.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1487_52x981_2003.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... . 623 patterns found. (out of a total of 981 sites) . 470 sites without polymorphism (47.91%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 78Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -25378.6008] [Alpha ][ 0.500960] . ( 5 sec) [ -25208.8340] [ 3853] [depth= 7] . ( 6 sec) [ -25144.3171] [ 3842] [depth= 6] . ( 7 sec) [ -24790.6158] [ 3803] [depth= 8] . ( 8 sec) [ -24731.9205] [ 3790] [depth= 1] . ( 9 sec) [ -24488.6162] [ 3744] [depth= 6] . ( 10 sec) [ -24238.6784] [ 3686] [depth= 8] . ( 11 sec) [ -24151.3288] [ 3684] [depth= 1] . ( 12 sec) [ -24008.2072] [ 3642] [depth= 8] . ( 13 sec) [ -23667.5776] [ 3630] [depth= 7] . ( 14 sec) [ -23645.1420] [ 3621] [depth= 1] . ( 16 sec) [ -23616.5587] [ 3622] [depth= 8] . ( 17 sec) [ -23454.8037] [ 3576] [depth= 7] . ( 18 sec) [ -23395.5114] [ 3579] [depth= 8] . ( 19 sec) [ -22924.9330] [ 3504] [depth= 7] . ( 21 sec) [ -22723.5004] [ 3493] [depth= 4] . ( 21 sec) [ -22681.4521] [ 3489] [depth= 1] . ( 22 sec) [ -22626.0124] [ 3482] [depth= 10] . ( 23 sec) [ -22574.2493] [ 3471] [depth= 1] . ( 24 sec) [ -22330.4479] [ 3473] [depth= 1] . ( 25 sec) [ -22328.9802] [ 3475] [depth= 1] . ( 26 sec) [ -22234.0483] [ 3448] [depth= 9] . ( 27 sec) [ -22222.6920] [ 3445] [depth= 1] . ( 28 sec) [ -22063.3472] [ 3423] [depth= 7] . ( 29 sec) [ -22062.2346] [ 3425] [depth= 1] . ( 30 sec) [ -21924.5884] [ 3418] [depth= 8] . ( 32 sec) [ -21917.1147] [ 3423] [depth= 1] . ( 33 sec) [ -21781.5971] [ 3421] [depth= 6] . ( 34 sec) [ -21609.1239] [ 3411] [depth= 3] . ( 35 sec) [ -21543.6934] [ 3405] [depth= 1] . ( 36 sec) [ -21392.1847] [ 3279] [depth= 3] . ( 37 sec) [ -21341.9610] [ 3276] [depth= 2] . ( 38 sec) [ -21223.7480] [ 3256] [depth= 3] . ( 39 sec) [ -21150.7541] [ 3248] [depth= 1] . ( 40 sec) [ -21088.7167] [ 3228] [depth= 18] . ( 41 sec) [ -21078.9628] [ 3230] [depth= 1] . ( 41 sec) [ -21060.1507] [ 3227] [depth= 1] . ( 43 sec) [ -20822.8137] [ 3197] [depth= 4] . ( 44 sec) [ -20770.8243] [ 3182] [depth= 1] . ( 45 sec) [ -20769.1962] [ 3191] [depth= 3] . ( 46 sec) [ -20746.4585] [ 3186] [depth= 5] . ( 47 sec) [ -20724.4623] [ 3187] [depth= 1] . ( 48 sec) [ -20713.3246] [ 3185] [depth= 6] . ( 49 sec) [ -20687.6683] [ 3186] [depth= 2] . ( 50 sec) [ -20673.4865] [ 3184] [depth= 1] . ( 52 sec) [ -20535.6479] [ 3163] [depth= 10] . ( 53 sec) [ -20341.4763] [ 3121] [depth= 8] . ( 54 sec) [ -20263.4164] [ 3114] [depth= 2] . ( 55 sec) [ -20103.8372] [ 3087] [depth= 4] . ( 56 sec) [ -19976.9666] [ 3072] [depth= 8] . ( 57 sec) [ -19902.5094] [ 3039] [depth= 1] . ( 58 sec) [ -19896.7052] [ 3036] [depth= 1] . ( 59 sec) [ -19893.1486] [ 3036] [depth= 1] . ( 60 sec) [ -19876.7582] [ 3039] [depth= 1] . ( 62 sec) [ -19391.3165] [ 3023] [depth= 5] . ( 63 sec) [ -19340.9041] [ 3005] [depth= 3] . ( 64 sec) [ -19331.2008] [ 3007] [depth= 1] . ( 65 sec) [ -19323.9340] [ 3003] [depth= 2] . ( 66 sec) [ -19231.8994] [ 2970] [depth= 12] . ( 67 sec) [ -19225.6937] [ 2970] [depth= 1] . ( 69 sec) [ -19225.0543] [ 2973] [depth= 1] . ( 70 sec) [ -19033.6733] [ 2912] [depth= 8] . ( 71 sec) [ -19019.1529] [ 2911] [depth= 1] . ( 72 sec) [ -19015.1431] [ 2910] [depth= 1] . ( 73 sec) [ -18964.8609] [ 2900] [depth= 7] . ( 74 sec) [ -18948.9862] [ 2899] [depth= 1] . ( 76 sec) [ -18936.5309] [ 2899] [depth= 2] . ( 76 sec) [ -18935.6891] [ 2899] [depth= 1] . ( 78 sec) [ -18744.8555] [ 2934] [depth= 7] . ( 79 sec) [ -18738.9552] [ 2930] [depth= 1] . ( 80 sec) [ -18737.1562] [ 2927] [depth= 6] . ( 81 sec) [ -18710.4055] [ 2930] [depth= 1] . ( 82 sec) [ -18578.9370] [ 2911] [depth= 6] . ( 83 sec) [ -18548.6458] [ 2903] [depth= 4] . ( 84 sec) [ -18423.3899] [ 2897] [depth= 6] . ( 85 sec) [ -18406.4383] [ 2889] [depth= 3] . ( 86 sec) [ -18331.1094] [ 2864] [depth= 9] . ( 87 sec) [ -18298.2597] [ 2856] [depth= 2] . ( 89 sec) [ -18283.3745] [ 2860] [depth= 1] . ( 91 sec) [ -18281.6192] [ 2862] [depth= 1] . ( 92 sec) [ -18158.8444] [ 2838] [depth= 8] . ( 98 sec) [ -18087.9146] [ 2816] [depth= 2] . ( 99 sec) [ -17724.4661] [ 2755] [depth= 1] . ( 100 sec) [ -17678.4913] [ 2738] [depth= 1] . ( 100 sec) [ -17656.1061] [ 2722] [depth= 1] . ( 101 sec) [ -17648.6597] [ 2721] [depth= 1] . ( 102 sec) [ -17596.5404] [ 2713] [depth= 1] . ( 103 sec) [ -17593.4392] [ 2709] [depth= 1] . ( 106 sec) [ -17556.9361] [ 2703] [depth= 3] . ( 107 sec) [ -17353.3943] [ 2696] [depth= 1] . ( 108 sec) [ -17343.5312] [ 2694] [depth= 2] . ( 110 sec) [ -17309.2124] [ 2695] [depth= 1] . ( 111 sec) [ -17288.4034] [ 2686] [depth= 2] . ( 113 sec) [ -17284.8136] [ 2684] [depth= 4] . ( 114 sec) [ -17247.9861] [ 2684] [depth= 1] . ( 115 sec) [ -17160.8318] [ 2674] [depth= 4] . ( 116 sec) [ -17058.4329] [ 2667] [depth= 2] . ( 117 sec) [ -17050.2758] [ 2667] [depth= 1] . ( 118 sec) [ -17044.6739] [ 2669] [depth= 1] . ( 119 sec) [ -17019.0260] [ 2661] [depth= 1] . ( 120 sec) [ -16968.1274] [ 2651] [depth= 4] . ( 121 sec) [ -16937.4051] [ 2643] [depth= 2] . ( 122 sec) [ -16924.8098] [ 2641] [depth= 1] . ( 123 sec) [ -16897.0021] [ 2630] [depth= 2] . ( 124 sec) [ -16887.6246] [ 2629] [depth= 1] . ( 125 sec) [ -16863.8439] [ 2626] [depth= 3] . ( 126 sec) [ -16807.2645] [ 2614] [depth= 2] . ( 128 sec) [ -16796.8862] [ 2615] [depth= 1] . ( 132 sec) [ -16777.4884] [ 2616] [depth= 1] . ( 133 sec) [ -16693.2870] [ 2598] [depth= 12] . ( 134 sec) [ -16671.8471] [ 2592] [depth= 2] . ( 137 sec) [ -16649.5850] [ 2588] [depth= 1] . ( 141 sec) [ -16479.6365] [Branch lengths ] . ( 143 sec) [ -16462.2130] [Alpha ][ 0.377903] . ( 147 sec) [ -16450.5118] [ 2584] [depth= 1] . ( 157 sec) [ -16445.5710] [ 2578] [depth= 5] . ( 158 sec) [ -16443.9802] [ 2577] [depth= 2] . ( 160 sec) [ -16433.2358] [ 2573] [depth= 1] . ( 164 sec) [ -16424.2549] [ 2574] [depth= 2] . ( 166 sec) [ -16423.4989] [ 2571] [depth= 1] . ( 172 sec) [ -16412.4185] [ 2573] [depth= 2] . ( 178 sec) [ -16410.5285] [ 2575] [depth= 2] . ( 183 sec) [ -16409.1879] [ 2571] [depth= 2] . ( 184 sec) [ -16399.6606] [ 2569] [depth= 2] . ( 192 sec) [ -16396.3766] [ 2570] [depth= 1] . ( 193 sec) [ -16388.0028] [ 2568] [depth= 2] . ( 201 sec) [ -16378.8420] [ 2564] [depth= 1] . ( 205 sec) [ -16377.9346] [ 2562] [depth= 1] . ( 213 sec) [ -16373.5926] [ 2561] [depth= 1] . ( 216 sec) [ -16371.6807] [ 2560] [depth= 1] . ( 235 sec) [ -16371.2535] [ 2563] [depth= 2] . ( 251 sec) [ -16352.5000] [ 2557] [depth= 4] . ( 254 sec) [ -16340.3721] [ 2554] [depth= 1] . ( 261 sec) [ -16332.6048] [ 2554] [depth= 1] . ( 279 sec) [ -16332.2708] [ 2554] [depth= 1] . ( 284 sec) [ -16327.0745] [ 2554] [depth= 4] . ( 302 sec) [ -16301.1234] [Branch lengths ] . ( 303 sec) [ -16301.1210] [Alpha ][ 0.376570] . ( 307 sec) [ -16285.0248] [ 2548] [depth= 1] . ( 395 sec) [ -16283.8525] [ 2545] [depth= 2] . ( 404 sec) [ -16282.1509] [ 2542] [depth= 1] . ( 439 sec) [ -16282.1345] [ 2543] [depth= 1] . ( 463 sec) [ -16278.4519] [Branch lengths ] . ( 465 sec) [ -16278.4503] [Alpha ][ 0.377559] . ( 628 sec) [ -16278.3101] [Branch lengths ] . ( 628 sec) [ -16278.3101] [Topology ] . ( 636 sec) [ -16278.0221] [Topology ] . ( 644 sec) [ -16277.7846] [Topology ] . ( 652 sec) [ -16277.7484] [Topology ] . ( 660 sec) [ -16277.7392] [Topology ] . ( 667 sec) [ -16277.7365] [Topology ] . ( 675 sec) [ -16277.7356] [Topology ] . ( 677 sec) [ -16277.7347] [Alpha ][ 0.378287] . ( 677 sec) [ -16277.7347] [Topology ] . ( 685 sec) [ -16277.7343] [Topology ] . ( 686 sec) [ -16277.7343] [Alpha ][ 0.378287] . Checking for NNIs, optimizing five branches... . ( 748 sec) [ -16277.7334] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16277.733354. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -27346.1914] [Alpha ][ 0.500960] . ( 4 sec) [ -27245.8446] [ 4108] [depth= 13] . ( 6 sec) [ -27059.3562] [ 4080] [depth= 10] . ( 6 sec) [ -26930.4228] [ 4048] [depth= 1] . ( 7 sec) [ -26848.8166] [ 4042] [depth= 9] . ( 8 sec) [ -26682.0812] [ 4005] [depth= 1] . ( 9 sec) [ -26514.9975] [ 3987] [depth= 7] . ( 10 sec) [ -26358.3247] [ 3955] [depth= 11] . ( 11 sec) [ -26300.2504] [ 3935] [depth= 1] . ( 12 sec) [ -26078.8406] [ 3903] [depth= 13] . ( 13 sec) [ -25743.3547] [ 3889] [depth= 3] . ( 14 sec) [ -25611.8476] [ 3872] [depth= 9] . ( 15 sec) [ -25472.2719] [ 3847] [depth= 3] . ( 16 sec) [ -25156.3297] [ 3839] [depth= 8] . ( 17 sec) [ -24979.8100] [ 3791] [depth= 3] . ( 18 sec) [ -24888.7748] [ 3773] [depth= 7] . ( 19 sec) [ -24801.5929] [ 3759] [depth= 2] . ( 20 sec) [ -24770.0695] [ 3764] [depth= 3] . ( 20 sec) [ -24696.8490] [ 3764] [depth= 1] . ( 21 sec) [ -24240.2627] [ 3765] [depth= 4] . ( 22 sec) [ -24220.8536] [ 3755] [depth= 2] . ( 23 sec) [ -24036.4343] [ 3707] [depth= 4] . ( 24 sec) [ -23701.3915] [ 3657] [depth= 3] . ( 26 sec) [ -23404.4470] [ 3619] [depth= 1] . ( 27 sec) [ -23380.5512] [ 3628] [depth= 3] . ( 28 sec) [ -23301.4940] [ 3595] [depth= 4] . ( 29 sec) [ -23229.8447] [ 3562] [depth= 8] . ( 30 sec) [ -23074.1080] [ 3530] [depth= 4] . ( 31 sec) [ -22996.9952] [ 3529] [depth= 2] . ( 32 sec) [ -22910.9424] [ 3517] [depth= 3] . ( 32 sec) [ -22420.3962] [ 3495] [depth= 4] . ( 34 sec) [ -22131.5798] [ 3475] [depth= 7] . ( 35 sec) [ -22049.6874] [ 3458] [depth= 14] . ( 36 sec) [ -21924.8379] [ 3449] [depth= 18] . ( 37 sec) [ -21791.0607] [ 3424] [depth= 2] . ( 39 sec) [ -21748.7633] [ 3407] [depth= 1] . ( 40 sec) [ -21472.4209] [ 3378] [depth= 2] . ( 41 sec) [ -21387.0937] [ 3354] [depth= 10] . ( 43 sec) [ -21328.8705] [ 3350] [depth= 1] . ( 44 sec) [ -21252.4109] [ 3323] [depth= 18] . ( 45 sec) [ -21117.5515] [ 3289] [depth= 14] . ( 46 sec) [ -20866.1867] [ 3246] [depth= 2] . ( 47 sec) [ -20860.7498] [ 3239] [depth= 2] . ( 48 sec) [ -20720.4082] [ 3198] [depth= 7] . ( 50 sec) [ -20240.0902] [ 3165] [depth= 4] . ( 50 sec) [ -20219.6454] [ 3159] [depth= 1] . ( 51 sec) [ -20056.3541] [ 3140] [depth= 9] . ( 52 sec) [ -20043.4172] [ 3134] [depth= 4] . ( 53 sec) [ -19927.3599] [ 3124] [depth= 3] . ( 54 sec) [ -19834.0008] [ 3110] [depth= 3] . ( 55 sec) [ -19715.5768] [ 3095] [depth= 5] . ( 57 sec) [ -19710.9320] [ 3096] [depth= 11] . ( 58 sec) [ -19636.2835] [ 3078] [depth= 1] . ( 59 sec) [ -19471.4190] [ 3055] [depth= 3] . ( 60 sec) [ -19398.6397] [ 3053] [depth= 2] . ( 61 sec) [ -19291.6261] [ 3047] [depth= 15] . ( 63 sec) [ -19258.4139] [ 3050] [depth= 12] . ( 64 sec) [ -19251.7692] [ 3044] [depth= 1] . ( 64 sec) [ -19229.3830] [ 3035] [depth= 2] . ( 66 sec) [ -19151.8077] [ 3011] [depth= 3] . ( 67 sec) [ -18960.8477] [ 2953] [depth= 14] . ( 68 sec) [ -18928.1896] [ 2950] [depth= 4] . ( 69 sec) [ -18913.8941] [ 2945] [depth= 1] . ( 70 sec) [ -18755.2919] [ 2912] [depth= 3] . ( 71 sec) [ -18698.2151] [ 2899] [depth= 5] . ( 72 sec) [ -18667.7773] [ 2898] [depth= 2] . ( 73 sec) [ -18660.0643] [ 2896] [depth= 2] . ( 74 sec) [ -18562.0837] [ 2874] [depth= 10] . ( 75 sec) [ -18522.1396] [ 2865] [depth= 4] . ( 76 sec) [ -18515.2623] [ 2865] [depth= 1] . ( 77 sec) [ -18480.9919] [ 2858] [depth= 10] . ( 80 sec) [ -18471.5669] [ 2856] [depth= 1] . ( 81 sec) [ -18438.2419] [ 2850] [depth= 2] . ( 82 sec) [ -18430.0829] [ 2852] [depth= 2] . ( 83 sec) [ -18410.4287] [ 2847] [depth= 8] . ( 84 sec) [ -18403.1668] [ 2844] [depth= 1] . ( 85 sec) [ -18396.5470] [ 2845] [depth= 1] . ( 86 sec) [ -18322.6921] [ 2834] [depth= 10] . ( 88 sec) [ -18286.4210] [ 2834] [depth= 14] . ( 89 sec) [ -18210.9588] [ 2816] [depth= 2] . ( 90 sec) [ -18131.3761] [ 2792] [depth= 11] . ( 92 sec) [ -18038.6844] [ 2774] [depth= 4] . ( 93 sec) [ -18023.0676] [ 2770] [depth= 1] . ( 94 sec) [ -18002.5144] [ 2770] [depth= 1] . ( 95 sec) [ -17945.8727] [ 2764] [depth= 3] . ( 97 sec) [ -17909.5850] [ 2766] [depth= 1] . ( 98 sec) [ -17890.2804] [ 2759] [depth= 2] . ( 99 sec) [ -17822.6109] [ 2738] [depth= 4] . ( 100 sec) [ -17810.6775] [ 2738] [depth= 3] . ( 102 sec) [ -17809.0130] [ 2741] [depth= 1] . ( 103 sec) [ -17806.7856] [ 2742] [depth= 1] . ( 104 sec) [ -17731.8126] [ 2732] [depth= 6] . ( 105 sec) [ -17706.5910] [ 2732] [depth= 1] . ( 106 sec) [ -17695.1813] [ 2729] [depth= 4] . ( 109 sec) [ -17690.2725] [ 2731] [depth= 1] . ( 109 sec) [ -17581.4405] [ 2759] [depth= 1] . ( 110 sec) [ -17485.9919] [ 2731] [depth= 1] . ( 111 sec) [ -17449.6156] [ 2717] [depth= 3] . ( 113 sec) [ -17445.4717] [ 2716] [depth= 1] . ( 114 sec) [ -17358.0887] [ 2713] [depth= 1] . ( 114 sec) [ -17346.2597] [ 2716] [depth= 1] . ( 116 sec) [ -17344.8043] [ 2716] [depth= 1] . ( 118 sec) [ -17322.7031] [ 2704] [depth= 3] . ( 119 sec) [ -17153.6103] [ 2650] [depth= 13] . ( 121 sec) [ -17107.6177] [ 2649] [depth= 1] . ( 121 sec) [ -16926.9841] [ 2654] [depth= 1] . ( 123 sec) [ -16821.6838] [ 2623] [depth= 10] . ( 125 sec) [ -16802.6050] [ 2620] [depth= 8] . ( 125 sec) [ -16800.4028] [ 2619] [depth= 1] . ( 126 sec) [ -16777.1095] [ 2618] [depth= 1] . ( 129 sec) [ -16775.2620] [ 2620] [depth= 2] . ( 133 sec) [ -16771.0647] [ 2621] [depth= 1] . ( 134 sec) [ -16764.3310] [ 2614] [depth= 1] . ( 136 sec) [ -16753.7597] [ 2607] [depth= 1] . ( 137 sec) [ -16727.2870] [ 2600] [depth= 1] . ( 140 sec) [ -16554.8597] [Branch lengths ] . ( 142 sec) [ -16536.4719] [Alpha ][ 0.374215] . ( 144 sec) [ -16532.6262] [ 2600] [depth= 1] . ( 145 sec) [ -16532.2128] [ 2597] [depth= 1] . ( 147 sec) [ -16531.4853] [ 2597] [depth= 1] . ( 147 sec) [ -16510.4662] [ 2585] [depth= 2] . ( 148 sec) [ -16493.2973] [ 2581] [depth= 2] . ( 153 sec) [ -16487.0779] [ 2579] [depth= 1] . ( 154 sec) [ -16485.1447] [ 2575] [depth= 1] . ( 156 sec) [ -16480.9428] [ 2573] [depth= 1] . ( 158 sec) [ -16467.1286] [ 2570] [depth= 1] . ( 161 sec) [ -16460.6373] [ 2569] [depth= 1] . ( 164 sec) [ -16456.1187] [ 2574] [depth= 1] . ( 167 sec) [ -16455.0329] [ 2576] [depth= 4] . ( 170 sec) [ -16440.6601] [ 2564] [depth= 5] . ( 171 sec) [ -16429.8435] [ 2562] [depth= 1] . ( 174 sec) [ -16428.9173] [ 2560] [depth= 2] . ( 179 sec) [ -16424.6080] [ 2557] [depth= 7] . ( 181 sec) [ -16424.2675] [ 2558] [depth= 1] . ( 182 sec) [ -16423.5097] [ 2558] [depth= 4] . ( 185 sec) [ -16422.5816] [ 2560] [depth= 1] . ( 192 sec) [ -16420.1411] [ 2563] [depth= 1] . ( 196 sec) [ -16412.7693] [ 2560] [depth= 1] . ( 201 sec) [ -16394.7854] [ 2558] [depth= 2] . ( 206 sec) [ -16391.5898] [ 2557] [depth= 2] . ( 210 sec) [ -16382.1120] [ 2557] [depth= 3] . ( 213 sec) [ -16371.7676] [ 2555] [depth= 2] . ( 215 sec) [ -16357.0556] [ 2549] [depth= 2] . ( 220 sec) [ -16350.4773] [ 2551] [depth= 1] . ( 234 sec) [ -16350.3063] [ 2552] [depth= 1] . ( 236 sec) [ -16349.1111] [ 2554] [depth= 1] . ( 238 sec) [ -16348.2836] [ 2554] [depth= 3] . ( 239 sec) [ -16343.3818] [ 2548] [depth= 1] . ( 240 sec) [ -16324.1738] [ 2544] [depth= 4] . ( 247 sec) [ -16322.9169] [ 2541] [depth= 3] . ( 248 sec) [ -16322.6365] [ 2542] [depth= 1] . ( 250 sec) [ -16322.1568] [ 2544] [depth= 1] . ( 252 sec) [ -16321.2954] [ 2542] [depth= 1] . ( 265 sec) [ -16310.0717] [ 2541] [depth= 2] . ( 271 sec) [ -16309.2603] [ 2543] [depth= 1] . ( 281 sec) [ -16278.6067] [Branch lengths ] . ( 283 sec) [ -16278.5883] [Alpha ][ 0.377659] . ( 371 sec) [ -16278.2023] [ 2541] [depth= 1] . ( 446 sec) [ -16277.2697] [Branch lengths ] . ( 448 sec) [ -16277.2693] [Alpha ][ 0.378127] . ( 610 sec) [ -16277.2307] [Branch lengths ] . ( 610 sec) [ -16277.2307] [Topology ] . ( 618 sec) [ -16277.0415] [Topology ] . ( 626 sec) [ -16276.8769] [Topology ] . ( 634 sec) [ -16276.8542] [Topology ] . ( 642 sec) [ -16276.8497] [Topology ] . ( 650 sec) [ -16276.8486] [Topology ] . ( 658 sec) [ -16276.8483] [Topology ] . ( 659 sec) [ -16276.8482] [Alpha ][ 0.377725] . ( 659 sec) [ -16276.8482] [Topology ] . ( 667 sec) [ -16276.8480] [Topology ] . ( 669 sec) [ -16276.8480] [Alpha ][ 0.377725] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16276.848001. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -25383.6869] [Alpha ][ 0.500960] . ( 4 sec) [ -25137.8657] [ 3966] [depth= 10] . ( 5 sec) [ -24903.8152] [ 3925] [depth= 10] . ( 6 sec) [ -24784.7793] [ 3920] [depth= 2] . ( 7 sec) [ -24675.0038] [ 3895] [depth= 7] . ( 8 sec) [ -24635.7352] [ 3872] [depth= 3] . ( 9 sec) [ -24414.5062] [ 3836] [depth= 6] . ( 10 sec) [ -24375.0032] [ 3832] [depth= 1] . ( 11 sec) [ -24202.4126] [ 3786] [depth= 5] . ( 12 sec) [ -24135.8823] [ 3781] [depth= 2] . ( 13 sec) [ -23911.1024] [ 3715] [depth= 9] . ( 13 sec) [ -23506.9413] [ 3694] [depth= 2] . ( 14 sec) [ -23426.6021] [ 3683] [depth= 3] . ( 15 sec) [ -23060.9180] [ 3616] [depth= 1] . ( 16 sec) [ -22973.3571] [ 3609] [depth= 3] . ( 17 sec) [ -22792.3560] [ 3592] [depth= 7] . ( 18 sec) [ -22691.8562] [ 3582] [depth= 2] . ( 19 sec) [ -22309.3484] [ 3490] [depth= 3] . ( 20 sec) [ -22097.7184] [ 3460] [depth= 9] . ( 21 sec) [ -22033.7280] [ 3449] [depth= 9] . ( 22 sec) [ -22026.5114] [ 3461] [depth= 1] . ( 23 sec) [ -22011.3612] [ 3450] [depth= 1] . ( 24 sec) [ -21778.9286] [ 3408] [depth= 10] . ( 25 sec) [ -21658.0696] [ 3401] [depth= 10] . ( 27 sec) [ -21640.3388] [ 3394] [depth= 3] . ( 27 sec) [ -21507.5610] [ 3366] [depth= 1] . ( 28 sec) [ -21288.7022] [ 3335] [depth= 7] . ( 29 sec) [ -21214.2393] [ 3328] [depth= 1] . ( 31 sec) [ -21125.6342] [ 3315] [depth= 10] . ( 32 sec) [ -20929.0750] [ 3294] [depth= 1] . ( 33 sec) [ -20863.0334] [ 3279] [depth= 10] . ( 34 sec) [ -20798.4192] [ 3261] [depth= 10] . ( 35 sec) [ -20716.0657] [ 3242] [depth= 14] . ( 36 sec) [ -20673.4975] [ 3244] [depth= 1] . ( 37 sec) [ -20585.3991] [ 3246] [depth= 4] . ( 38 sec) [ -20526.2975] [ 3234] [depth= 11] . ( 39 sec) [ -20402.5645] [ 3216] [depth= 5] . ( 40 sec) [ -20239.8739] [ 3193] [depth= 7] . ( 41 sec) [ -20123.6620] [ 3184] [depth= 4] . ( 43 sec) [ -20116.5454] [ 3176] [depth= 4] . ( 44 sec) [ -19718.3219] [ 3171] [depth= 5] . ( 45 sec) [ -19645.3335] [ 3166] [depth= 8] . ( 47 sec) [ -19567.0175] [ 3150] [depth= 1] . ( 49 sec) [ -19458.3197] [ 3132] [depth= 6] . ( 50 sec) [ -19378.6227] [ 3123] [depth= 4] . ( 51 sec) [ -19352.6206] [ 3124] [depth= 1] . ( 51 sec) [ -19299.1590] [ 3113] [depth= 2] . ( 53 sec) [ -19290.9610] [ 3112] [depth= 1] . ( 54 sec) [ -19286.7044] [ 3111] [depth= 1] . ( 56 sec) [ -19243.7427] [ 3112] [depth= 1] . ( 58 sec) [ -19222.7569] [ 3112] [depth= 1] . ( 59 sec) [ -19212.7072] [ 3110] [depth= 1] . ( 60 sec) [ -19124.9723] [ 3093] [depth= 5] . ( 60 sec) [ -19105.6343] [ 3087] [depth= 2] . ( 62 sec) [ -18971.8911] [ 3064] [depth= 5] . ( 63 sec) [ -18904.1940] [ 3035] [depth= 3] . ( 64 sec) [ -18898.6933] [ 3033] [depth= 1] . ( 69 sec) [ -18842.4979] [ 3029] [depth= 7] . ( 70 sec) [ -18752.2385] [ 2997] [depth= 6] . ( 71 sec) [ -18743.1344] [ 3001] [depth= 1] . ( 72 sec) [ -18717.2812] [ 2981] [depth= 4] . ( 73 sec) [ -18478.3710] [ 2951] [depth= 5] . ( 74 sec) [ -18275.9496] [ 2952] [depth= 4] . ( 75 sec) [ -18233.2088] [ 2932] [depth= 3] . ( 76 sec) [ -18121.1270] [ 2873] [depth= 1] . ( 77 sec) [ -18077.1707] [ 2848] [depth= 1] . ( 79 sec) [ -18049.4566] [ 2845] [depth= 7] . ( 79 sec) [ -18027.4629] [ 2848] [depth= 1] . ( 80 sec) [ -18002.2220] [ 2846] [depth= 3] . ( 81 sec) [ -17889.2120] [ 2831] [depth= 6] . ( 82 sec) [ -17802.6205] [ 2814] [depth= 5] . ( 83 sec) [ -17756.9767] [ 2803] [depth= 1] . ( 84 sec) [ -17735.7821] [ 2793] [depth= 1] . ( 85 sec) [ -17695.4316] [ 2785] [depth= 1] . ( 86 sec) [ -17654.1915] [ 2783] [depth= 1] . ( 89 sec) [ -17646.1566] [ 2787] [depth= 2] . ( 90 sec) [ -17614.9987] [ 2785] [depth= 1] . ( 91 sec) [ -17586.4472] [ 2781] [depth= 1] . ( 92 sec) [ -17560.5890] [ 2778] [depth= 1] . ( 94 sec) [ -17544.4939] [ 2771] [depth= 1] . ( 95 sec) [ -17543.2686] [ 2773] [depth= 1] . ( 96 sec) [ -17463.5869] [ 2769] [depth= 8] . ( 97 sec) [ -17456.0214] [ 2769] [depth= 1] . ( 99 sec) [ -17428.9135] [ 2768] [depth= 1] . ( 99 sec) [ -17427.8728] [ 2772] [depth= 1] . ( 101 sec) [ -17392.9572] [ 2776] [depth= 9] . ( 102 sec) [ -17390.0587] [ 2771] [depth= 2] . ( 103 sec) [ -17355.7989] [ 2757] [depth= 1] . ( 104 sec) [ -17337.3193] [ 2758] [depth= 1] . ( 105 sec) [ -17332.7721] [ 2760] [depth= 1] . ( 106 sec) [ -17331.8401] [ 2763] [depth= 1] . ( 107 sec) [ -17309.4247] [ 2757] [depth= 3] . ( 109 sec) [ -17277.5118] [ 2753] [depth= 1] . ( 110 sec) [ -17255.0082] [ 2748] [depth= 2] . ( 111 sec) [ -17242.7580] [ 2751] [depth= 3] . ( 112 sec) [ -17235.3990] [ 2753] [depth= 1] . ( 113 sec) [ -17219.3279] [ 2752] [depth= 5] . ( 114 sec) [ -17209.8466] [ 2754] [depth= 1] . ( 115 sec) [ -17124.2517] [ 2719] [depth= 8] . ( 117 sec) [ -17111.0673] [ 2720] [depth= 1] . ( 117 sec) [ -17044.8559] [ 2720] [depth= 1] . ( 119 sec) [ -17038.4368] [ 2720] [depth= 1] . ( 120 sec) [ -17031.2339] [ 2708] [depth= 5] . ( 121 sec) [ -16913.7478] [ 2665] [depth= 4] . ( 122 sec) [ -16830.7922] [ 2647] [depth= 13] . ( 126 sec) [ -16830.0508] [ 2652] [depth= 2] . ( 128 sec) [ -16768.3569] [ 2637] [depth= 3] . ( 130 sec) [ -16764.9849] [ 2636] [depth= 1] . ( 133 sec) [ -16760.8876] [ 2636] [depth= 1] . ( 134 sec) [ -16661.2804] [ 2597] [depth= 9] . ( 137 sec) [ -16493.3844] [Branch lengths ] . ( 139 sec) [ -16475.4060] [Alpha ][ 0.376130] . ( 144 sec) [ -16468.0138] [ 2601] [depth= 3] . ( 148 sec) [ -16455.0751] [ 2596] [depth= 2] . ( 160 sec) [ -16451.5783] [ 2596] [depth= 1] . ( 161 sec) [ -16444.6170] [ 2593] [depth= 2] . ( 162 sec) [ -16431.3458] [ 2590] [depth= 1] . ( 163 sec) [ -16430.6274] [ 2592] [depth= 1] . ( 179 sec) [ -16365.1653] [ 2561] [depth= 8] . ( 184 sec) [ -16358.7109] [ 2553] [depth= 3] . ( 190 sec) [ -16351.7580] [ 2557] [depth= 1] . ( 203 sec) [ -16348.9423] [ 2553] [depth= 2] . ( 212 sec) [ -16347.7976] [ 2556] [depth= 1] . ( 221 sec) [ -16345.2159] [ 2557] [depth= 1] . ( 229 sec) [ -16338.2988] [ 2562] [depth= 4] . ( 253 sec) [ -16335.8714] [ 2563] [depth= 3] . ( 287 sec) [ -16335.4532] [ 2563] [depth= 1] . ( 289 sec) [ -16332.6801] [ 2564] [depth= 1] . ( 308 sec) [ -16332.4772] [ 2563] [depth= 1] . ( 318 sec) [ -16319.4491] [Branch lengths ] . ( 319 sec) [ -16319.4401] [Alpha ][ 0.378498] . ( 345 sec) [ -16319.3656] [ 2563] [depth= 1] . ( 406 sec) [ -16318.3704] [ 2562] [depth= 1] . ( 422 sec) [ -16318.0757] [ 2561] [depth= 1] . ( 428 sec) [ -16294.1828] [ 2548] [depth= 5] . ( 479 sec) [ -16294.0971] [ 2545] [depth= 2] . ( 485 sec) [ -16293.9088] [ 2546] [depth= 1] . ( 487 sec) [ -16292.7536] [ 2544] [depth= 2] . ( 490 sec) [ -16292.6557] [ 2542] [depth= 1] . ( 510 sec) [ -16286.5454] [Branch lengths ] . ( 511 sec) [ -16286.5414] [Alpha ][ 0.376797] . ( 520 sec) [ -16285.6455] [ 2544] [depth= 1] . ( 544 sec) [ -16280.2076] [ 2538] [depth= 4] . ( 631 sec) [ -16279.4390] [ 2540] [depth= 1] . ( 665 sec) [ -16278.9765] [ 2541] [depth= 1] . ( 676 sec) [ -16276.9224] [Branch lengths ] . ( 678 sec) [ -16276.9224] [Alpha ][ 0.376797] . ( 847 sec) [ -16276.8650] [Branch lengths ] . ( 848 sec) [ -16276.8650] [Topology ] . ( 856 sec) [ -16276.8519] [Topology ] . ( 864 sec) [ -16276.8499] [Topology ] . ( 871 sec) [ -16276.8492] [Topology ] . ( 873 sec) [ -16276.8489] [Alpha ][ 0.377235] . ( 873 sec) [ -16276.8489] [Topology ] . ( 881 sec) [ -16276.8485] [Topology ] . ( 883 sec) [ -16276.8485] [Alpha ][ 0.377235] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16276.848472. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -25650.6608] [Alpha ][ 0.500960] . ( 5 sec) [ -25309.5274] [ 4008] [depth= 10] . ( 6 sec) [ -25139.8086] [ 3988] [depth= 13] . ( 7 sec) [ -24850.0436] [ 3956] [depth= 5] . ( 8 sec) [ -24807.4203] [ 3950] [depth= 1] . ( 9 sec) [ -24443.5053] [ 3889] [depth= 8] . ( 10 sec) [ -24280.2324] [ 3885] [depth= 4] . ( 11 sec) [ -23678.8218] [ 3873] [depth= 3] . ( 12 sec) [ -23095.6683] [ 3736] [depth= 4] . ( 13 sec) [ -22761.6100] [ 3643] [depth= 7] . ( 14 sec) [ -22658.5487] [ 3649] [depth= 1] . ( 15 sec) [ -22531.5507] [ 3622] [depth= 1] . ( 16 sec) [ -22510.5294] [ 3618] [depth= 1] . ( 17 sec) [ -22434.3309] [ 3619] [depth= 5] . ( 18 sec) [ -22150.5630] [ 3580] [depth= 4] . ( 19 sec) [ -22025.8070] [ 3549] [depth= 4] . ( 20 sec) [ -22005.0875] [ 3546] [depth= 5] . ( 21 sec) [ -21805.4513] [ 3505] [depth= 6] . ( 22 sec) [ -21665.8243] [ 3485] [depth= 3] . ( 23 sec) [ -21586.2180] [ 3474] [depth= 15] . ( 24 sec) [ -21485.5796] [ 3454] [depth= 1] . ( 25 sec) [ -21481.5588] [ 3455] [depth= 1] . ( 26 sec) [ -21479.8337] [ 3456] [depth= 1] . ( 27 sec) [ -21476.0748] [ 3454] [depth= 2] . ( 28 sec) [ -21286.2933] [ 3417] [depth= 6] . ( 29 sec) [ -21108.4913] [ 3378] [depth= 10] . ( 30 sec) [ -20916.9363] [ 3328] [depth= 2] . ( 31 sec) [ -20880.2791] [ 3324] [depth= 2] . ( 32 sec) [ -20850.1822] [ 3311] [depth= 1] . ( 33 sec) [ -20777.1449] [ 3309] [depth= 1] . ( 34 sec) [ -20707.4562] [ 3293] [depth= 1] . ( 35 sec) [ -20696.3416] [ 3291] [depth= 3] . ( 36 sec) [ -20636.5462] [ 3280] [depth= 1] . ( 37 sec) [ -20425.3038] [ 3273] [depth= 4] . ( 38 sec) [ -20406.7669] [ 3256] [depth= 4] . ( 39 sec) [ -20287.8823] [ 3230] [depth= 3] . ( 40 sec) [ -20264.5142] [ 3233] [depth= 2] . ( 41 sec) [ -20226.1093] [ 3228] [depth= 2] . ( 42 sec) [ -20201.7901] [ 3215] [depth= 13] . ( 43 sec) [ -20132.5526] [ 3214] [depth= 1] . ( 44 sec) [ -19980.3261] [ 3201] [depth= 7] . ( 45 sec) [ -19966.7962] [ 3200] [depth= 1] . ( 46 sec) [ -19930.7078] [ 3194] [depth= 9] . ( 47 sec) [ -19896.1625] [ 3170] [depth= 6] . ( 48 sec) [ -19818.5799] [ 3159] [depth= 10] . ( 49 sec) [ -19812.5030] [ 3161] [depth= 1] . ( 50 sec) [ -19768.7181] [ 3156] [depth= 4] . ( 52 sec) [ -19766.9404] [ 3157] [depth= 2] . ( 53 sec) [ -19756.8927] [ 3154] [depth= 8] . ( 54 sec) [ -19716.3737] [ 3148] [depth= 11] . ( 55 sec) [ -19640.4748] [ 3124] [depth= 3] . ( 57 sec) [ -19534.6882] [ 3108] [depth= 4] . ( 57 sec) [ -19431.2631] [ 3095] [depth= 1] . ( 58 sec) [ -19263.5967] [ 3056] [depth= 7] . ( 59 sec) [ -19251.1030] [ 3056] [depth= 1] . ( 60 sec) [ -19248.7912] [ 3063] [depth= 7] . ( 62 sec) [ -19157.0276] [ 3040] [depth= 6] . ( 63 sec) [ -19144.1913] [ 3037] [depth= 1] . ( 64 sec) [ -19026.7528] [ 3023] [depth= 4] . ( 65 sec) [ -18910.2046] [ 3020] [depth= 1] . ( 66 sec) [ -18898.0499] [ 3016] [depth= 2] . ( 67 sec) [ -18889.6444] [ 3012] [depth= 2] . ( 68 sec) [ -18885.7911] [ 3010] [depth= 2] . ( 69 sec) [ -18875.3095] [ 2994] [depth= 12] . ( 70 sec) [ -18772.1971] [ 2957] [depth= 12] . ( 71 sec) [ -18378.2521] [ 2883] [depth= 9] . ( 72 sec) [ -18376.8243] [ 2886] [depth= 1] . ( 73 sec) [ -18257.5533] [ 2883] [depth= 9] . ( 75 sec) [ -18252.5590] [ 2880] [depth= 1] . ( 76 sec) [ -18192.1997] [ 2875] [depth= 3] . ( 77 sec) [ -18191.8471] [ 2875] [depth= 1] . ( 79 sec) [ -18186.4463] [ 2879] [depth= 1] . ( 79 sec) [ -18182.7528] [ 2879] [depth= 1] . ( 81 sec) [ -18174.8917] [ 2880] [depth= 9] . ( 85 sec) [ -18114.9927] [ 2861] [depth= 4] . ( 86 sec) [ -17989.4987] [ 2811] [depth= 15] . ( 87 sec) [ -17974.2486] [ 2812] [depth= 1] . ( 88 sec) [ -17949.1354] [ 2804] [depth= 1] . ( 89 sec) [ -17945.2992] [ 2803] [depth= 1] . ( 91 sec) [ -17945.2468] [ 2808] [depth= 1] . ( 92 sec) [ -17825.5319] [ 2782] [depth= 3] . ( 92 sec) [ -17728.1727] [ 2757] [depth= 2] . ( 94 sec) [ -17723.8529] [ 2754] [depth= 2] . ( 95 sec) [ -17720.7617] [ 2758] [depth= 2] . ( 96 sec) [ -17720.0394] [ 2756] [depth= 1] . ( 97 sec) [ -17664.9191] [ 2748] [depth= 2] . ( 98 sec) [ -17632.6625] [ 2726] [depth= 3] . ( 99 sec) [ -17596.2911] [ 2722] [depth= 1] . ( 100 sec) [ -17529.8183] [ 2717] [depth= 3] . ( 101 sec) [ -17522.5214] [ 2715] [depth= 1] . ( 102 sec) [ -17520.8339] [ 2714] [depth= 2] . ( 103 sec) [ -17446.6184] [ 2686] [depth= 5] . ( 104 sec) [ -17385.9663] [ 2686] [depth= 1] . ( 105 sec) [ -17362.4734] [ 2677] [depth= 5] . ( 106 sec) [ -16993.4714] [ 2647] [depth= 5] . ( 108 sec) [ -16938.9461] [ 2639] [depth= 2] . ( 109 sec) [ -16914.2304] [ 2634] [depth= 2] . ( 111 sec) [ -16913.4597] [ 2636] [depth= 1] . ( 113 sec) [ -16850.3784] [ 2625] [depth= 2] . ( 113 sec) [ -16842.3037] [ 2626] [depth= 1] . ( 115 sec) [ -16833.6288] [ 2630] [depth= 1] . ( 116 sec) [ -16823.1741] [ 2628] [depth= 1] . ( 117 sec) [ -16820.6301] [ 2629] [depth= 1] . ( 119 sec) [ -16771.7653] [ 2616] [depth= 2] . ( 120 sec) [ -16756.2619] [ 2608] [depth= 2] . ( 121 sec) [ -16750.9902] [ 2610] [depth= 2] . ( 122 sec) [ -16750.7629] [ 2608] [depth= 3] . ( 126 sec) [ -16705.6265] [ 2592] [depth= 2] . ( 128 sec) [ -16692.2299] [ 2592] [depth= 1] . ( 129 sec) [ -16689.6728] [ 2594] [depth= 1] . ( 131 sec) [ -16686.1001] [ 2591] [depth= 4] . ( 132 sec) [ -16661.1227] [ 2587] [depth= 1] . ( 133 sec) [ -16650.7292] [ 2587] [depth= 2] . ( 134 sec) [ -16607.0304] [ 2575] [depth= 5] . ( 137 sec) [ -16464.3711] [Branch lengths ] . ( 139 sec) [ -16444.9629] [Alpha ][ 0.370285] . ( 140 sec) [ -16441.9813] [ 2573] [depth= 1] . ( 142 sec) [ -16430.5699] [ 2572] [depth= 1] . ( 147 sec) [ -16429.3993] [ 2577] [depth= 7] . ( 148 sec) [ -16427.4189] [ 2574] [depth= 1] . ( 150 sec) [ -16414.0372] [ 2570] [depth= 3] . ( 158 sec) [ -16413.7695] [ 2571] [depth= 1] . ( 160 sec) [ -16392.5803] [ 2568] [depth= 3] . ( 161 sec) [ -16378.4617] [ 2565] [depth= 2] . ( 162 sec) [ -16376.8076] [ 2564] [depth= 3] . ( 167 sec) [ -16374.4470] [ 2564] [depth= 1] . ( 168 sec) [ -16369.4780] [ 2561] [depth= 2] . ( 171 sec) [ -16368.6808] [ 2560] [depth= 1] . ( 175 sec) [ -16362.8136] [ 2557] [depth= 1] . ( 177 sec) [ -16355.5896] [ 2554] [depth= 1] . ( 179 sec) [ -16355.5236] [ 2553] [depth= 1] . ( 186 sec) [ -16354.3365] [ 2556] [depth= 1] . ( 192 sec) [ -16353.3868] [ 2559] [depth= 1] . ( 194 sec) [ -16351.2690] [ 2555] [depth= 1] . ( 200 sec) [ -16348.0607] [ 2556] [depth= 1] . ( 201 sec) [ -16344.0471] [ 2554] [depth= 2] . ( 208 sec) [ -16343.3652] [ 2555] [depth= 2] . ( 215 sec) [ -16339.5015] [ 2559] [depth= 3] . ( 224 sec) [ -16336.3105] [ 2552] [depth= 2] . ( 232 sec) [ -16333.9439] [ 2549] [depth= 1] . ( 233 sec) [ -16332.6684] [ 2547] [depth= 1] . ( 239 sec) [ -16330.4486] [ 2547] [depth= 1] . ( 252 sec) [ -16323.5774] [ 2543] [depth= 1] . ( 265 sec) [ -16322.3128] [ 2542] [depth= 1] . ( 269 sec) [ -16321.9584] [ 2543] [depth= 1] . ( 270 sec) [ -16321.0701] [ 2543] [depth= 1] . ( 271 sec) [ -16310.9217] [ 2546] [depth= 1] . ( 275 sec) [ -16310.1864] [ 2543] [depth= 1] . ( 280 sec) [ -16306.9978] [ 2542] [depth= 1] . ( 286 sec) [ -16305.6407] [ 2541] [depth= 1] . ( 289 sec) [ -16280.4616] [Branch lengths ] . ( 291 sec) [ -16280.4616] [Alpha ][ 0.370285] . ( 334 sec) [ -16280.4229] [ 2539] [depth= 1] . ( 364 sec) [ -16280.1833] [ 2539] [depth= 1] . ( 424 sec) [ -16279.9056] [ 2541] [depth= 1] . ( 443 sec) [ -16277.2212] [Branch lengths ] . ( 445 sec) [ -16277.2073] [Alpha ][ 0.373250] . ( 614 sec) [ -16276.9391] [Branch lengths ] . ( 614 sec) [ -16276.9391] [Topology ] . ( 622 sec) [ -16276.8990] [Topology ] . ( 630 sec) [ -16276.8879] [Topology ] . ( 638 sec) [ -16276.8820] [Topology ] . ( 646 sec) [ -16276.8786] [Topology ] . ( 654 sec) [ -16276.8766] [Topology ] . ( 662 sec) [ -16276.8754] [Topology ] . ( 670 sec) [ -16276.8746] [Topology ] . ( 671 sec) [ -16276.8567] [Alpha ][ 0.376647] . ( 672 sec) [ -16276.8567] [Topology ] . ( 680 sec) [ -16276.8535] [Topology ] . ( 687 sec) [ -16276.8518] [Topology ] . ( 695 sec) [ -16276.8507] [Topology ] . ( 703 sec) [ -16276.8500] [Topology ] . ( 705 sec) [ -16276.8496] [Alpha ][ 0.377108] . ( 705 sec) [ -16276.8496] [Topology ] . ( 713 sec) [ -16276.8491] [Topology ] . ( 715 sec) [ -16276.8491] [Alpha ][ 0.377108] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16276.849052. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -26278.9357] [Alpha ][ 0.500960] . ( 5 sec) [ -26171.5464] [ 3994] [depth= 10] . ( 6 sec) [ -26126.2375] [ 3975] [depth= 9] . ( 7 sec) [ -26017.4551] [ 3950] [depth= 7] . ( 8 sec) [ -25966.3522] [ 3937] [depth= 1] . ( 9 sec) [ -25895.6735] [ 3929] [depth= 5] . ( 10 sec) [ -25797.7946] [ 3921] [depth= 1] . ( 11 sec) [ -25640.4279] [ 3911] [depth= 6] . ( 11 sec) [ -25288.6710] [ 3860] [depth= 5] . ( 13 sec) [ -25173.7688] [ 3849] [depth= 4] . ( 13 sec) [ -24887.5345] [ 3849] [depth= 1] . ( 14 sec) [ -23979.4001] [ 3835] [depth= 6] . ( 15 sec) [ -23746.4894] [ 3811] [depth= 6] . ( 16 sec) [ -23722.0003] [ 3802] [depth= 1] . ( 17 sec) [ -23602.9156] [ 3778] [depth= 1] . ( 18 sec) [ -23580.8486] [ 3778] [depth= 1] . ( 19 sec) [ -23559.4674] [ 3771] [depth= 3] . ( 21 sec) [ -23386.4594] [ 3705] [depth= 2] . ( 22 sec) [ -23200.4730] [ 3688] [depth= 14] . ( 22 sec) [ -23117.0480] [ 3684] [depth= 1] . ( 24 sec) [ -23042.6428] [ 3672] [depth= 1] . ( 24 sec) [ -22900.6311] [ 3662] [depth= 6] . ( 25 sec) [ -22789.8021] [ 3611] [depth= 5] . ( 26 sec) [ -22763.0301] [ 3610] [depth= 1] . ( 27 sec) [ -22620.2077] [ 3587] [depth= 15] . ( 28 sec) [ -22605.7951] [ 3583] [depth= 1] . ( 29 sec) [ -22449.3036] [ 3561] [depth= 4] . ( 30 sec) [ -22318.3919] [ 3536] [depth= 15] . ( 31 sec) [ -22276.6021] [ 3533] [depth= 11] . ( 32 sec) [ -22271.8400] [ 3527] [depth= 2] . ( 34 sec) [ -22209.2162] [ 3515] [depth= 13] . ( 34 sec) [ -22205.4909] [ 3517] [depth= 1] . ( 35 sec) [ -21928.6470] [ 3415] [depth= 9] . ( 37 sec) [ -21869.5569] [ 3404] [depth= 1] . ( 38 sec) [ -21641.3712] [ 3379] [depth= 17] . ( 40 sec) [ -21636.0006] [ 3377] [depth= 1] . ( 41 sec) [ -21542.1503] [ 3362] [depth= 2] . ( 42 sec) [ -21484.8476] [ 3366] [depth= 12] . ( 43 sec) [ -21376.7923] [ 3320] [depth= 7] . ( 45 sec) [ -21337.1203] [ 3324] [depth= 5] . ( 46 sec) [ -21257.1162] [ 3323] [depth= 1] . ( 47 sec) [ -21164.4689] [ 3302] [depth= 12] . ( 48 sec) [ -21052.7318] [ 3304] [depth= 1] . ( 49 sec) [ -21044.8984] [ 3299] [depth= 6] . ( 51 sec) [ -20939.2197] [ 3283] [depth= 1] . ( 52 sec) [ -20916.7887] [ 3278] [depth= 12] . ( 53 sec) [ -20841.6944] [ 3259] [depth= 3] . ( 54 sec) [ -20804.2820] [ 3253] [depth= 1] . ( 55 sec) [ -20695.0868] [ 3218] [depth= 9] . ( 56 sec) [ -20678.2630] [ 3214] [depth= 1] . ( 57 sec) [ -20619.7083] [ 3210] [depth= 2] . ( 58 sec) [ -20571.0384] [ 3204] [depth= 1] . ( 59 sec) [ -20457.7898] [ 3188] [depth= 4] . ( 60 sec) [ -20452.7034] [ 3188] [depth= 2] . ( 61 sec) [ -20400.2554] [ 3176] [depth= 12] . ( 62 sec) [ -20389.3227] [ 3174] [depth= 3] . ( 63 sec) [ -20315.3585] [ 3172] [depth= 2] . ( 64 sec) [ -20004.1504] [ 3101] [depth= 5] . ( 65 sec) [ -19933.2834] [ 3079] [depth= 6] . ( 67 sec) [ -19931.7719] [ 3080] [depth= 1] . ( 70 sec) [ -19895.5196] [ 3069] [depth= 12] . ( 73 sec) [ -19559.7010] [ 3036] [depth= 7] . ( 75 sec) [ -19548.6530] [ 3036] [depth= 2] . ( 76 sec) [ -19450.3932] [ 2996] [depth= 11] . ( 77 sec) [ -19289.6370] [ 2967] [depth= 5] . ( 78 sec) [ -19039.1828] [ 2935] [depth= 10] . ( 80 sec) [ -19038.6062] [ 2934] [depth= 1] . ( 82 sec) [ -19013.4500] [ 2932] [depth= 2] . ( 82 sec) [ -18935.2865] [ 2933] [depth= 1] . ( 83 sec) [ -18787.8889] [ 2901] [depth= 10] . ( 85 sec) [ -18737.1791] [ 2903] [depth= 2] . ( 86 sec) [ -18361.4057] [ 2857] [depth= 9] . ( 87 sec) [ -18358.2352] [ 2856] [depth= 1] . ( 88 sec) [ -18247.9461] [ 2809] [depth= 3] . ( 89 sec) [ -18129.2286] [ 2781] [depth= 7] . ( 90 sec) [ -18105.6376] [ 2780] [depth= 1] . ( 91 sec) [ -18087.0420] [ 2778] [depth= 1] . ( 93 sec) [ -18082.5273] [ 2781] [depth= 1] . ( 94 sec) [ -18067.0246] [ 2782] [depth= 1] . ( 95 sec) [ -18060.4061] [ 2784] [depth= 1] . ( 96 sec) [ -18038.8456] [ 2788] [depth= 1] . ( 97 sec) [ -17964.1968] [ 2784] [depth= 1] . ( 98 sec) [ -17851.3161] [ 2772] [depth= 2] . ( 100 sec) [ -17638.1947] [ 2744] [depth= 4] . ( 101 sec) [ -17593.1678] [ 2744] [depth= 4] . ( 102 sec) [ -17455.4027] [ 2735] [depth= 6] . ( 103 sec) [ -17442.1856] [ 2736] [depth= 1] . ( 104 sec) [ -17440.6620] [ 2735] [depth= 1] . ( 105 sec) [ -17398.5020] [ 2737] [depth= 1] . ( 106 sec) [ -17392.0336] [ 2737] [depth= 3] . ( 107 sec) [ -17378.1670] [ 2723] [depth= 6] . ( 108 sec) [ -17346.9934] [ 2712] [depth= 1] . ( 110 sec) [ -17346.2208] [ 2710] [depth= 2] . ( 112 sec) [ -17296.3027] [ 2697] [depth= 4] . ( 115 sec) [ -17294.8485] [ 2698] [depth= 1] . ( 118 sec) [ -17265.9014] [ 2689] [depth= 4] . ( 120 sec) [ -17264.3431] [ 2689] [depth= 3] . ( 121 sec) [ -17263.5124] [ 2689] [depth= 1] . ( 122 sec) [ -17263.3933] [ 2698] [depth= 5] . ( 123 sec) [ -17119.4520] [ 2687] [depth= 2] . ( 125 sec) [ -17082.3567] [ 2681] [depth= 8] . ( 126 sec) [ -17062.3354] [ 2680] [depth= 2] . ( 127 sec) [ -16952.0855] [ 2651] [depth= 14] . ( 131 sec) [ -16945.2790] [ 2653] [depth= 1] . ( 132 sec) [ -16944.9180] [ 2653] [depth= 1] . ( 133 sec) [ -16925.5067] [ 2651] [depth= 1] . ( 134 sec) [ -16916.3760] [ 2649] [depth= 1] . ( 137 sec) [ -16727.0454] [Branch lengths ] . ( 139 sec) [ -16705.5505] [Alpha ][ 0.365454] . ( 141 sec) [ -16705.3805] [ 2649] [depth= 1] . ( 144 sec) [ -16695.9005] [ 2644] [depth= 1] . ( 145 sec) [ -16655.1901] [ 2635] [depth= 2] . ( 146 sec) [ -16653.2101] [ 2635] [depth= 2] . ( 147 sec) [ -16645.2473] [ 2635] [depth= 2] . ( 153 sec) [ -16643.9989] [ 2634] [depth= 1] . ( 154 sec) [ -16637.3673] [ 2635] [depth= 1] . ( 158 sec) [ -16631.9647] [ 2632] [depth= 1] . ( 164 sec) [ -16525.4585] [ 2594] [depth= 7] . ( 164 sec) [ -16514.6496] [ 2594] [depth= 1] . ( 166 sec) [ -16511.2392] [ 2594] [depth= 1] . ( 166 sec) [ -16507.1428] [ 2592] [depth= 1] . ( 179 sec) [ -16505.4917] [ 2593] [depth= 1] . ( 182 sec) [ -16505.2763] [ 2592] [depth= 1] . ( 184 sec) [ -16451.0232] [ 2576] [depth= 2] . ( 188 sec) [ -16448.9710] [ 2576] [depth= 1] . ( 189 sec) [ -16369.3829] [ 2555] [depth= 4] . ( 190 sec) [ -16359.1338] [ 2553] [depth= 2] . ( 191 sec) [ -16357.6005] [ 2550] [depth= 1] . ( 195 sec) [ -16351.6507] [ 2547] [depth= 1] . ( 198 sec) [ -16345.2487] [ 2546] [depth= 1] . ( 203 sec) [ -16344.3593] [ 2545] [depth= 1] . ( 206 sec) [ -16344.1919] [ 2546] [depth= 1] . ( 208 sec) [ -16341.9246] [ 2545] [depth= 1] . ( 209 sec) [ -16337.1399] [ 2547] [depth= 1] . ( 218 sec) [ -16332.9496] [ 2549] [depth= 3] . ( 221 sec) [ -16326.6940] [ 2548] [depth= 1] . ( 225 sec) [ -16324.9445] [ 2549] [depth= 1] . ( 229 sec) [ -16322.5440] [ 2548] [depth= 1] . ( 231 sec) [ -16321.6698] [ 2548] [depth= 1] . ( 237 sec) [ -16319.1320] [ 2547] [depth= 2] . ( 240 sec) [ -16317.5655] [ 2546] [depth= 1] . ( 255 sec) [ -16314.8645] [ 2546] [depth= 1] . ( 259 sec) [ -16314.4828] [ 2548] [depth= 1] . ( 286 sec) [ -16291.1386] [Branch lengths ] . ( 287 sec) [ -16291.1282] [Alpha ][ 0.367981] . ( 339 sec) [ -16287.4682] [ 2547] [depth= 1] . ( 441 sec) [ -16287.0623] [ 2547] [depth= 1] . ( 477 sec) [ -16284.8923] [Branch lengths ] . ( 479 sec) [ -16284.8787] [Alpha ][ 0.370890] . ( 492 sec) [ -16282.5837] [ 2543] [depth= 4] . ( 506 sec) [ -16281.6532] [ 2543] [depth= 1] . ( 508 sec) [ -16281.5373] [ 2543] [depth= 1] . ( 580 sec) [ -16281.2513] [ 2544] [depth= 1] . ( 644 sec) [ -16279.1448] [Branch lengths ] . ( 646 sec) [ -16279.1370] [Alpha ][ 0.373090] . ( 676 sec) [ -16279.0122] [ 2542] [depth= 2] . ( 729 sec) [ -16278.8218] [ 2543] [depth= 1] . ( 745 sec) [ -16278.6119] [ 2543] [depth= 1] . ( 810 sec) [ -16277.3182] [Branch lengths ] . ( 812 sec) [ -16277.3106] [Alpha ][ 0.375277] . ( 862 sec) [ -16277.0283] [ 2541] [depth= 1] . ( 979 sec) [ -16276.8851] [Branch lengths ] . ( 980 sec) [ -16276.8821] [Alpha ][ 0.376628] . ( 981 sec) [ -16276.8821] [Topology ] . ( 989 sec) [ -16276.8684] [Topology ] . ( 997 sec) [ -16276.8532] [Topology ] . ( 1005 sec) [ -16276.8507] [Topology ] . ( 1012 sec) [ -16276.8499] [Topology ] . ( 1014 sec) [ -16276.8493] [Alpha ][ 0.377170] . ( 1014 sec) [ -16276.8493] [Topology ] . ( 1022 sec) [ -16276.8487] [Topology ] . ( 1024 sec) [ -16276.8487] [Alpha ][ 0.377170] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16276.848748. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -16605.2876] [Alpha ][ 0.500960] . ( 5 sec) [ -16605.2876] [Topology ] . ( 11 sec) [ -16414.2448] [Topology ] . ( 19 sec) [ -16352.8333] [Topology ] . ( 27 sec) [ -16338.9484] [Topology ] . ( 34 sec) [ -16328.2423] [Topology ] . ( 42 sec) [ -16325.0301] [Topology ] . ( 50 sec) [ -16323.8529] [Topology ] . ( 58 sec) [ -16322.4261] [Topology ] . ( 65 sec) [ -16319.2864] [Topology ] . ( 73 sec) [ -16312.8466] [Topology ] . ( 82 sec) [ -16294.9689] [Alpha ][ 0.387752] . ( 83 sec) [ -16294.9689] [Topology ] . ( 91 sec) [ -16292.1804] [Topology ] . ( 98 sec) [ -16291.4873] [Topology ] . ( 106 sec) [ -16291.2953] [Topology ] . ( 114 sec) [ -16291.2163] [Topology ] . ( 122 sec) [ -16291.1787] [Topology ] . ( 129 sec) [ -16291.1592] [Topology ] . ( 137 sec) [ -16291.1484] [Topology ] . Checking for NNIs, optimizing five branches... . ( 199 sec) [ -16291.0909] [Alpha ][ 0.381762] . ( 200 sec) [ -16291.0909] [Topology ] . ( 208 sec) [ -16291.0737] [Topology ] . ( 215 sec) [ -16291.0635] [Topology ] . ( 223 sec) [ -16291.0572] [Topology ] . ( 231 sec) [ -16291.0534] [Topology ] . ( 238 sec) [ -16291.0510] [Topology ] . ( 246 sec) [ -16291.0495] [Topology ] . Checking for NNIs, optimizing five branches... . ( 309 sec) [ -16291.0454] [Alpha ][ 0.380025] . ( 309 sec) [ -16291.0454] [Topology ] . ( 317 sec) [ -16291.0433] [Topology ] . ( 325 sec) [ -16291.0420] [Topology ] . ( 333 sec) [ -16291.0412] [Topology ] . Checking for NNIs, optimizing five branches... . ( 395 sec) [ -16291.0411] [Alpha ][ 0.379644] . ( 396 sec) [ -16291.0411] [Topology ] . ( 403 sec) [ -16291.0404] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 530 sec) [ -16605.2876] [Alpha ][ 0.500960] . ( 531 sec) [ -16595.4016] [ 2560] [depth= 1] . ( 532 sec) [ -16593.3251] [ 2559] [depth= 1] . ( 535 sec) [ -16591.2562] [ 2558] [depth= 1] . ( 552 sec) [ -16581.8807] [ 2559] [depth= 1] . ( 553 sec) [ -16572.7899] [ 2558] [depth= 1] . ( 557 sec) [ -16569.0639] [ 2559] [depth= 1] . ( 565 sec) [ -16562.4481] [ 2557] [depth= 1] . ( 569 sec) [ -16561.5336] [ 2558] [depth= 1] . ( 578 sec) [ -16554.3289] [ 2558] [depth= 1] . ( 579 sec) [ -16550.8681] [ 2558] [depth= 1] . ( 580 sec) [ -16542.7190] [ 2558] [depth= 3] . ( 581 sec) [ -16541.9999] [ 2558] [depth= 1] . ( 591 sec) [ -16525.8312] [ 2553] [depth= 3] . ( 593 sec) [ -16522.8339] [ 2552] [depth= 1] . ( 594 sec) [ -16520.3052] [ 2551] [depth= 1] . ( 595 sec) [ -16517.7199] [ 2551] [depth= 1] . ( 597 sec) [ -16516.4984] [ 2556] [depth= 2] . ( 602 sec) [ -16507.2109] [ 2559] [depth= 3] . ( 603 sec) [ -16499.0775] [ 2555] [depth= 3] . ( 604 sec) [ -16486.0382] [ 2550] [depth= 1] . ( 605 sec) [ -16470.9384] [ 2551] [depth= 1] . ( 606 sec) [ -16469.5869] [ 2550] [depth= 2] . ( 607 sec) [ -16469.4201] [ 2549] [depth= 1] . ( 608 sec) [ -16463.8042] [ 2551] [depth= 1] . ( 612 sec) [ -16460.9952] [ 2552] [depth= 1] . ( 614 sec) [ -16458.6746] [ 2547] [depth= 1] . ( 616 sec) [ -16456.2940] [ 2549] [depth= 1] . ( 617 sec) [ -16455.7503] [ 2546] [depth= 1] . ( 618 sec) [ -16445.6869] [ 2546] [depth= 1] . ( 619 sec) [ -16444.6771] [ 2545] [depth= 1] . ( 620 sec) [ -16439.3687] [ 2548] [depth= 1] . ( 624 sec) [ -16438.0344] [ 2551] [depth= 1] . ( 626 sec) [ -16434.4046] [ 2548] [depth= 1] . ( 629 sec) [ -16430.2810] [ 2549] [depth= 1] . ( 635 sec) [ -16416.3164] [ 2548] [depth= 1] . ( 646 sec) [ -16415.7550] [ 2548] [depth= 1] . ( 647 sec) [ -16414.6868] [ 2548] [depth= 1] . ( 648 sec) [ -16413.3543] [ 2549] [depth= 2] . ( 650 sec) [ -16413.0612] [ 2546] [depth= 3] . ( 651 sec) [ -16407.3849] [ 2545] [depth= 3] . ( 652 sec) [ -16405.8978] [ 2546] [depth= 1] . ( 661 sec) [ -16405.3278] [ 2545] [depth= 1] . ( 667 sec) [ -16404.8001] [ 2546] [depth= 1] . ( 669 sec) [ -16402.0362] [ 2545] [depth= 3] . ( 674 sec) [ -16401.4646] [ 2546] [depth= 1] . ( 677 sec) [ -16321.5849] [Branch lengths ] . ( 679 sec) [ -16300.1920] [Alpha ][ 0.362572] . ( 716 sec) [ -16294.2916] [ 2545] [depth= 1] . ( 767 sec) [ -16294.2145] [ 2546] [depth= 1] . ( 769 sec) [ -16293.2434] [ 2546] [depth= 1] . ( 813 sec) [ -16286.6503] [ 2546] [depth= 3] . ( 815 sec) [ -16285.1681] [ 2545] [depth= 1] . ( 819 sec) [ -16284.9352] [ 2545] [depth= 1] . ( 820 sec) [ -16284.8298] [ 2543] [depth= 2] . ( 851 sec) [ -16277.9422] [Branch lengths ] . ( 852 sec) [ -16277.8551] [Alpha ][ 0.369611] . ( 953 sec) [ -16277.5752] [ 2541] [depth= 1] . ( 1025 sec) [ -16277.0647] [Branch lengths ] . ( 1026 sec) [ -16277.0386] [Alpha ][ 0.373691] . ( 1027 sec) [ -16277.0386] [Topology ] . ( 1035 sec) [ -16276.9571] [Topology ] . ( 1042 sec) [ -16276.9103] [Topology ] . ( 1050 sec) [ -16276.8919] [Topology ] . ( 1058 sec) [ -16276.8822] [Topology ] . ( 1066 sec) [ -16276.8767] [Topology ] . ( 1074 sec) [ -16276.8734] [Topology ] . ( 1082 sec) [ -16276.8715] [Topology ] . ( 1090 sec) [ -16276.8703] [Topology ] . ( 1091 sec) [ -16276.8569] [Alpha ][ 0.376619] . ( 1092 sec) [ -16276.8569] [Topology ] . ( 1100 sec) [ -16276.8537] [Topology ] . ( 1107 sec) [ -16276.8519] [Topology ] . ( 1115 sec) [ -16276.8508] [Topology ] . ( 1123 sec) [ -16276.8502] [Topology ] . ( 1125 sec) [ -16276.8497] [Alpha ][ 0.377100] . ( 1125 sec) [ -16276.8497] [Topology ] . ( 1133 sec) [ -16276.8491] [Topology ] . ( 1134 sec) [ -16276.8491] [Alpha ][ 0.377100] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -16291.040410 . Log likelihood obtained after SPR moves : -16276.849102 . Log likelihood of the current tree: -16276.849102. . Printing the most likely tree in file 'proteic_M1487_52x981_2003.phy_phyml_tree.txt'... . Best log likelihood : -16276.848001 . Time used 0h19m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 5514.71user 0.00system 1:32:28elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps