.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2565_51x1951_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 763 patterns found. (out of a total of 1951 sites) . 1244 sites without polymorphism (63.76%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -31190.6048] [GTR parameters ] . ( 2 sec) [ -30413.2312] [Alpha ][ 0.500960] . ( 2 sec) [ -29179.3434] [ 4635] [depth= 13] . ( 3 sec) [ -28605.4852] [ 4577] [depth= 6] . ( 3 sec) [ -28508.6164] [ 4572] [depth= 1] . ( 3 sec) [ -28507.1239] [ 4574] [depth= 6] . ( 3 sec) [ -28407.2229] [ 4531] [depth= 2] . ( 3 sec) [ -28253.6794] [ 4486] [depth= 8] . ( 3 sec) [ -27917.9713] [ 4469] [depth= 2] . ( 3 sec) [ -27888.6204] [ 4455] [depth= 9] . ( 3 sec) [ -27748.1239] [ 4395] [depth= 3] . ( 4 sec) [ -27334.6372] [ 4372] [depth= 8] . ( 4 sec) [ -26855.9608] [ 4358] [depth= 2] . ( 4 sec) [ -26851.0664] [ 4357] [depth= 1] . ( 4 sec) [ -26800.9174] [ 4350] [depth= 2] . ( 4 sec) [ -26466.0962] [ 4349] [depth= 3] . ( 4 sec) [ -25589.8920] [ 4342] [depth= 3] . ( 4 sec) [ -24819.0937] [ 4254] [depth= 6] . ( 4 sec) [ -24494.9861] [ 4180] [depth= 15] . ( 4 sec) [ -24462.2741] [ 4159] [depth= 1] . ( 4 sec) [ -24257.3154] [ 4151] [depth= 4] . ( 4 sec) [ -24240.6193] [ 4143] [depth= 3] . ( 4 sec) [ -24167.7726] [ 4143] [depth= 1] . ( 5 sec) [ -24076.8421] [ 4093] [depth= 5] . ( 5 sec) [ -23985.3429] [ 4085] [depth= 1] . ( 5 sec) [ -23980.9004] [ 4085] [depth= 4] . ( 5 sec) [ -23905.4969] [ 4076] [depth= 1] . ( 5 sec) [ -23881.8377] [ 4076] [depth= 1] . ( 5 sec) [ -23465.7582] [ 4037] [depth= 7] . ( 5 sec) [ -22847.4036] [ 4032] [depth= 2] . ( 5 sec) [ -22474.6439] [ 4003] [depth= 3] . ( 5 sec) [ -22034.9208] [ 3946] [depth= 1] . ( 5 sec) [ -21785.0810] [ 3901] [depth= 7] . ( 6 sec) [ -21243.5572] [ 3845] [depth= 3] . ( 6 sec) [ -21019.5255] [ 3803] [depth= 8] . ( 6 sec) [ -20925.8401] [ 3762] [depth= 8] . ( 6 sec) [ -20907.2865] [ 3766] [depth= 1] . ( 6 sec) [ -20660.4832] [ 3705] [depth= 7] . ( 6 sec) [ -20653.8255] [ 3703] [depth= 1] . ( 6 sec) [ -20568.6371] [ 3679] [depth= 13] . ( 6 sec) [ -20521.1403] [ 3651] [depth= 2] . ( 6 sec) [ -20475.2583] [ 3647] [depth= 1] . ( 6 sec) [ -20281.4258] [ 3580] [depth= 12] . ( 7 sec) [ -20172.4371] [ 3566] [depth= 4] . ( 7 sec) [ -19956.0241] [ 3528] [depth= 6] . ( 7 sec) [ -19840.1248] [ 3519] [depth= 17] . ( 7 sec) [ -19812.9018] [ 3518] [depth= 1] . ( 7 sec) [ -19361.7849] [ 3410] [depth= 17] . ( 7 sec) [ -19319.2685] [ 3410] [depth= 2] . ( 7 sec) [ -19251.1684] [ 3390] [depth= 14] . ( 7 sec) [ -19241.6229] [ 3389] [depth= 19] . ( 7 sec) [ -19222.2565] [ 3388] [depth= 2] . ( 8 sec) [ -19153.7773] [ 3373] [depth= 20] . ( 8 sec) [ -19151.9491] [ 3370] [depth= 2] . ( 8 sec) [ -18956.1743] [ 3325] [depth= 5] . ( 8 sec) [ -18834.7596] [ 3289] [depth= 4] . ( 8 sec) [ -18810.4412] [ 3285] [depth= 1] . ( 8 sec) [ -18674.8421] [ 3247] [depth= 4] . ( 8 sec) [ -18642.2673] [ 3249] [depth= 1] . ( 8 sec) [ -18612.9270] [ 3234] [depth= 3] . ( 8 sec) [ -18609.2001] [ 3235] [depth= 1] . ( 8 sec) [ -18602.7777] [ 3234] [depth= 1] . ( 9 sec) [ -18547.3683] [ 3226] [depth= 1] . ( 9 sec) [ -18345.0275] [ 3186] [depth= 8] . ( 9 sec) [ -18330.3176] [ 3178] [depth= 2] . ( 9 sec) [ -18320.0185] [ 3172] [depth= 1] . ( 9 sec) [ -18153.5587] [ 3132] [depth= 9] . ( 9 sec) [ -18152.6750] [ 3137] [depth= 1] . ( 9 sec) [ -18141.9081] [ 3132] [depth= 1] . ( 9 sec) [ -18131.1321] [ 3123] [depth= 1] . ( 10 sec) [ -18123.0438] [ 3118] [depth= 1] . ( 10 sec) [ -18100.5662] [ 3113] [depth= 1] . ( 10 sec) [ -18016.3555] [ 3070] [depth= 6] . ( 10 sec) [ -17713.7250] [ 3037] [depth= 11] . ( 10 sec) [ -17699.6379] [ 3051] [depth= 11] . ( 10 sec) [ -17622.5652] [ 3032] [depth= 3] . ( 10 sec) [ -17564.6131] [ 3008] [depth= 1] . ( 10 sec) [ -17547.0896] [ 3001] [depth= 1] . ( 10 sec) [ -17435.0272] [ 2981] [depth= 8] . ( 10 sec) [ -17138.5346] [ 2938] [depth= 2] . ( 11 sec) [ -17135.4775] [ 2939] [depth= 1] . ( 11 sec) [ -17005.8316] [ 2921] [depth= 2] . ( 11 sec) [ -16996.9172] [ 2918] [depth= 1] . ( 11 sec) [ -16994.8950] [ 2918] [depth= 1] . ( 11 sec) [ -16857.7111] [ 2878] [depth= 8] . ( 12 sec) [ -16854.7090] [ 2881] [depth= 1] . ( 12 sec) [ -16765.3005] [ 2849] [depth= 2] . ( 12 sec) [ -16753.6069] [ 2837] [depth= 2] . ( 12 sec) [ -16725.0246] [ 2830] [depth= 1] . ( 12 sec) [ -16614.4281] [ 2794] [depth= 3] . ( 12 sec) [ -16551.8370] [ 2779] [depth= 10] . ( 12 sec) [ -16532.7263] [ 2773] [depth= 1] . ( 12 sec) [ -16323.6701] [ 2783] [depth= 3] . ( 13 sec) [ -16053.8480] [ 2677] [depth= 12] . ( 13 sec) [ -16042.7939] [ 2675] [depth= 1] . ( 13 sec) [ -16027.5829] [ 2670] [depth= 1] . ( 13 sec) [ -16012.8495] [ 2647] [depth= 5] . ( 13 sec) [ -15918.9931] [ 2645] [depth= 1] . ( 13 sec) [ -15918.3777] [ 2646] [depth= 1] . ( 13 sec) [ -15904.4829] [ 2643] [depth= 1] . ( 14 sec) [ -15902.1058] [ 2646] [depth= 3] . ( 14 sec) [ -15826.8502] [ 2620] [depth= 6] . ( 14 sec) [ -15767.1219] [ 2600] [depth= 3] . ( 14 sec) [ -15766.5092] [ 2601] [depth= 2] . ( 14 sec) [ -15735.3626] [ 2597] [depth= 3] . ( 14 sec) [ -15730.6348] [ 2596] [depth= 1] . ( 14 sec) [ -15730.2670] [ 2598] [depth= 1] . ( 14 sec) [ -15673.3628] [ 2569] [depth= 1] . ( 14 sec) [ -15661.8598] [ 2566] [depth= 1] . ( 15 sec) [ -15650.0007] [ 2567] [depth= 1] . ( 15 sec) [ -15648.0335] [ 2566] [depth= 1] . ( 16 sec) [ -15514.8783] [Branch lengths ] . ( 19 sec) [ -15485.4225] [GTR parameters ] . ( 19 sec) [ -15341.0272] [Alpha ][ 0.250961] . ( 19 sec) [ -15339.9552] [ 2565] [depth= 1] . ( 20 sec) [ -15143.8453] [ 2514] [depth= 5] . ( 20 sec) [ -15073.5104] [ 2499] [depth= 7] . ( 20 sec) [ -15066.0056] [ 2495] [depth= 3] . ( 20 sec) [ -15015.1288] [ 2495] [depth= 2] . ( 20 sec) [ -15007.9739] [ 2490] [depth= 2] . ( 20 sec) [ -14987.7995] [ 2477] [depth= 1] . ( 21 sec) [ -14986.0844] [ 2477] [depth= 1] . ( 21 sec) [ -14911.8045] [ 2462] [depth= 1] . ( 21 sec) [ -14910.4919] [ 2462] [depth= 1] . ( 22 sec) [ -14909.0751] [ 2461] [depth= 1] . ( 22 sec) [ -14899.3953] [ 2466] [depth= 1] . ( 22 sec) [ -14838.4233] [ 2443] [depth= 1] . ( 23 sec) [ -14834.3204] [ 2442] [depth= 1] . ( 23 sec) [ -14834.3100] [ 2442] [depth= 1] . ( 24 sec) [ -14831.8132] [ 2438] [depth= 2] . ( 24 sec) [ -14711.2902] [ 2402] [depth= 2] . ( 24 sec) [ -14711.1931] [ 2399] [depth= 1] . ( 25 sec) [ -14710.0403] [ 2404] [depth= 1] . ( 25 sec) [ -14708.0280] [ 2406] [depth= 3] . ( 25 sec) [ -14707.7897] [ 2408] [depth= 1] . ( 25 sec) [ -14706.2929] [ 2408] [depth= 1] . ( 27 sec) [ -14706.0756] [ 2402] [depth= 1] . ( 27 sec) [ -14704.3292] [ 2405] [depth= 1] . ( 28 sec) [ -14700.7407] [ 2407] [depth= 1] . ( 28 sec) [ -14696.4759] [ 2407] [depth= 1] . ( 28 sec) [ -14694.8637] [ 2404] [depth= 1] . ( 28 sec) [ -14693.6660] [ 2405] [depth= 1] . ( 29 sec) [ -14693.5246] [ 2406] [depth= 1] . ( 29 sec) [ -14692.3370] [ 2405] [depth= 1] . ( 29 sec) [ -14690.5766] [ 2401] [depth= 3] . ( 31 sec) [ -14663.3183] [Branch lengths ] . ( 34 sec) [ -14662.3730] [GTR parameters ] . ( 34 sec) [ -14662.1371] [Alpha ][ 0.244091] . ( 35 sec) [ -14661.8181] [ 2404] [depth= 2] . ( 37 sec) [ -14660.7911] [ 2401] [depth= 1] . ( 46 sec) [ -14658.0768] [Branch lengths ] . ( 47 sec) [ -14658.0640] [GTR parameters ] . ( 48 sec) [ -14658.0640] [Alpha ][ 0.244091] . ( 60 sec) [ -14657.8045] [Branch lengths ] . ( 113 sec) [ -14657.7767] [Branch lengths ] . ( 113 sec) [ -14657.7767] [Topology ] . ( 115 sec) [ -14657.7743] [Topology ] . ( 116 sec) [ -14657.7734] [Topology ] . ( 117 sec) [ -14657.7733] [GTR parameters ] . ( 117 sec) [ -14657.7720] [Alpha ][ 0.244553] . ( 117 sec) [ -14657.7720] [Topology ] . ( 119 sec) [ -14657.7713] [Topology ] . ( 120 sec) [ -14657.7691] [GTR parameters ] . ( 120 sec) [ -14657.7691] [Alpha ][ 0.244553] . ( 120 sec) [ -14657.7691] [Topology ] . ( 122 sec) [ -14657.7685] [Topology ] . ( 122 sec) [ -14657.7676] [GTR parameters ] . ( 122 sec) [ -14657.7676] [Alpha ][ 0.244553] . ( 122 sec) [ -14657.7676] [Topology ] . ( 124 sec) [ -14657.7673] [Topology ] . ( 124 sec) [ -14657.7673] [GTR parameters ] . ( 124 sec) [ -14657.7673] [Alpha ][ 0.244553] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14657.767254. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -29654.4211] [GTR parameters ] . ( 1 sec) [ -28908.3215] [Alpha ][ 0.500960] . ( 1 sec) [ -28581.0336] [ 4620] [depth= 13] . ( 1 sec) [ -28368.9991] [ 4572] [depth= 11] . ( 1 sec) [ -28255.2035] [ 4568] [depth= 1] . ( 1 sec) [ -28056.1056] [ 4559] [depth= 6] . ( 1 sec) [ -27917.0412] [ 4535] [depth= 1] . ( 1 sec) [ -27730.0730] [ 4528] [depth= 7] . ( 2 sec) [ -27583.3739] [ 4519] [depth= 8] . ( 2 sec) [ -27441.0847] [ 4466] [depth= 1] . ( 2 sec) [ -27333.3304] [ 4428] [depth= 9] . ( 2 sec) [ -27329.1856] [ 4428] [depth= 2] . ( 2 sec) [ -27228.8713] [ 4421] [depth= 4] . ( 2 sec) [ -27148.2395] [ 4400] [depth= 4] . ( 2 sec) [ -26986.8685] [ 4380] [depth= 7] . ( 2 sec) [ -26950.0188] [ 4361] [depth= 9] . ( 2 sec) [ -26240.7199] [ 4357] [depth= 4] . ( 2 sec) [ -26056.9320] [ 4337] [depth= 13] . ( 2 sec) [ -26048.2393] [ 4338] [depth= 2] . ( 3 sec) [ -24770.6163] [ 4230] [depth= 8] . ( 3 sec) [ -24734.2455] [ 4225] [depth= 1] . ( 3 sec) [ -24704.5173] [ 4222] [depth= 1] . ( 3 sec) [ -24703.6930] [ 4217] [depth= 1] . ( 3 sec) [ -24658.9300] [ 4190] [depth= 3] . ( 3 sec) [ -24446.3594] [ 4149] [depth= 8] . ( 3 sec) [ -24351.5425] [ 4176] [depth= 1] . ( 3 sec) [ -24323.6793] [ 4171] [depth= 1] . ( 3 sec) [ -24146.6314] [ 4088] [depth= 9] . ( 3 sec) [ -23921.8138] [ 4030] [depth= 8] . ( 4 sec) [ -23346.3630] [ 4017] [depth= 10] . ( 4 sec) [ -22915.6191] [ 3966] [depth= 15] . ( 4 sec) [ -22886.4753] [ 3949] [depth= 2] . ( 4 sec) [ -22883.0676] [ 3941] [depth= 13] . ( 4 sec) [ -22810.6989] [ 3916] [depth= 1] . ( 4 sec) [ -22769.7170] [ 3907] [depth= 8] . ( 4 sec) [ -22746.5261] [ 3924] [depth= 14] . ( 4 sec) [ -22658.6542] [ 3915] [depth= 13] . ( 4 sec) [ -22444.1587] [ 3915] [depth= 3] . ( 4 sec) [ -22027.8627] [ 3819] [depth= 6] . ( 5 sec) [ -21734.4917] [ 3849] [depth= 1] . ( 5 sec) [ -21429.9359] [ 3819] [depth= 1] . ( 5 sec) [ -21335.5651] [ 3788] [depth= 1] . ( 5 sec) [ -21319.7330] [ 3786] [depth= 1] . ( 5 sec) [ -21019.9791] [ 3738] [depth= 8] . ( 5 sec) [ -20910.1672] [ 3713] [depth= 8] . ( 5 sec) [ -20766.0567] [ 3689] [depth= 9] . ( 5 sec) [ -20763.7850] [ 3688] [depth= 1] . ( 5 sec) [ -20698.7181] [ 3675] [depth= 1] . ( 5 sec) [ -20463.1986] [ 3613] [depth= 15] . ( 6 sec) [ -20454.1373] [ 3598] [depth= 5] . ( 6 sec) [ -20191.4621] [ 3534] [depth= 12] . ( 6 sec) [ -19951.6269] [ 3501] [depth= 6] . ( 6 sec) [ -19614.9546] [ 3493] [depth= 5] . ( 6 sec) [ -19560.0719] [ 3478] [depth= 4] . ( 6 sec) [ -19550.2520] [ 3477] [depth= 1] . ( 7 sec) [ -19408.1346] [ 3436] [depth= 2] . ( 7 sec) [ -19363.8221] [ 3415] [depth= 6] . ( 7 sec) [ -19216.9039] [ 3385] [depth= 3] . ( 7 sec) [ -19063.4614] [ 3388] [depth= 1] . ( 7 sec) [ -18927.8740] [ 3321] [depth= 5] . ( 7 sec) [ -18882.5040] [ 3311] [depth= 6] . ( 7 sec) [ -18764.0011] [ 3272] [depth= 5] . ( 8 sec) [ -18762.9949] [ 3272] [depth= 1] . ( 8 sec) [ -18656.0687] [ 3243] [depth= 2] . ( 8 sec) [ -18460.5003] [ 3202] [depth= 4] . ( 8 sec) [ -18272.0202] [ 3139] [depth= 7] . ( 8 sec) [ -18078.7751] [ 3094] [depth= 3] . ( 8 sec) [ -18018.4897] [ 3078] [depth= 3] . ( 8 sec) [ -17989.3287] [ 3068] [depth= 8] . ( 8 sec) [ -17923.6232] [ 3070] [depth= 1] . ( 8 sec) [ -17844.3458] [ 3075] [depth= 10] . ( 8 sec) [ -17833.9851] [ 3066] [depth= 2] . ( 8 sec) [ -17555.0271] [ 2982] [depth= 9] . ( 9 sec) [ -17372.9696] [ 2971] [depth= 3] . ( 9 sec) [ -17372.6092] [ 2971] [depth= 2] . ( 9 sec) [ -17363.7165] [ 2969] [depth= 9] . ( 9 sec) [ -17174.0771] [ 2913] [depth= 2] . ( 9 sec) [ -17134.8769] [ 2872] [depth= 3] . ( 9 sec) [ -17129.5968] [ 2868] [depth= 1] . ( 9 sec) [ -16935.7132] [ 2813] [depth= 3] . ( 10 sec) [ -16933.7104] [ 2814] [depth= 1] . ( 10 sec) [ -16924.9435] [ 2811] [depth= 11] . ( 10 sec) [ -16866.2470] [ 2806] [depth= 1] . ( 10 sec) [ -16696.0165] [ 2811] [depth= 1] . ( 10 sec) [ -16639.1607] [ 2788] [depth= 2] . ( 10 sec) [ -16637.7352] [ 2788] [depth= 1] . ( 10 sec) [ -16620.3814] [ 2777] [depth= 1] . ( 10 sec) [ -16607.7335] [ 2779] [depth= 1] . ( 10 sec) [ -16569.0761] [ 2769] [depth= 1] . ( 10 sec) [ -16519.1682] [ 2759] [depth= 2] . ( 11 sec) [ -16518.7807] [ 2762] [depth= 1] . ( 11 sec) [ -16503.3821] [ 2756] [depth= 2] . ( 11 sec) [ -16284.1238] [ 2692] [depth= 7] . ( 11 sec) [ -16276.4605] [ 2687] [depth= 1] . ( 11 sec) [ -16218.5053] [ 2680] [depth= 3] . ( 11 sec) [ -16074.4475] [ 2646] [depth= 4] . ( 11 sec) [ -16063.7841] [ 2644] [depth= 1] . ( 11 sec) [ -16002.3983] [ 2629] [depth= 7] . ( 11 sec) [ -16001.1530] [ 2623] [depth= 1] . ( 12 sec) [ -16000.0714] [ 2623] [depth= 1] . ( 12 sec) [ -15999.6763] [ 2623] [depth= 1] . ( 12 sec) [ -15990.2669] [ 2618] [depth= 2] . ( 12 sec) [ -15962.5670] [ 2620] [depth= 7] . ( 12 sec) [ -15913.2702] [ 2602] [depth= 6] . ( 12 sec) [ -15899.5906] [ 2605] [depth= 1] . ( 12 sec) [ -15879.6608] [ 2602] [depth= 1] . ( 13 sec) [ -15876.1740] [ 2602] [depth= 1] . ( 13 sec) [ -15823.5345] [ 2578] [depth= 1] . ( 13 sec) [ -15817.8504] [ 2577] [depth= 1] . ( 13 sec) [ -15813.5671] [ 2579] [depth= 1] . ( 13 sec) [ -15810.1516] [ 2579] [depth= 2] . ( 13 sec) [ -15804.8530] [ 2578] [depth= 2] . ( 13 sec) [ -15800.0963] [ 2576] [depth= 1] . ( 13 sec) [ -15696.7859] [ 2546] [depth= 5] . ( 13 sec) [ -15685.6761] [ 2538] [depth= 5] . ( 13 sec) [ -15682.8671] [ 2529] [depth= 1] . ( 14 sec) [ -15669.9523] [ 2529] [depth= 1] . ( 14 sec) [ -15555.9640] [Branch lengths ] . ( 17 sec) [ -15302.6902] [GTR parameters ] . ( 18 sec) [ -15159.9736] [Alpha ][ 0.250961] . ( 18 sec) [ -15151.0213] [ 2525] [depth= 1] . ( 18 sec) [ -15137.4965] [ 2521] [depth= 1] . ( 18 sec) [ -15104.3679] [ 2511] [depth= 2] . ( 18 sec) [ -15104.1100] [ 2509] [depth= 1] . ( 19 sec) [ -15054.1428] [ 2488] [depth= 1] . ( 19 sec) [ -14979.9551] [ 2470] [depth= 7] . ( 19 sec) [ -14917.3535] [ 2460] [depth= 1] . ( 19 sec) [ -14916.8981] [ 2458] [depth= 1] . ( 19 sec) [ -14915.2178] [ 2457] [depth= 2] . ( 19 sec) [ -14912.2248] [ 2455] [depth= 1] . ( 20 sec) [ -14857.0893] [ 2438] [depth= 2] . ( 20 sec) [ -14856.9923] [ 2438] [depth= 1] . ( 21 sec) [ -14847.1279] [ 2439] [depth= 1] . ( 21 sec) [ -14784.9302] [ 2409] [depth= 9] . ( 21 sec) [ -14784.3073] [ 2412] [depth= 1] . ( 21 sec) [ -14782.6537] [ 2411] [depth= 1] . ( 22 sec) [ -14782.1937] [ 2411] [depth= 1] . ( 22 sec) [ -14782.0340] [ 2411] [depth= 1] . ( 23 sec) [ -14781.1909] [ 2410] [depth= 2] . ( 23 sec) [ -14779.6367] [ 2414] [depth= 1] . ( 23 sec) [ -14758.5515] [ 2409] [depth= 1] . ( 24 sec) [ -14758.4535] [ 2410] [depth= 1] . ( 24 sec) [ -14753.6347] [ 2410] [depth= 1] . ( 25 sec) [ -14753.5966] [ 2410] [depth= 1] . ( 25 sec) [ -14714.3715] [ 2400] [depth= 2] . ( 25 sec) [ -14713.8996] [ 2401] [depth= 1] . ( 26 sec) [ -14713.8616] [ 2401] [depth= 1] . ( 26 sec) [ -14713.4727] [ 2400] [depth= 1] . ( 27 sec) [ -14712.0704] [ 2399] [depth= 1] . ( 28 sec) [ -14696.7062] [ 2397] [depth= 1] . ( 28 sec) [ -14693.6066] [ 2398] [depth= 1] . ( 29 sec) [ -14664.0851] [Branch lengths ] . ( 32 sec) [ -14662.9863] [GTR parameters ] . ( 33 sec) [ -14662.6835] [Alpha ][ 0.243118] . ( 35 sec) [ -14662.6654] [ 2398] [depth= 1] . ( 40 sec) [ -14660.7223] [ 2401] [depth= 1] . ( 43 sec) [ -14660.3919] [ 2403] [depth= 1] . ( 45 sec) [ -14658.1658] [Branch lengths ] . ( 45 sec) [ -14658.1656] [GTR parameters ] . ( 45 sec) [ -14658.1633] [Alpha ][ 0.243763] . ( 57 sec) [ -14657.9475] [Branch lengths ] . ( 90 sec) [ -14657.9169] [ 2401] [depth= 1] . ( 109 sec) [ -14657.8129] [Branch lengths ] . ( 112 sec) [ -14657.7847] [GTR parameters ] . ( 112 sec) [ -14657.7822] [Alpha ][ 0.244436] . ( 112 sec) [ -14657.7822] [Topology ] . ( 113 sec) [ -14657.7742] [Topology ] . ( 115 sec) [ -14657.7710] [Topology ] . ( 117 sec) [ -14657.7693] [Topology ] . ( 118 sec) [ -14657.7684] [Topology ] . ( 119 sec) [ -14657.7684] [GTR parameters ] . ( 119 sec) [ -14657.7683] [Alpha ][ 0.244680] . ( 119 sec) [ -14657.7683] [Topology ] . ( 120 sec) [ -14657.7677] [Topology ] . ( 122 sec) [ -14657.7676] [GTR parameters ] . ( 122 sec) [ -14657.7676] [Alpha ][ 0.244680] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14657.767618. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -30672.1497] [GTR parameters ] . ( 2 sec) [ -29897.2861] [Alpha ][ 0.500960] . ( 2 sec) [ -29699.7195] [ 4719] [depth= 5] . ( 2 sec) [ -28594.3240] [ 4660] [depth= 7] . ( 2 sec) [ -28200.2362] [ 4615] [depth= 1] . ( 2 sec) [ -28053.7216] [ 4598] [depth= 8] . ( 2 sec) [ -27991.4773] [ 4572] [depth= 1] . ( 2 sec) [ -27861.3352] [ 4552] [depth= 2] . ( 2 sec) [ -27823.0721] [ 4543] [depth= 7] . ( 2 sec) [ -27654.2767] [ 4543] [depth= 1] . ( 3 sec) [ -26957.3888] [ 4541] [depth= 1] . ( 3 sec) [ -26873.6859] [ 4533] [depth= 3] . ( 3 sec) [ -26703.3504] [ 4469] [depth= 7] . ( 3 sec) [ -26649.6783] [ 4467] [depth= 1] . ( 3 sec) [ -26373.9075] [ 4429] [depth= 4] . ( 3 sec) [ -26291.3063] [ 4426] [depth= 1] . ( 3 sec) [ -25755.2482] [ 4358] [depth= 8] . ( 3 sec) [ -25331.1818] [ 4294] [depth= 8] . ( 3 sec) [ -24813.0454] [ 4192] [depth= 8] . ( 3 sec) [ -24617.0517] [ 4142] [depth= 10] . ( 3 sec) [ -24128.9736] [ 4051] [depth= 1] . ( 4 sec) [ -23990.3158] [ 3986] [depth= 1] . ( 4 sec) [ -23941.7475] [ 3983] [depth= 6] . ( 4 sec) [ -23895.9346] [ 3975] [depth= 7] . ( 4 sec) [ -23502.4248] [ 3968] [depth= 8] . ( 4 sec) [ -23481.2314] [ 3943] [depth= 3] . ( 4 sec) [ -23350.6999] [ 3943] [depth= 6] . ( 4 sec) [ -23063.6293] [ 3983] [depth= 2] . ( 4 sec) [ -22686.9882] [ 3890] [depth= 9] . ( 4 sec) [ -22527.5689] [ 3848] [depth= 1] . ( 5 sec) [ -22401.1963] [ 3818] [depth= 6] . ( 5 sec) [ -22347.2943] [ 3808] [depth= 6] . ( 5 sec) [ -22324.0674] [ 3807] [depth= 1] . ( 5 sec) [ -21948.1412] [ 3685] [depth= 6] . ( 5 sec) [ -21715.2685] [ 3671] [depth= 7] . ( 5 sec) [ -21703.6734] [ 3669] [depth= 1] . ( 5 sec) [ -21654.7167] [ 3663] [depth= 9] . ( 5 sec) [ -21346.7404] [ 3609] [depth= 6] . ( 5 sec) [ -21223.3446] [ 3616] [depth= 1] . ( 5 sec) [ -20986.2998] [ 3616] [depth= 1] . ( 6 sec) [ -20971.2832] [ 3612] [depth= 1] . ( 6 sec) [ -20652.2184] [ 3515] [depth= 9] . ( 6 sec) [ -20558.6301] [ 3515] [depth= 1] . ( 6 sec) [ -20398.5853] [ 3498] [depth= 4] . ( 6 sec) [ -20328.9523] [ 3488] [depth= 4] . ( 6 sec) [ -20296.2058] [ 3477] [depth= 3] . ( 6 sec) [ -20240.3031] [ 3469] [depth= 1] . ( 6 sec) [ -20199.2355] [ 3455] [depth= 12] . ( 6 sec) [ -20146.4420] [ 3441] [depth= 1] . ( 6 sec) [ -19952.1671] [ 3395] [depth= 9] . ( 6 sec) [ -19943.3453] [ 3402] [depth= 12] . ( 7 sec) [ -19513.2672] [ 3345] [depth= 13] . ( 7 sec) [ -19392.3051] [ 3273] [depth= 3] . ( 7 sec) [ -19277.8414] [ 3270] [depth= 2] . ( 7 sec) [ -19096.0737] [ 3192] [depth= 4] . ( 7 sec) [ -19082.6114] [ 3189] [depth= 1] . ( 7 sec) [ -19055.2975] [ 3167] [depth= 6] . ( 7 sec) [ -18950.4464] [ 3164] [depth= 2] . ( 7 sec) [ -18636.7295] [ 3148] [depth= 12] . ( 7 sec) [ -18128.3005] [ 3127] [depth= 1] . ( 7 sec) [ -18056.7954] [ 3110] [depth= 7] . ( 7 sec) [ -18036.5482] [ 3105] [depth= 1] . ( 8 sec) [ -18029.3093] [ 3099] [depth= 3] . ( 8 sec) [ -17750.0188] [ 3085] [depth= 4] . ( 8 sec) [ -17546.7314] [ 3052] [depth= 8] . ( 8 sec) [ -17465.7682] [ 3021] [depth= 1] . ( 8 sec) [ -17437.7795] [ 2997] [depth= 1] . ( 8 sec) [ -17326.4007] [ 2936] [depth= 12] . ( 8 sec) [ -17286.6473] [ 2936] [depth= 1] . ( 8 sec) [ -17085.9555] [ 2878] [depth= 9] . ( 8 sec) [ -17074.0914] [ 2877] [depth= 1] . ( 8 sec) [ -17072.4452] [ 2857] [depth= 5] . ( 9 sec) [ -16976.5928] [ 2853] [depth= 1] . ( 9 sec) [ -16929.2717] [ 2842] [depth= 2] . ( 9 sec) [ -16813.6341] [ 2828] [depth= 1] . ( 9 sec) [ -16794.8589] [ 2830] [depth= 1] . ( 9 sec) [ -16788.6323] [ 2842] [depth= 1] . ( 9 sec) [ -16772.9476] [ 2830] [depth= 1] . ( 9 sec) [ -16737.8003] [ 2819] [depth= 1] . ( 9 sec) [ -16459.4831] [ 2781] [depth= 11] . ( 9 sec) [ -16437.0658] [ 2758] [depth= 8] . ( 10 sec) [ -16309.5127] [ 2726] [depth= 9] . ( 10 sec) [ -16209.5357] [ 2698] [depth= 3] . ( 10 sec) [ -16196.3083] [ 2697] [depth= 2] . ( 10 sec) [ -16164.8289] [ 2685] [depth= 1] . ( 10 sec) [ -16020.6677] [ 2664] [depth= 6] . ( 10 sec) [ -15920.4317] [ 2659] [depth= 2] . ( 10 sec) [ -15793.4527] [ 2625] [depth= 1] . ( 11 sec) [ -15700.3748] [ 2604] [depth= 3] . ( 11 sec) [ -15695.7699] [ 2604] [depth= 1] . ( 11 sec) [ -15559.7067] [ 2571] [depth= 2] . ( 11 sec) [ -15483.8823] [ 2552] [depth= 1] . ( 11 sec) [ -15453.3700] [ 2540] [depth= 1] . ( 11 sec) [ -15425.1093] [ 2528] [depth= 1] . ( 11 sec) [ -15402.5840] [ 2518] [depth= 1] . ( 11 sec) [ -15400.9897] [ 2519] [depth= 1] . ( 11 sec) [ -15400.2565] [ 2519] [depth= 1] . ( 12 sec) [ -15400.1893] [ 2519] [depth= 1] . ( 12 sec) [ -15389.0286] [ 2514] [depth= 3] . ( 12 sec) [ -15383.5254] [ 2514] [depth= 2] . ( 12 sec) [ -15290.3692] [ 2488] [depth= 2] . ( 12 sec) [ -15287.4527] [ 2485] [depth= 1] . ( 12 sec) [ -15209.4630] [ 2470] [depth= 6] . ( 12 sec) [ -15201.6505] [ 2469] [depth= 2] . ( 12 sec) [ -15192.3351] [ 2468] [depth= 2] . ( 12 sec) [ -15191.1164] [ 2468] [depth= 1] . ( 13 sec) [ -15141.6035] [ 2457] [depth= 1] . ( 13 sec) [ -15135.4450] [ 2457] [depth= 1] . ( 13 sec) [ -15134.4935] [ 2458] [depth= 2] . ( 13 sec) [ -15132.1136] [ 2460] [depth= 1] . ( 13 sec) [ -15131.6220] [ 2460] [depth= 1] . ( 13 sec) [ -15129.5605] [ 2461] [depth= 1] . ( 13 sec) [ -15123.2221] [ 2460] [depth= 1] . ( 14 sec) [ -15025.4397] [Branch lengths ] . ( 17 sec) [ -14993.6280] [GTR parameters ] . ( 17 sec) [ -14857.4946] [Alpha ][ 0.250961] . ( 18 sec) [ -14852.0558] [ 2456] [depth= 2] . ( 18 sec) [ -14851.3049] [ 2456] [depth= 1] . ( 18 sec) [ -14850.8351] [ 2455] [depth= 1] . ( 19 sec) [ -14847.2777] [ 2459] [depth= 1] . ( 20 sec) [ -14841.2953] [ 2454] [depth= 1] . ( 20 sec) [ -14729.8113] [ 2420] [depth= 1] . ( 21 sec) [ -14710.0214] [ 2410] [depth= 2] . ( 21 sec) [ -14709.0161] [ 2407] [depth= 1] . ( 22 sec) [ -14706.7155] [ 2408] [depth= 1] . ( 22 sec) [ -14703.5408] [ 2407] [depth= 1] . ( 24 sec) [ -14701.6792] [ 2409] [depth= 1] . ( 24 sec) [ -14700.9855] [ 2407] [depth= 1] . ( 25 sec) [ -14698.0531] [ 2411] [depth= 1] . ( 25 sec) [ -14686.3699] [ 2408] [depth= 2] . ( 26 sec) [ -14686.2106] [ 2409] [depth= 1] . ( 27 sec) [ -14684.8007] [ 2406] [depth= 3] . ( 27 sec) [ -14683.9960] [ 2402] [depth= 1] . ( 27 sec) [ -14683.9572] [ 2402] [depth= 1] . ( 27 sec) [ -14681.2457] [ 2404] [depth= 1] . ( 28 sec) [ -14679.2498] [ 2402] [depth= 1] . ( 29 sec) [ -14679.1931] [ 2402] [depth= 1] . ( 31 sec) [ -14661.6409] [Branch lengths ] . ( 34 sec) [ -14660.8032] [GTR parameters ] . ( 34 sec) [ -14660.5830] [Alpha ][ 0.244335] . ( 40 sec) [ -14660.4057] [ 2401] [depth= 1] . ( 45 sec) [ -14657.8787] [Branch lengths ] . ( 46 sec) [ -14657.8740] [GTR parameters ] . ( 46 sec) [ -14657.8740] [Alpha ][ 0.244335] . ( 58 sec) [ -14657.7771] [Branch lengths ] . ( 109 sec) [ -14657.7704] [Branch lengths ] . ( 109 sec) [ -14657.7704] [Topology ] . ( 110 sec) [ -14657.7696] [Topology ] . ( 111 sec) [ -14657.7695] [GTR parameters ] . ( 111 sec) [ -14657.7692] [Alpha ][ 0.244579] . ( 111 sec) [ -14657.7692] [Topology ] . ( 112 sec) [ -14657.7688] [Topology ] . ( 113 sec) [ -14657.7687] [GTR parameters ] . ( 113 sec) [ -14657.7687] [Alpha ][ 0.244579] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14657.768747. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -30392.4001] [GTR parameters ] . ( 2 sec) [ -29637.4448] [Alpha ][ 0.500960] . ( 2 sec) [ -29379.0200] [ 4480] [depth= 9] . ( 2 sec) [ -29058.8830] [ 4430] [depth= 9] . ( 2 sec) [ -28953.5314] [ 4416] [depth= 1] . ( 3 sec) [ -28686.6158] [ 4387] [depth= 2] . ( 3 sec) [ -28486.6050] [ 4326] [depth= 1] . ( 3 sec) [ -28348.4889] [ 4276] [depth= 11] . ( 3 sec) [ -28220.5356] [ 4260] [depth= 2] . ( 3 sec) [ -28127.7206] [ 4245] [depth= 5] . ( 3 sec) [ -28001.9935] [ 4227] [depth= 2] . ( 3 sec) [ -27869.9415] [ 4202] [depth= 5] . ( 3 sec) [ -27840.7792] [ 4208] [depth= 1] . ( 3 sec) [ -27777.6611] [ 4200] [depth= 7] . ( 3 sec) [ -27563.7898] [ 4189] [depth= 10] . ( 4 sec) [ -27553.9252] [ 4189] [depth= 1] . ( 4 sec) [ -27085.6575] [ 4151] [depth= 6] . ( 4 sec) [ -26810.5107] [ 4151] [depth= 1] . ( 4 sec) [ -26799.6926] [ 4154] [depth= 1] . ( 4 sec) [ -26797.5118] [ 4138] [depth= 18] . ( 4 sec) [ -26788.8605] [ 4130] [depth= 1] . ( 4 sec) [ -26642.9603] [ 4120] [depth= 9] . ( 4 sec) [ -26585.0008] [ 4116] [depth= 8] . ( 4 sec) [ -26573.7499] [ 4113] [depth= 9] . ( 4 sec) [ -26215.0896] [ 4027] [depth= 19] . ( 5 sec) [ -26139.2399] [ 4004] [depth= 1] . ( 5 sec) [ -26095.3680] [ 3985] [depth= 1] . ( 5 sec) [ -25958.1595] [ 3963] [depth= 14] . ( 5 sec) [ -25940.8829] [ 3967] [depth= 10] . ( 5 sec) [ -25831.7362] [ 3941] [depth= 8] . ( 5 sec) [ -25558.8124] [ 3939] [depth= 2] . ( 5 sec) [ -25487.5237] [ 3933] [depth= 9] . ( 5 sec) [ -24992.2393] [ 3880] [depth= 8] . ( 6 sec) [ -24821.0162] [ 3831] [depth= 3] . ( 6 sec) [ -24707.3478] [ 3808] [depth= 4] . ( 6 sec) [ -24688.6319] [ 3804] [depth= 1] . ( 6 sec) [ -24392.8312] [ 3783] [depth= 4] . ( 6 sec) [ -24305.8953] [ 3779] [depth= 9] . ( 6 sec) [ -24277.4650] [ 3762] [depth= 1] . ( 6 sec) [ -24158.3115] [ 3719] [depth= 4] . ( 6 sec) [ -24050.2438] [ 3698] [depth= 6] . ( 6 sec) [ -23492.1560] [ 3677] [depth= 13] . ( 7 sec) [ -23407.0404] [ 3653] [depth= 7] . ( 7 sec) [ -23376.6634] [ 3644] [depth= 2] . ( 7 sec) [ -23297.3949] [ 3613] [depth= 1] . ( 7 sec) [ -23106.6907] [ 3569] [depth= 10] . ( 7 sec) [ -23099.1305] [ 3570] [depth= 2] . ( 7 sec) [ -23094.2343] [ 3568] [depth= 2] . ( 7 sec) [ -23089.0818] [ 3569] [depth= 1] . ( 7 sec) [ -22447.0133] [ 3542] [depth= 15] . ( 7 sec) [ -21808.6350] [ 3536] [depth= 1] . ( 7 sec) [ -20750.0536] [ 3529] [depth= 3] . ( 8 sec) [ -19999.0136] [ 3512] [depth= 4] . ( 8 sec) [ -19758.2163] [ 3493] [depth= 16] . ( 8 sec) [ -19595.5021] [ 3457] [depth= 2] . ( 8 sec) [ -19255.6768] [ 3437] [depth= 15] . ( 8 sec) [ -18902.0216] [ 3348] [depth= 10] . ( 8 sec) [ -18684.9871] [ 3297] [depth= 4] . ( 8 sec) [ -18512.7220] [ 3249] [depth= 1] . ( 8 sec) [ -18338.3879] [ 3190] [depth= 15] . ( 8 sec) [ -18137.6295] [ 3177] [depth= 12] . ( 9 sec) [ -18122.9048] [ 3167] [depth= 1] . ( 9 sec) [ -17897.2364] [ 3079] [depth= 11] . ( 9 sec) [ -17891.7222] [ 3080] [depth= 1] . ( 9 sec) [ -17816.7563] [ 3077] [depth= 1] . ( 9 sec) [ -17668.9344] [ 3068] [depth= 1] . ( 9 sec) [ -17644.6122] [ 3067] [depth= 1] . ( 9 sec) [ -17636.3870] [ 3048] [depth= 4] . ( 9 sec) [ -17488.6701] [ 2996] [depth= 1] . ( 9 sec) [ -17476.9139] [ 2986] [depth= 1] . ( 10 sec) [ -17318.5098] [ 2938] [depth= 6] . ( 10 sec) [ -17301.8301] [ 2941] [depth= 2] . ( 10 sec) [ -17250.3094] [ 2945] [depth= 2] . ( 10 sec) [ -17244.5709] [ 2954] [depth= 1] . ( 10 sec) [ -17232.6640] [ 2929] [depth= 3] . ( 10 sec) [ -17232.5752] [ 2927] [depth= 13] . ( 10 sec) [ -17060.1403] [ 2906] [depth= 3] . ( 10 sec) [ -17030.6164] [ 2900] [depth= 2] . ( 11 sec) [ -17028.5401] [ 2902] [depth= 1] . ( 11 sec) [ -16840.0538] [ 2864] [depth= 2] . ( 11 sec) [ -16823.9718] [ 2865] [depth= 2] . ( 11 sec) [ -16597.6340] [ 2813] [depth= 3] . ( 11 sec) [ -16572.1410] [ 2811] [depth= 1] . ( 11 sec) [ -16570.3581] [ 2805] [depth= 1] . ( 11 sec) [ -16464.6630] [ 2778] [depth= 6] . ( 11 sec) [ -16462.3508] [ 2777] [depth= 1] . ( 11 sec) [ -16438.9201] [ 2767] [depth= 2] . ( 11 sec) [ -16420.1521] [ 2760] [depth= 5] . ( 11 sec) [ -16359.0845] [ 2740] [depth= 1] . ( 12 sec) [ -16337.6462] [ 2742] [depth= 3] . ( 12 sec) [ -16327.8847] [ 2742] [depth= 1] . ( 12 sec) [ -16313.6536] [ 2742] [depth= 2] . ( 12 sec) [ -16133.9466] [ 2705] [depth= 5] . ( 12 sec) [ -16070.7435] [ 2686] [depth= 6] . ( 12 sec) [ -16053.0078] [ 2689] [depth= 1] . ( 13 sec) [ -16039.3765] [ 2680] [depth= 7] . ( 13 sec) [ -15969.9227] [ 2662] [depth= 2] . ( 13 sec) [ -15887.3339] [ 2642] [depth= 4] . ( 13 sec) [ -15879.8587] [ 2642] [depth= 1] . ( 13 sec) [ -15874.9444] [ 2642] [depth= 1] . ( 13 sec) [ -15853.0741] [ 2642] [depth= 1] . ( 13 sec) [ -15831.6132] [ 2643] [depth= 1] . ( 13 sec) [ -15831.3898] [ 2643] [depth= 1] . ( 13 sec) [ -15831.3213] [ 2643] [depth= 1] . ( 14 sec) [ -15831.2448] [ 2641] [depth= 1] . ( 14 sec) [ -15799.5224] [ 2635] [depth= 1] . ( 14 sec) [ -15799.3423] [ 2635] [depth= 1] . ( 14 sec) [ -15799.1797] [ 2635] [depth= 1] . ( 14 sec) [ -15796.8478] [ 2638] [depth= 1] . ( 14 sec) [ -15706.2471] [ 2609] [depth= 1] . ( 15 sec) [ -15705.9165] [ 2608] [depth= 1] . ( 15 sec) [ -15663.7178] [ 2600] [depth= 2] . ( 15 sec) [ -15656.2169] [ 2600] [depth= 1] . ( 15 sec) [ -15656.0950] [ 2600] [depth= 1] . ( 15 sec) [ -15636.0659] [ 2600] [depth= 10] . ( 15 sec) [ -15625.9087] [ 2599] [depth= 2] . ( 16 sec) [ -15509.3023] [Branch lengths ] . ( 19 sec) [ -15494.0518] [GTR parameters ] . ( 19 sec) [ -15330.7439] [Alpha ][ 0.250961] . ( 19 sec) [ -15312.5514] [ 2582] [depth= 1] . ( 20 sec) [ -15308.5171] [ 2580] [depth= 1] . ( 20 sec) [ -15301.1174] [ 2572] [depth= 3] . ( 20 sec) [ -15293.7883] [ 2571] [depth= 5] . ( 20 sec) [ -15292.3596] [ 2569] [depth= 1] . ( 21 sec) [ -15268.4895] [ 2548] [depth= 7] . ( 21 sec) [ -15267.7888] [ 2553] [depth= 3] . ( 21 sec) [ -15266.2186] [ 2555] [depth= 2] . ( 21 sec) [ -15242.3785] [ 2542] [depth= 1] . ( 21 sec) [ -15239.1347] [ 2533] [depth= 1] . ( 22 sec) [ -15204.9451] [ 2520] [depth= 1] . ( 22 sec) [ -15195.0124] [ 2506] [depth= 5] . ( 23 sec) [ -15133.4675] [ 2473] [depth= 1] . ( 23 sec) [ -15117.7911] [ 2467] [depth= 2] . ( 24 sec) [ -15115.5174] [ 2467] [depth= 1] . ( 24 sec) [ -15101.9828] [ 2454] [depth= 2] . ( 24 sec) [ -14895.1188] [ 2444] [depth= 1] . ( 24 sec) [ -14893.0621] [ 2447] [depth= 2] . ( 24 sec) [ -14864.7321] [ 2433] [depth= 5] . ( 25 sec) [ -14831.7084] [ 2425] [depth= 1] . ( 25 sec) [ -14825.8046] [ 2424] [depth= 1] . ( 25 sec) [ -14794.6853] [ 2419] [depth= 1] . ( 26 sec) [ -14788.9356] [ 2424] [depth= 1] . ( 26 sec) [ -14734.6548] [ 2412] [depth= 1] . ( 26 sec) [ -14732.4540] [ 2413] [depth= 1] . ( 26 sec) [ -14731.7385] [ 2414] [depth= 1] . ( 26 sec) [ -14731.3691] [ 2413] [depth= 1] . ( 26 sec) [ -14731.1906] [ 2413] [depth= 1] . ( 27 sec) [ -14731.1400] [ 2412] [depth= 1] . ( 27 sec) [ -14730.5644] [ 2415] [depth= 1] . ( 28 sec) [ -14719.8129] [ 2410] [depth= 2] . ( 29 sec) [ -14714.8669] [ 2411] [depth= 1] . ( 30 sec) [ -14714.5778] [ 2410] [depth= 1] . ( 31 sec) [ -14708.6823] [ 2403] [depth= 1] . ( 32 sec) [ -14668.7932] [Branch lengths ] . ( 34 sec) [ -14667.9063] [GTR parameters ] . ( 35 sec) [ -14667.6623] [Alpha ][ 0.244042] . ( 36 sec) [ -14666.5060] [ 2404] [depth= 1] . ( 47 sec) [ -14663.9982] [Branch lengths ] . ( 47 sec) [ -14663.9947] [GTR parameters ] . ( 47 sec) [ -14663.9940] [Alpha ][ 0.244366] . ( 48 sec) [ -14663.9745] [ 2405] [depth= 1] . ( 59 sec) [ -14662.9331] [Branch lengths ] . ( 60 sec) [ -14662.9326] [GTR parameters ] . ( 60 sec) [ -14662.9326] [Alpha ][ 0.244611] . ( 73 sec) [ -14659.8711] [Branch lengths ] . ( 103 sec) [ -14659.8252] [ 2403] [depth= 1] . ( 124 sec) [ -14659.4762] [Branch lengths ] . ( 124 sec) [ -14659.4760] [GTR parameters ] . ( 124 sec) [ -14659.4760] [Alpha ][ 0.244611] . ( 124 sec) [ -14659.4760] [Topology ] . ( 126 sec) [ -14659.4748] [Topology ] . ( 128 sec) [ -14659.4746] [Topology ] . ( 128 sec) [ -14659.4746] [GTR parameters ] . ( 128 sec) [ -14659.4746] [Alpha ][ 0.244611] . ( 128 sec) [ -14659.4746] [Topology ] . ( 130 sec) [ -14659.4745] [Topology ] . ( 130 sec) [ -14659.4745] [GTR parameters ] . ( 130 sec) [ -14659.4745] [Alpha ][ 0.244611] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14659.474533. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29826.0168] [GTR parameters ] . ( 2 sec) [ -29078.0927] [Alpha ][ 0.500960] . ( 2 sec) [ -28584.1946] [ 4493] [depth= 8] . ( 2 sec) [ -28114.1602] [ 4422] [depth= 6] . ( 2 sec) [ -28044.6597] [ 4412] [depth= 1] . ( 2 sec) [ -27913.2728] [ 4394] [depth= 4] . ( 2 sec) [ -27844.8063] [ 4376] [depth= 1] . ( 2 sec) [ -27514.0210] [ 4356] [depth= 9] . ( 2 sec) [ -27193.1975] [ 4339] [depth= 3] . ( 2 sec) [ -27094.1711] [ 4338] [depth= 1] . ( 2 sec) [ -27045.4315] [ 4330] [depth= 7] . ( 3 sec) [ -26987.7398] [ 4324] [depth= 7] . ( 3 sec) [ -26847.9723] [ 4321] [depth= 2] . ( 3 sec) [ -26800.9666] [ 4318] [depth= 3] . ( 3 sec) [ -26553.6551] [ 4263] [depth= 14] . ( 3 sec) [ -26527.6779] [ 4262] [depth= 4] . ( 3 sec) [ -26496.6248] [ 4248] [depth= 2] . ( 3 sec) [ -26378.6010] [ 4242] [depth= 12] . ( 3 sec) [ -26277.3549] [ 4241] [depth= 4] . ( 3 sec) [ -26109.7032] [ 4213] [depth= 2] . ( 3 sec) [ -25736.9323] [ 4155] [depth= 12] . ( 3 sec) [ -25617.1298] [ 4128] [depth= 1] . ( 4 sec) [ -25611.0674] [ 4129] [depth= 2] . ( 4 sec) [ -25558.0422] [ 4116] [depth= 1] . ( 4 sec) [ -25348.4779] [ 4112] [depth= 11] . ( 4 sec) [ -24943.4379] [ 4024] [depth= 15] . ( 4 sec) [ -24865.1772] [ 4005] [depth= 16] . ( 4 sec) [ -24851.4334] [ 4003] [depth= 1] . ( 4 sec) [ -24634.9958] [ 3994] [depth= 1] . ( 4 sec) [ -24503.0164] [ 3990] [depth= 12] . ( 4 sec) [ -24409.3903] [ 3958] [depth= 10] . ( 5 sec) [ -24258.8023] [ 3946] [depth= 4] . ( 5 sec) [ -24229.8632] [ 3949] [depth= 1] . ( 5 sec) [ -23986.5700] [ 3917] [depth= 10] . ( 5 sec) [ -23965.5509] [ 3920] [depth= 1] . ( 5 sec) [ -23958.3467] [ 3919] [depth= 1] . ( 5 sec) [ -23832.4266] [ 3963] [depth= 1] . ( 5 sec) [ -23717.7425] [ 3915] [depth= 3] . ( 5 sec) [ -23713.5839] [ 3915] [depth= 1] . ( 5 sec) [ -23565.7431] [ 3919] [depth= 12] . ( 5 sec) [ -23541.4751] [ 3913] [depth= 1] . ( 6 sec) [ -23329.1517] [ 3807] [depth= 12] . ( 6 sec) [ -23063.7947] [ 3717] [depth= 13] . ( 6 sec) [ -23040.6911] [ 3701] [depth= 1] . ( 6 sec) [ -23024.4808] [ 3709] [depth= 1] . ( 6 sec) [ -22892.5818] [ 3677] [depth= 8] . ( 6 sec) [ -21774.7033] [ 3592] [depth= 6] . ( 6 sec) [ -21721.3533] [ 3592] [depth= 3] . ( 6 sec) [ -21697.3865] [ 3595] [depth= 1] . ( 6 sec) [ -20687.2183] [ 3597] [depth= 10] . ( 6 sec) [ -20651.9792] [ 3597] [depth= 3] . ( 7 sec) [ -20281.2949] [ 3559] [depth= 7] . ( 7 sec) [ -20251.5387] [ 3537] [depth= 1] . ( 7 sec) [ -20084.5250] [ 3524] [depth= 3] . ( 7 sec) [ -20075.0741] [ 3524] [depth= 1] . ( 7 sec) [ -19931.8279] [ 3486] [depth= 1] . ( 7 sec) [ -19888.2332] [ 3485] [depth= 1] . ( 7 sec) [ -19886.1379] [ 3485] [depth= 1] . ( 7 sec) [ -19454.9004] [ 3366] [depth= 13] . ( 8 sec) [ -18814.3506] [ 3323] [depth= 1] . ( 8 sec) [ -18453.7161] [ 3222] [depth= 11] . ( 8 sec) [ -18448.1065] [ 3222] [depth= 1] . ( 8 sec) [ -18446.0862] [ 3222] [depth= 1] . ( 8 sec) [ -18336.2765] [ 3191] [depth= 2] . ( 8 sec) [ -18314.8076] [ 3182] [depth= 1] . ( 8 sec) [ -18298.6795] [ 3179] [depth= 16] . ( 8 sec) [ -18260.0406] [ 3165] [depth= 1] . ( 8 sec) [ -18201.5562] [ 3140] [depth= 1] . ( 8 sec) [ -17936.4566] [ 3101] [depth= 8] . ( 9 sec) [ -17790.5093] [ 3062] [depth= 9] . ( 9 sec) [ -17787.3750] [ 3059] [depth= 3] . ( 9 sec) [ -17731.7619] [ 3033] [depth= 1] . ( 9 sec) [ -17677.2304] [ 3021] [depth= 9] . ( 9 sec) [ -17675.2142] [ 3020] [depth= 2] . ( 9 sec) [ -17585.2441] [ 2971] [depth= 4] . ( 9 sec) [ -17374.0780] [ 2903] [depth= 8] . ( 9 sec) [ -17361.0399] [ 2907] [depth= 2] . ( 9 sec) [ -17266.4328] [ 2894] [depth= 7] . ( 9 sec) [ -17246.1144] [ 2882] [depth= 1] . ( 10 sec) [ -17200.2580] [ 2877] [depth= 2] . ( 10 sec) [ -17159.5827] [ 2852] [depth= 2] . ( 10 sec) [ -17122.2935] [ 2844] [depth= 1] . ( 10 sec) [ -17121.6400] [ 2844] [depth= 1] . ( 10 sec) [ -17020.3129] [ 2803] [depth= 3] . ( 10 sec) [ -16462.5756] [ 2806] [depth= 1] . ( 10 sec) [ -16458.9193] [ 2801] [depth= 2] . ( 10 sec) [ -16443.4954] [ 2797] [depth= 2] . ( 10 sec) [ -16412.3610] [ 2796] [depth= 1] . ( 11 sec) [ -16296.3570] [ 2784] [depth= 4] . ( 11 sec) [ -16294.4170] [ 2780] [depth= 3] . ( 11 sec) [ -16155.4307] [ 2741] [depth= 3] . ( 11 sec) [ -16145.0549] [ 2738] [depth= 1] . ( 11 sec) [ -16136.2959] [ 2728] [depth= 1] . ( 11 sec) [ -16125.1222] [ 2714] [depth= 5] . ( 11 sec) [ -16068.4823] [ 2695] [depth= 1] . ( 11 sec) [ -16060.2068] [ 2671] [depth= 4] . ( 12 sec) [ -16052.4747] [ 2675] [depth= 4] . ( 12 sec) [ -16042.7273] [ 2675] [depth= 1] . ( 12 sec) [ -16035.6327] [ 2664] [depth= 7] . ( 12 sec) [ -16034.8461] [ 2660] [depth= 4] . ( 12 sec) [ -15975.5147] [ 2650] [depth= 2] . ( 12 sec) [ -15959.4785] [ 2641] [depth= 1] . ( 12 sec) [ -15801.3659] [ 2591] [depth= 5] . ( 12 sec) [ -15731.7893] [ 2575] [depth= 3] . ( 12 sec) [ -15731.2071] [ 2575] [depth= 1] . ( 13 sec) [ -15678.7480] [ 2553] [depth= 1] . ( 13 sec) [ -15557.1997] [ 2523] [depth= 4] . ( 13 sec) [ -15532.4058] [ 2514] [depth= 2] . ( 13 sec) [ -15416.3817] [ 2479] [depth= 3] . ( 13 sec) [ -15368.0244] [ 2476] [depth= 1] . ( 13 sec) [ -15367.8656] [ 2478] [depth= 1] . ( 13 sec) [ -15360.5848] [ 2498] [depth= 1] . ( 13 sec) [ -15343.4629] [ 2488] [depth= 2] . ( 14 sec) [ -15178.3395] [Branch lengths ] . ( 17 sec) [ -15148.0432] [GTR parameters ] . ( 17 sec) [ -15010.3781] [Alpha ][ 0.250961] . ( 18 sec) [ -15007.9724] [ 2488] [depth= 1] . ( 18 sec) [ -14998.8985] [ 2492] [depth= 1] . ( 18 sec) [ -14998.7606] [ 2492] [depth= 1] . ( 18 sec) [ -14973.7120] [ 2481] [depth= 2] . ( 19 sec) [ -14971.7278] [ 2482] [depth= 1] . ( 19 sec) [ -14883.7884] [ 2462] [depth= 1] . ( 19 sec) [ -14880.6944] [ 2461] [depth= 1] . ( 20 sec) [ -14873.4938] [ 2459] [depth= 1] . ( 20 sec) [ -14870.9212] [ 2459] [depth= 2] . ( 20 sec) [ -14861.9685] [ 2454] [depth= 3] . ( 21 sec) [ -14829.8738] [ 2443] [depth= 3] . ( 21 sec) [ -14829.6212] [ 2443] [depth= 1] . ( 22 sec) [ -14820.5443] [ 2440] [depth= 1] . ( 22 sec) [ -14815.2029] [ 2440] [depth= 4] . ( 22 sec) [ -14767.3629] [ 2418] [depth= 1] . ( 23 sec) [ -14755.8551] [ 2417] [depth= 1] . ( 23 sec) [ -14746.6149] [ 2418] [depth= 1] . ( 23 sec) [ -14743.6476] [ 2418] [depth= 1] . ( 23 sec) [ -14740.4045] [ 2419] [depth= 1] . ( 24 sec) [ -14737.5321] [ 2420] [depth= 1] . ( 24 sec) [ -14731.6542] [ 2411] [depth= 2] . ( 25 sec) [ -14730.4092] [ 2413] [depth= 1] . ( 25 sec) [ -14729.7849] [ 2413] [depth= 2] . ( 25 sec) [ -14716.9255] [ 2414] [depth= 1] . ( 26 sec) [ -14716.8306] [ 2416] [depth= 1] . ( 27 sec) [ -14704.6523] [ 2409] [depth= 1] . ( 27 sec) [ -14701.0935] [ 2409] [depth= 1] . ( 27 sec) [ -14700.0439] [ 2408] [depth= 1] . ( 28 sec) [ -14693.8512] [ 2400] [depth= 1] . ( 28 sec) [ -14664.5513] [Branch lengths ] . ( 31 sec) [ -14663.7351] [GTR parameters ] . ( 31 sec) [ -14663.4993] [Alpha ][ 0.244091] . ( 41 sec) [ -14661.4237] [ 2403] [depth= 1] . ( 43 sec) [ -14659.8005] [Branch lengths ] . ( 44 sec) [ -14659.7948] [GTR parameters ] . ( 44 sec) [ -14659.7946] [Alpha ][ 0.244335] . ( 55 sec) [ -14659.6564] [Branch lengths ] . ( 105 sec) [ -14659.6415] [Branch lengths ] . ( 105 sec) [ -14659.6415] [Topology ] . ( 107 sec) [ -14659.6400] [Topology ] . ( 108 sec) [ -14659.6394] [Topology ] . ( 110 sec) [ -14659.6341] [GTR parameters ] . ( 110 sec) [ -14659.6338] [Alpha ][ 0.244579] . ( 110 sec) [ -14659.6338] [Topology ] . ( 112 sec) [ -14659.6331] [Topology ] . ( 112 sec) [ -14659.6331] [GTR parameters ] . ( 112 sec) [ -14659.6331] [Alpha ][ 0.244579] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14659.633128. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -15365.1345] [GTR parameters ] . ( 3 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 3 sec) [ -15101.1310] [Topology ] . ( 5 sec) [ -14867.9767] [Topology ] . ( 7 sec) [ -14827.6590] [Topology ] . ( 8 sec) [ -14813.5467] [Topology ] . ( 10 sec) [ -14806.6086] [Topology ] . ( 11 sec) [ -14803.6705] [Topology ] . ( 13 sec) [ -14802.4499] [Topology ] . ( 15 sec) [ -14801.9650] [Topology ] . ( 16 sec) [ -14801.0546] [Topology ] . ( 18 sec) [ -14798.5980] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -14797.1571] [Topology ] . ( 35 sec) [ -14794.9999] [GTR parameters ] . ( 35 sec) [ -14662.2856] [Alpha ][ 0.250961] . ( 35 sec) [ -14662.2856] [Topology ] . ( 37 sec) [ -14660.9408] [Topology ] . ( 38 sec) [ -14660.5526] [Topology ] . ( 40 sec) [ -14660.3874] [Topology ] . ( 41 sec) [ -14660.3135] [Topology ] . ( 43 sec) [ -14660.2777] [Topology ] . ( 45 sec) [ -14660.2591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -14659.7059] [GTR parameters ] . ( 60 sec) [ -14659.4964] [Alpha ][ 0.244536] . ( 60 sec) [ -14659.4964] [Topology ] . ( 61 sec) [ -14659.4851] [Topology ] . ( 63 sec) [ -14659.4811] [Topology ] . ( 65 sec) [ -14659.4791] [Topology ] . ( 66 sec) [ -14659.4781] [Topology ] . ( 68 sec) [ -14659.4775] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -14659.4757] [GTR parameters ] . ( 82 sec) [ -14659.4757] [Alpha ][ 0.244536] . ( 82 sec) [ -14659.4757] [Topology ] . ( 83 sec) [ -14659.4753] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -14659.4752] [GTR parameters ] . ( 97 sec) [ -14659.4752] [Alpha ][ 0.244536] . ( 97 sec) [ -14659.4752] [Topology ] . ( 99 sec) [ -14659.4750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 129 sec) [ -15365.1345] [GTR parameters ] . ( 129 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 129 sec) [ -15101.1009] [ 2403] [depth= 1] . ( 130 sec) [ -15098.8715] [ 2402] [depth= 1] . ( 130 sec) [ -15093.6818] [ 2401] [depth= 1] . ( 132 sec) [ -15092.8612] [ 2406] [depth= 1] . ( 132 sec) [ -15081.3237] [ 2407] [depth= 1] . ( 132 sec) [ -15080.2997] [ 2406] [depth= 1] . ( 132 sec) [ -15077.9949] [ 2407] [depth= 1] . ( 132 sec) [ -15075.3447] [ 2409] [depth= 2] . ( 132 sec) [ -15066.2616] [ 2405] [depth= 2] . ( 133 sec) [ -15042.6033] [ 2407] [depth= 1] . ( 133 sec) [ -15042.2844] [ 2409] [depth= 1] . ( 133 sec) [ -15037.4363] [ 2414] [depth= 2] . ( 133 sec) [ -15034.8203] [ 2407] [depth= 2] . ( 133 sec) [ -15033.3611] [ 2405] [depth= 1] . ( 133 sec) [ -15028.4546] [ 2411] [depth= 1] . ( 133 sec) [ -15024.4674] [ 2405] [depth= 1] . ( 134 sec) [ -15013.3167] [ 2407] [depth= 1] . ( 134 sec) [ -15010.1207] [ 2410] [depth= 1] . ( 134 sec) [ -14999.2240] [ 2408] [depth= 1] . ( 135 sec) [ -14998.0467] [ 2407] [depth= 1] . ( 135 sec) [ -14993.0069] [ 2408] [depth= 1] . ( 136 sec) [ -14990.9335] [ 2404] [depth= 2] . ( 136 sec) [ -14984.5772] [ 2399] [depth= 1] . ( 136 sec) [ -14983.2566] [ 2404] [depth= 1] . ( 136 sec) [ -14957.0542] [ 2403] [depth= 1] . ( 136 sec) [ -14948.7024] [ 2400] [depth= 1] . ( 136 sec) [ -14944.2341] [ 2404] [depth= 2] . ( 137 sec) [ -14942.0251] [ 2404] [depth= 1] . ( 137 sec) [ -14935.9613] [ 2405] [depth= 1] . ( 137 sec) [ -14932.2116] [ 2408] [depth= 1] . ( 137 sec) [ -14930.9248] [ 2405] [depth= 1] . ( 137 sec) [ -14924.1668] [ 2404] [depth= 1] . ( 137 sec) [ -14923.1236] [ 2407] [depth= 1] . ( 138 sec) [ -14921.4219] [ 2410] [depth= 1] . ( 138 sec) [ -14920.9806] [ 2407] [depth= 1] . ( 139 sec) [ -14919.6076] [ 2410] [depth= 3] . ( 139 sec) [ -14918.9091] [ 2410] [depth= 1] . ( 139 sec) [ -14918.8393] [ 2410] [depth= 1] . ( 139 sec) [ -14918.7493] [ 2410] [depth= 1] . ( 140 sec) [ -14916.7639] [ 2410] [depth= 1] . ( 140 sec) [ -14913.6688] [ 2409] [depth= 2] . ( 141 sec) [ -14818.6887] [Branch lengths ] . ( 143 sec) [ -14816.9403] [GTR parameters ] . ( 143 sec) [ -14684.1683] [Alpha ][ 0.250961] . ( 145 sec) [ -14680.5537] [ 2404] [depth= 1] . ( 148 sec) [ -14680.3275] [ 2408] [depth= 1] . ( 150 sec) [ -14680.2820] [ 2404] [depth= 1] . ( 151 sec) [ -14677.0815] [ 2406] [depth= 1] . ( 151 sec) [ -14675.9054] [ 2410] [depth= 1] . ( 154 sec) [ -14674.7975] [ 2406] [depth= 3] . ( 154 sec) [ -14674.6222] [ 2406] [depth= 1] . ( 156 sec) [ -14664.5296] [Branch lengths ] . ( 158 sec) [ -14664.1216] [GTR parameters ] . ( 158 sec) [ -14663.7831] [Alpha ][ 0.242689] . ( 168 sec) [ -14663.7647] [ 2406] [depth= 1] . ( 170 sec) [ -14662.5765] [Branch lengths ] . ( 172 sec) [ -14662.5623] [GTR parameters ] . ( 172 sec) [ -14662.5565] [Alpha ][ 0.243734] . ( 183 sec) [ -14662.3659] [Branch lengths ] . ( 233 sec) [ -14662.3234] [Branch lengths ] . ( 233 sec) [ -14662.3234] [Topology ] . ( 235 sec) [ -14662.0968] [Topology ] . ( 236 sec) [ -14661.6754] [Topology ] . ( 238 sec) [ -14660.2749] [Topology ] . ( 239 sec) [ -14658.2223] [Topology ] . ( 241 sec) [ -14657.8743] [Topology ] . ( 243 sec) [ -14657.7992] [Topology ] . ( 244 sec) [ -14657.7815] [Topology ] . ( 246 sec) [ -14657.7771] [Topology ] . ( 247 sec) [ -14657.7732] [GTR parameters ] . ( 247 sec) [ -14657.7689] [Alpha ][ 0.244620] . ( 247 sec) [ -14657.7689] [Topology ] . ( 249 sec) [ -14657.7678] [Topology ] . ( 250 sec) [ -14657.7675] [Topology ] . ( 251 sec) [ -14657.7667] [GTR parameters ] . ( 251 sec) [ -14657.7667] [Alpha ][ 0.244620] . ( 251 sec) [ -14657.7667] [Topology ] . ( 253 sec) [ -14657.7666] [Topology ] . ( 253 sec) [ -14657.7665] [GTR parameters ] . ( 253 sec) [ -14657.7665] [Alpha ][ 0.244620] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -14659.474973 . Log likelihood obtained after SPR moves : -14657.766539 . Log likelihood of the current tree: -14657.766539. . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Best log likelihood : -14657.766539 . Time used 0h4m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 933.01user 0.00system 15:43.86elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps