Branch lengths ] . ( 266 sec) [ -2697.3105] [Alpha ][ 0.346531] . ( 357 sec) [ -2697.2351] [Branch lengths ] . ( 357 sec) [ -2697.2351] [Topology ] . ( 358 sec) [ -2697.2303] [Topology ] . ( 358 sec) [ -2697.2290] [Topology ] . ( 359 sec) [ -2697.2285] [Topology ] . ( 360 sec) [ -2697.2270] [Alpha ][ 0.348618] . ( 360 sec) [ -2697.2270] [Topology ] . ( 361 sec) [ -2697.2265] [Topology ] . ( 361 sec) [ -2697.2265] [Alpha ][ 0.348618] . Checking for NNIs, optimizing five branches... . ( 367 sec) [ -2697.1624] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2712.457654 . Log likelihood obtained after SPR moves : -2697.162387 . Log likelihood of the current tree: -2697.162387. . Printing the most likely tree in file 'proteic_M2382_28x162_2005.phy_phyml_tree.txt'... . Best log likelihood : -2695.766816 . Time used 0h6m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1612.76user 0.00system 26:55.01elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps