.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data71.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 . Compressing sequences... . 455 patterns found. (out of a total of 500 sites) . 44 sites without polymorphism (8.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22782.8963] [GTR parameters ] . ( 1 sec) [ -22331.4465] [Alpha ][ 0.500960] . ( 1 sec) [ -22148.6558] [ 5817] [depth= 6] . ( 1 sec) [ -21784.7601] [ 5764] [depth= 11] . ( 1 sec) [ -21370.1431] [ 5753] [depth= 1] . ( 1 sec) [ -20963.2472] [ 5745] [depth= 7] . ( 1 sec) [ -20666.2321] [ 5613] [depth= 5] . ( 1 sec) [ -20421.4202] [ 5600] [depth= 2] . ( 1 sec) [ -20283.8655] [ 5573] [depth= 5] . ( 1 sec) [ -20234.2771] [ 5544] [depth= 1] . ( 1 sec) [ -20203.1194] [ 5500] [depth= 14] . ( 1 sec) [ -20009.1298] [ 5351] [depth= 15] . ( 1 sec) [ -19870.2042] [ 5322] [depth= 5] . ( 1 sec) [ -19809.2587] [ 5317] [depth= 8] . ( 1 sec) [ -19706.0943] [ 5295] [depth= 3] . ( 1 sec) [ -19436.6172] [ 5283] [depth= 9] . ( 1 sec) [ -18924.2087] [ 5070] [depth= 5] . ( 1 sec) [ -18858.8277] [ 5067] [depth= 2] . ( 1 sec) [ -18563.4972] [ 4997] [depth= 3] . ( 2 sec) [ -18268.7941] [ 4917] [depth= 1] . ( 2 sec) [ -18001.5604] [ 4879] [depth= 6] . ( 2 sec) [ -17921.4361] [ 4867] [depth= 17] . ( 2 sec) [ -17853.7184] [ 4843] [depth= 1] . ( 2 sec) [ -17810.5428] [ 4827] [depth= 1] . ( 2 sec) [ -17567.1083] [ 4786] [depth= 3] . ( 2 sec) [ -16992.5160] [ 4597] [depth= 20] . ( 2 sec) [ -16603.7399] [ 4523] [depth= 10] . ( 2 sec) [ -16468.3330] [ 4531] [depth= 20] . ( 2 sec) [ -16270.0736] [ 4478] [depth= 15] . ( 2 sec) [ -15991.3004] [ 4282] [depth= 13] . ( 2 sec) [ -15328.5984] [ 4152] [depth= 9] . ( 2 sec) [ -15229.9902] [ 4138] [depth= 2] . ( 2 sec) [ -15227.2184] [ 4159] [depth= 1] . ( 2 sec) [ -15209.2638] [ 4162] [depth= 1] . ( 2 sec) [ -14820.2647] [ 4051] [depth= 2] . ( 2 sec) [ -14680.8962] [ 3975] [depth= 1] . ( 2 sec) [ -14415.5467] [ 3892] [depth= 14] . ( 2 sec) [ -14269.0042] [ 3838] [depth= 8] . ( 2 sec) [ -14062.8836] [ 3755] [depth= 10] . ( 3 sec) [ -13947.8125] [ 3597] [depth= 6] . ( 3 sec) [ -13212.4027] [ 3381] [depth= 8] . ( 3 sec) [ -13202.7641] [ 3382] [depth= 1] . ( 3 sec) [ -13187.4684] [ 3389] [depth= 1] . ( 3 sec) [ -13179.0547] [ 3388] [depth= 1] . ( 3 sec) [ -13175.0503] [ 3399] [depth= 2] . ( 3 sec) [ -13062.1004] [ 3289] [depth= 9] . ( 3 sec) [ -13042.2531] [ 3315] [depth= 1] . ( 3 sec) [ -12942.1918] [ 3331] [depth= 1] . ( 3 sec) [ -12941.6328] [ 3329] [depth= 1] . ( 3 sec) [ -12750.7021] [ 3211] [depth= 2] . ( 3 sec) [ -12683.0468] [ 3207] [depth= 1] . ( 3 sec) [ -12580.9032] [ 3174] [depth= 9] . ( 3 sec) [ -12575.8363] [ 3170] [depth= 1] . ( 3 sec) [ -12436.9686] [ 3137] [depth= 9] . ( 3 sec) [ -12360.9235] [ 3095] [depth= 3] . ( 3 sec) [ -12346.9497] [ 3092] [depth= 1] . ( 3 sec) [ -12323.0911] [ 3068] [depth= 1] . ( 3 sec) [ -12130.3693] [ 2903] [depth= 5] . ( 4 sec) [ -12049.1538] [ 2900] [depth= 7] . ( 4 sec) [ -12026.9270] [ 2880] [depth= 5] . ( 4 sec) [ -11989.1983] [ 2879] [depth= 4] . ( 4 sec) [ -11980.1580] [ 2870] [depth= 1] . ( 4 sec) [ -11949.4558] [ 2864] [depth= 1] . ( 4 sec) [ -11941.2440] [ 2861] [depth= 1] . ( 4 sec) [ -11926.0562] [ 2867] [depth= 1] . ( 4 sec) [ -11921.9967] [ 2884] [depth= 1] . ( 4 sec) [ -11789.5583] [ 2788] [depth= 2] . ( 4 sec) [ -11737.1901] [ 2765] [depth= 2] . ( 4 sec) [ -11383.8612] [ 2652] [depth= 11] . ( 4 sec) [ -11350.0997] [ 2644] [depth= 1] . ( 4 sec) [ -11292.3061] [ 2626] [depth= 1] . ( 4 sec) [ -11268.2326] [ 2629] [depth= 1] . ( 4 sec) [ -11267.0030] [ 2630] [depth= 1] . ( 5 sec) [ -11265.0298] [ 2632] [depth= 1] . ( 5 sec) [ -11243.8070] [ 2640] [depth= 1] . ( 5 sec) [ -11242.3140] [ 2640] [depth= 1] . ( 5 sec) [ -11233.7431] [ 2646] [depth= 1] . ( 5 sec) [ -11114.0416] [Branch lengths ] . ( 6 sec) [ -11112.2108] [GTR parameters ] . ( 6 sec) [ -11065.2284] [Alpha ][ 0.972302] . ( 6 sec) [ -11064.8279] [ 2645] [depth= 1] . ( 6 sec) [ -11057.8554] [ 2637] [depth= 1] . ( 6 sec) [ -11046.5271] [ 2629] [depth= 1] . ( 6 sec) [ -11041.8540] [ 2637] [depth= 1] . ( 6 sec) [ -11041.4968] [ 2638] [depth= 2] . ( 7 sec) [ -11039.6540] [ 2638] [depth= 1] . ( 7 sec) [ -11039.5034] [ 2642] [depth= 1] . ( 7 sec) [ -11037.3260] [ 2643] [depth= 2] . ( 7 sec) [ -11021.9709] [ 2612] [depth= 2] . ( 7 sec) [ -10977.6129] [ 2548] [depth= 7] . ( 7 sec) [ -10972.1139] [ 2533] [depth= 2] . ( 7 sec) [ -10962.8491] [ 2524] [depth= 1] . ( 7 sec) [ -10959.9086] [ 2518] [depth= 1] . ( 8 sec) [ -10951.8534] [ 2524] [depth= 1] . ( 8 sec) [ -10951.6614] [ 2526] [depth= 1] . ( 9 sec) [ -10940.4225] [ 2522] [depth= 1] . ( 9 sec) [ -10940.4074] [ 2516] [depth= 1] . ( 9 sec) [ -10929.2102] [Branch lengths ] . ( 10 sec) [ -10928.9598] [GTR parameters ] . ( 10 sec) [ -10927.5172] [Alpha ][ 1.094171] . ( 12 sec) [ -10927.4515] [ 2511] [depth= 1] . ( 12 sec) [ -10927.4054] [ 2514] [depth= 1] . ( 13 sec) [ -10925.6005] [Branch lengths ] . ( 14 sec) [ -10925.5966] [GTR parameters ] . ( 14 sec) [ -10925.5822] [Alpha ][ 1.107377] . ( 14 sec) [ -10925.4909] [ 2513] [depth= 3] . ( 17 sec) [ -10924.4027] [Branch lengths ] . ( 17 sec) [ -10924.3993] [GTR parameters ] . ( 17 sec) [ -10924.3991] [Alpha ][ 1.108816] . ( 21 sec) [ -10924.3256] [Branch lengths ] . ( 43 sec) [ -10924.3123] [Branch lengths ] . ( 43 sec) [ -10924.3123] [Topology ] . ( 44 sec) [ -10924.3111] [Topology ] . ( 45 sec) [ -10924.3106] [Topology ] . ( 45 sec) [ -10924.3106] [GTR parameters ] . ( 45 sec) [ -10924.3105] [Alpha ][ 1.110084] . ( 45 sec) [ -10924.3105] [Topology ] . ( 46 sec) [ -10924.3102] [Topology ] . ( 46 sec) [ -10924.3102] [GTR parameters ] . ( 46 sec) [ -10924.3102] [Alpha ][ 1.110084] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.310169. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -24515.3481] [GTR parameters ] . ( 0 sec) [ -24016.8361] [Alpha ][ 0.500960] . ( 0 sec) [ -23895.6627] [ 5806] [depth= 9] . ( 0 sec) [ -23726.8450] [ 5772] [depth= 11] . ( 1 sec) [ -23509.6030] [ 5718] [depth= 4] . ( 1 sec) [ -23207.1301] [ 5700] [depth= 7] . ( 1 sec) [ -22810.2933] [ 5645] [depth= 6] . ( 1 sec) [ -22636.7375] [ 5648] [depth= 9] . ( 1 sec) [ -22416.7050] [ 5648] [depth= 1] . ( 1 sec) [ -22152.7510] [ 5623] [depth= 10] . ( 1 sec) [ -22039.9390] [ 5572] [depth= 2] . ( 1 sec) [ -21215.6732] [ 5520] [depth= 11] . ( 1 sec) [ -20872.5643] [ 5490] [depth= 9] . ( 1 sec) [ -20740.2621] [ 5480] [depth= 4] . ( 1 sec) [ -20512.8877] [ 5404] [depth= 4] . ( 1 sec) [ -20459.8949] [ 5357] [depth= 5] . ( 1 sec) [ -19702.7321] [ 5191] [depth= 9] . ( 1 sec) [ -19187.5284] [ 5012] [depth= 8] . ( 1 sec) [ -18679.3163] [ 4875] [depth= 9] . ( 1 sec) [ -18464.5995] [ 4872] [depth= 1] . ( 1 sec) [ -18246.7049] [ 4873] [depth= 1] . ( 1 sec) [ -18228.5342] [ 4868] [depth= 1] . ( 1 sec) [ -18164.5119] [ 4854] [depth= 2] . ( 1 sec) [ -17757.4851] [ 4718] [depth= 4] . ( 1 sec) [ -17741.4964] [ 4684] [depth= 1] . ( 1 sec) [ -17180.2027] [ 4498] [depth= 11] . ( 1 sec) [ -17090.8733] [ 4500] [depth= 1] . ( 2 sec) [ -16866.6199] [ 4392] [depth= 4] . ( 2 sec) [ -16747.3837] [ 4380] [depth= 1] . ( 2 sec) [ -16656.7652] [ 4345] [depth= 1] . ( 2 sec) [ -16385.8980] [ 4352] [depth= 1] . ( 2 sec) [ -15945.4117] [ 4122] [depth= 13] . ( 2 sec) [ -15920.1822] [ 4124] [depth= 1] . ( 2 sec) [ -15916.6673] [ 4122] [depth= 4] . ( 2 sec) [ -15916.5797] [ 4122] [depth= 1] . ( 2 sec) [ -15793.4123] [ 4020] [depth= 3] . ( 2 sec) [ -15643.7535] [ 4019] [depth= 3] . ( 2 sec) [ -15395.1434] [ 3896] [depth= 9] . ( 2 sec) [ -15355.7990] [ 3889] [depth= 1] . ( 2 sec) [ -15202.8216] [ 3869] [depth= 10] . ( 2 sec) [ -15056.2369] [ 3792] [depth= 8] . ( 2 sec) [ -14984.8511] [ 3716] [depth= 7] . ( 2 sec) [ -14666.0179] [ 3651] [depth= 5] . ( 2 sec) [ -14626.8015] [ 3647] [depth= 1] . ( 2 sec) [ -14596.3724] [ 3649] [depth= 1] . ( 2 sec) [ -14260.6603] [ 3504] [depth= 8] . ( 2 sec) [ -14069.4365] [ 3417] [depth= 7] . ( 3 sec) [ -14050.8770] [ 3421] [depth= 2] . ( 3 sec) [ -13810.7227] [ 3448] [depth= 1] . ( 3 sec) [ -13732.2688] [ 3446] [depth= 2] . ( 3 sec) [ -13718.2628] [ 3448] [depth= 1] . ( 3 sec) [ -13708.1122] [ 3446] [depth= 1] . ( 3 sec) [ -13698.6084] [ 3477] [depth= 1] . ( 3 sec) [ -13694.6533] [ 3462] [depth= 2] . ( 3 sec) [ -13414.6741] [ 3427] [depth= 6] . ( 3 sec) [ -13041.0741] [ 3429] [depth= 1] . ( 3 sec) [ -13034.0607] [ 3423] [depth= 2] . ( 3 sec) [ -12994.8328] [ 3347] [depth= 1] . ( 3 sec) [ -12986.0277] [ 3346] [depth= 1] . ( 3 sec) [ -12725.1888] [ 3230] [depth= 15] . ( 3 sec) [ -12698.9167] [ 3210] [depth= 2] . ( 3 sec) [ -12632.2793] [ 3213] [depth= 7] . ( 3 sec) [ -12394.4379] [ 3011] [depth= 7] . ( 3 sec) [ -12393.5543] [ 3012] [depth= 1] . ( 3 sec) [ -12382.5166] [ 2992] [depth= 1] . ( 3 sec) [ -12354.2582] [ 2999] [depth= 1] . ( 3 sec) [ -12342.4764] [ 2990] [depth= 1] . ( 4 sec) [ -12339.0064] [ 2983] [depth= 1] . ( 4 sec) [ -12232.4914] [ 2971] [depth= 1] . ( 4 sec) [ -12228.8957] [ 2970] [depth= 2] . ( 4 sec) [ -12190.0031] [ 2967] [depth= 3] . ( 4 sec) [ -12152.9536] [ 2964] [depth= 1] . ( 4 sec) [ -12073.0929] [ 2972] [depth= 1] . ( 4 sec) [ -11806.4119] [ 2866] [depth= 6] . ( 4 sec) [ -11796.6670] [ 2863] [depth= 1] . ( 4 sec) [ -11642.2059] [ 2846] [depth= 2] . ( 4 sec) [ -11640.8176] [ 2845] [depth= 1] . ( 4 sec) [ -11622.4205] [ 2812] [depth= 3] . ( 4 sec) [ -11574.7046] [ 2799] [depth= 3] . ( 4 sec) [ -11465.8532] [ 2706] [depth= 4] . ( 4 sec) [ -11403.1449] [ 2691] [depth= 1] . ( 5 sec) [ -11219.2355] [Branch lengths ] . ( 5 sec) [ -11216.7003] [GTR parameters ] . ( 5 sec) [ -11178.0477] [Alpha ][ 0.903200] . ( 5 sec) [ -11172.4869] [ 2693] [depth= 1] . ( 6 sec) [ -11171.2668] [ 2693] [depth= 1] . ( 6 sec) [ -11170.2999] [ 2691] [depth= 1] . ( 6 sec) [ -11170.1622] [ 2689] [depth= 1] . ( 6 sec) [ -11167.4534] [ 2694] [depth= 4] . ( 6 sec) [ -11166.8691] [ 2692] [depth= 1] . ( 6 sec) [ -11150.4739] [ 2686] [depth= 1] . ( 6 sec) [ -11138.4188] [ 2590] [depth= 1] . ( 6 sec) [ -11138.1495] [ 2594] [depth= 1] . ( 6 sec) [ -11138.1306] [ 2596] [depth= 2] . ( 7 sec) [ -11133.7717] [ 2605] [depth= 1] . ( 7 sec) [ -11133.3624] [ 2601] [depth= 2] . ( 7 sec) [ -11133.2066] [ 2606] [depth= 1] . ( 7 sec) [ -11129.6849] [ 2601] [depth= 1] . ( 7 sec) [ -11126.4820] [ 2605] [depth= 1] . ( 7 sec) [ -11005.0991] [ 2564] [depth= 3] . ( 7 sec) [ -10992.9607] [ 2567] [depth= 1] . ( 7 sec) [ -10989.6398] [ 2538] [depth= 1] . ( 8 sec) [ -10966.8376] [ 2527] [depth= 1] . ( 8 sec) [ -10966.6597] [ 2531] [depth= 1] . ( 9 sec) [ -10966.6300] [ 2534] [depth= 1] . ( 9 sec) [ -10941.9841] [Branch lengths ] . ( 10 sec) [ -10941.7877] [GTR parameters ] . ( 10 sec) [ -10938.6570] [Alpha ][ 1.074386] . ( 10 sec) [ -10938.5618] [ 2536] [depth= 1] . ( 10 sec) [ -10936.8512] [ 2536] [depth= 1] . ( 11 sec) [ -10936.8170] [ 2529] [depth= 1] . ( 11 sec) [ -10936.5704] [ 2533] [depth= 1] . ( 11 sec) [ -10936.5359] [ 2530] [depth= 1] . ( 13 sec) [ -10935.9453] [ 2529] [depth= 2] . ( 14 sec) [ -10928.3564] [Branch lengths ] . ( 14 sec) [ -10928.3524] [GTR parameters ] . ( 14 sec) [ -10928.2821] [Alpha ][ 1.102288] . ( 14 sec) [ -10928.2369] [ 2530] [depth= 1] . ( 14 sec) [ -10927.4638] [ 2535] [depth= 1] . ( 15 sec) [ -10926.7389] [ 2534] [depth= 1] . ( 15 sec) [ -10926.4692] [ 2533] [depth= 1] . ( 16 sec) [ -10926.4356] [ 2530] [depth= 1] . ( 18 sec) [ -10925.1871] [Branch lengths ] . ( 19 sec) [ -10925.1807] [GTR parameters ] . ( 19 sec) [ -10925.1787] [Alpha ][ 1.107172] . ( 23 sec) [ -10924.9672] [Branch lengths ] . ( 32 sec) [ -10924.4772] [ 2536] [depth= 1] . ( 45 sec) [ -10924.4000] [Branch lengths ] . ( 45 sec) [ -10924.3982] [GTR parameters ] . ( 45 sec) [ -10924.3974] [Alpha ][ 1.110124] . ( 45 sec) [ -10924.3974] [Topology ] . ( 46 sec) [ -10924.3883] [Topology ] . ( 47 sec) [ -10924.3838] [Topology ] . ( 47 sec) [ -10924.3809] [Topology ] . ( 48 sec) [ -10924.3790] [Topology ] . ( 49 sec) [ -10924.3776] [Topology ] . ( 50 sec) [ -10924.3767] [Topology ] . ( 50 sec) [ -10924.3767] [GTR parameters ] . ( 50 sec) [ -10924.3767] [Alpha ][ 1.111234] . ( 50 sec) [ -10924.3767] [Topology ] . ( 51 sec) [ -10924.3760] [Topology ] . ( 51 sec) [ -10924.3759] [GTR parameters ] . ( 51 sec) [ -10924.3759] [Alpha ][ 1.111234] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -10924.3399] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.339938. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23116.0068] [GTR parameters ] . ( 1 sec) [ -22647.3687] [Alpha ][ 0.500960] . ( 1 sec) [ -22467.2217] [ 6060] [depth= 4] . ( 1 sec) [ -22395.2138] [ 6027] [depth= 4] . ( 1 sec) [ -22274.1366] [ 6008] [depth= 2] . ( 1 sec) [ -22057.4567] [ 5990] [depth= 6] . ( 1 sec) [ -21936.6269] [ 5840] [depth= 6] . ( 1 sec) [ -21879.4893] [ 5838] [depth= 1] . ( 2 sec) [ -21212.0829] [ 5684] [depth= 16] . ( 2 sec) [ -20976.6902] [ 5637] [depth= 15] . ( 2 sec) [ -20346.0240] [ 5435] [depth= 17] . ( 2 sec) [ -19843.7248] [ 5247] [depth= 9] . ( 2 sec) [ -19537.3129] [ 5171] [depth= 9] . ( 2 sec) [ -19374.7758] [ 5144] [depth= 1] . ( 2 sec) [ -19254.8510] [ 5117] [depth= 1] . ( 2 sec) [ -19058.6217] [ 5046] [depth= 6] . ( 2 sec) [ -18834.4203] [ 5034] [depth= 3] . ( 2 sec) [ -18692.1820] [ 4978] [depth= 10] . ( 2 sec) [ -18547.1718] [ 4917] [depth= 1] . ( 2 sec) [ -18418.2204] [ 4906] [depth= 7] . ( 2 sec) [ -18208.2640] [ 4846] [depth= 10] . ( 2 sec) [ -17969.1507] [ 4732] [depth= 1] . ( 2 sec) [ -17671.8365] [ 4674] [depth= 9] . ( 2 sec) [ -17570.1478] [ 4666] [depth= 6] . ( 2 sec) [ -17320.2307] [ 4638] [depth= 1] . ( 2 sec) [ -16915.5941] [ 4485] [depth= 5] . ( 2 sec) [ -16691.1858] [ 4428] [depth= 7] . ( 2 sec) [ -16685.8903] [ 4428] [depth= 1] . ( 3 sec) [ -16601.2264] [ 4410] [depth= 17] . ( 3 sec) [ -16140.7464] [ 4265] [depth= 1] . ( 3 sec) [ -15881.3317] [ 4108] [depth= 8] . ( 3 sec) [ -15797.1331] [ 4119] [depth= 1] . ( 3 sec) [ -15262.0385] [ 3929] [depth= 12] . ( 3 sec) [ -15129.6877] [ 3905] [depth= 1] . ( 3 sec) [ -15066.1647] [ 3893] [depth= 2] . ( 3 sec) [ -14847.7943] [ 3794] [depth= 6] . ( 3 sec) [ -14813.4337] [ 3781] [depth= 1] . ( 3 sec) [ -14770.6887] [ 3783] [depth= 8] . ( 3 sec) [ -14634.0772] [ 3705] [depth= 8] . ( 3 sec) [ -14619.6438] [ 3679] [depth= 1] . ( 3 sec) [ -14615.6235] [ 3670] [depth= 1] . ( 3 sec) [ -14452.2728] [ 3629] [depth= 6] . ( 3 sec) [ -14442.5268] [ 3584] [depth= 1] . ( 3 sec) [ -14219.4769] [ 3572] [depth= 1] . ( 3 sec) [ -14004.6959] [ 3454] [depth= 7] . ( 3 sec) [ -13836.3647] [ 3446] [depth= 1] . ( 4 sec) [ -13756.3189] [ 3442] [depth= 2] . ( 4 sec) [ -13502.9762] [ 3341] [depth= 3] . ( 4 sec) [ -13492.8651] [ 3345] [depth= 1] . ( 4 sec) [ -13491.2954] [ 3349] [depth= 1] . ( 4 sec) [ -13462.7485] [ 3279] [depth= 9] . ( 4 sec) [ -13432.7877] [ 3273] [depth= 1] . ( 4 sec) [ -13424.3975] [ 3253] [depth= 8] . ( 4 sec) [ -13263.4691] [ 3255] [depth= 1] . ( 4 sec) [ -13242.4202] [ 3253] [depth= 1] . ( 4 sec) [ -13010.5825] [ 3112] [depth= 8] . ( 4 sec) [ -13008.2070] [ 3110] [depth= 1] . ( 4 sec) [ -12970.2985] [ 3110] [depth= 1] . ( 4 sec) [ -12760.4005] [ 2984] [depth= 7] . ( 4 sec) [ -12720.7010] [ 2971] [depth= 1] . ( 4 sec) [ -12193.5784] [ 2950] [depth= 4] . ( 4 sec) [ -12139.2650] [ 2942] [depth= 3] . ( 4 sec) [ -12040.5398] [ 2910] [depth= 1] . ( 4 sec) [ -11959.8608] [ 2841] [depth= 4] . ( 4 sec) [ -11955.8798] [ 2844] [depth= 1] . ( 4 sec) [ -11929.7413] [ 2839] [depth= 2] . ( 5 sec) [ -11902.2498] [ 2831] [depth= 1] . ( 5 sec) [ -11893.5784] [ 2826] [depth= 1] . ( 5 sec) [ -11853.8889] [ 2716] [depth= 1] . ( 5 sec) [ -11844.4799] [ 2715] [depth= 1] . ( 5 sec) [ -11792.9852] [ 2704] [depth= 2] . ( 5 sec) [ -11730.7308] [ 2692] [depth= 1] . ( 5 sec) [ -11626.7131] [ 2643] [depth= 2] . ( 5 sec) [ -11617.6872] [ 2645] [depth= 2] . ( 5 sec) [ -11480.6805] [ 2653] [depth= 1] . ( 5 sec) [ -11394.8232] [ 2631] [depth= 1] . ( 5 sec) [ -11386.0745] [ 2637] [depth= 1] . ( 5 sec) [ -11381.8174] [ 2635] [depth= 1] . ( 5 sec) [ -11380.7736] [ 2640] [depth= 1] . ( 6 sec) [ -11154.4924] [Branch lengths ] . ( 6 sec) [ -11151.7822] [GTR parameters ] . ( 6 sec) [ -11113.6965] [Alpha ][ 0.916426] . ( 6 sec) [ -11111.3069] [ 2644] [depth= 1] . ( 6 sec) [ -11110.8155] [ 2640] [depth= 1] . ( 6 sec) [ -11101.9503] [ 2589] [depth= 3] . ( 6 sec) [ -11090.7251] [ 2590] [depth= 1] . ( 6 sec) [ -11090.3249] [ 2591] [depth= 1] . ( 7 sec) [ -11082.9827] [ 2586] [depth= 2] . ( 7 sec) [ -11082.6707] [ 2587] [depth= 1] . ( 7 sec) [ -11081.2967] [ 2587] [depth= 1] . ( 7 sec) [ -11080.1235] [ 2587] [depth= 1] . ( 7 sec) [ -11054.5692] [ 2538] [depth= 3] . ( 7 sec) [ -11010.8083] [ 2519] [depth= 1] . ( 7 sec) [ -11009.5052] [ 2533] [depth= 1] . ( 7 sec) [ -11009.3167] [ 2534] [depth= 1] . ( 7 sec) [ -11009.2674] [ 2535] [depth= 1] . ( 7 sec) [ -11003.6608] [ 2536] [depth= 1] . ( 7 sec) [ -11001.4060] [ 2536] [depth= 1] . ( 7 sec) [ -10995.4771] [ 2546] [depth= 1] . ( 7 sec) [ -10985.5914] [ 2547] [depth= 3] . ( 8 sec) [ -10978.8594] [ 2533] [depth= 1] . ( 8 sec) [ -10975.0113] [ 2530] [depth= 1] . ( 8 sec) [ -10957.5250] [ 2532] [depth= 2] . ( 8 sec) [ -10957.0774] [ 2533] [depth= 1] . ( 8 sec) [ -10956.6533] [ 2527] [depth= 1] . ( 9 sec) [ -10956.4430] [ 2531] [depth= 1] . ( 9 sec) [ -10956.3707] [ 2533] [depth= 1] . ( 9 sec) [ -10956.2086] [ 2523] [depth= 1] . ( 9 sec) [ -10955.5763] [ 2524] [depth= 1] . ( 10 sec) [ -10934.1478] [Branch lengths ] . ( 10 sec) [ -10933.9779] [GTR parameters ] . ( 10 sec) [ -10931.0022] [Alpha ][ 1.088441] . ( 11 sec) [ -10930.9872] [ 2526] [depth= 1] . ( 11 sec) [ -10930.7193] [ 2531] [depth= 1] . ( 12 sec) [ -10930.5867] [ 2528] [depth= 3] . ( 13 sec) [ -10929.5714] [ 2523] [depth= 1] . ( 13 sec) [ -10929.5456] [ 2528] [depth= 1] . ( 14 sec) [ -10927.0245] [Branch lengths ] . ( 14 sec) [ -10927.0209] [GTR parameters ] . ( 14 sec) [ -10926.9966] [Alpha ][ 1.105674] . ( 15 sec) [ -10926.9779] [ 2532] [depth= 2] . ( 17 sec) [ -10926.9490] [ 2535] [depth= 1] . ( 18 sec) [ -10926.4508] [Branch lengths ] . ( 18 sec) [ -10926.4502] [GTR parameters ] . ( 18 sec) [ -10926.4499] [Alpha ][ 1.107549] . ( 19 sec) [ -10926.1302] [ 2528] [depth= 1] . ( 19 sec) [ -10924.8530] [ 2535] [depth= 2] . ( 40 sec) [ -10924.6654] [Branch lengths ] . ( 40 sec) [ -10924.6643] [GTR parameters ] . ( 40 sec) [ -10924.6624] [Alpha ][ 1.112306] . ( 62 sec) [ -10924.6280] [Branch lengths ] . ( 62 sec) [ -10924.6280] [Topology ] . ( 63 sec) [ -10924.6211] [Topology ] . ( 64 sec) [ -10924.6173] [Topology ] . ( 65 sec) [ -10924.6146] [Topology ] . ( 66 sec) [ -10924.6126] [Topology ] . ( 66 sec) [ -10924.6111] [Topology ] . ( 67 sec) [ -10924.6100] [Topology ] . ( 67 sec) [ -10924.6099] [GTR parameters ] . ( 67 sec) [ -10924.6099] [Alpha ][ 1.112306] . ( 67 sec) [ -10924.6099] [Topology ] . ( 68 sec) [ -10924.6091] [Topology ] . ( 68 sec) [ -10924.6091] [GTR parameters ] . ( 68 sec) [ -10924.6091] [Alpha ][ 1.112306] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -10924.6089] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.608893. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22750.0841] [GTR parameters ] . ( 1 sec) [ -22254.5644] [Alpha ][ 0.500960] . ( 1 sec) [ -22060.0291] [ 6001] [depth= 10] . ( 1 sec) [ -21792.3288] [ 5918] [depth= 9] . ( 1 sec) [ -21410.9507] [ 5863] [depth= 2] . ( 1 sec) [ -21228.5512] [ 5782] [depth= 1] . ( 1 sec) [ -21118.1193] [ 5717] [depth= 4] . ( 1 sec) [ -20901.9795] [ 5668] [depth= 3] . ( 1 sec) [ -20753.2442] [ 5664] [depth= 1] . ( 1 sec) [ -20549.4591] [ 5582] [depth= 1] . ( 1 sec) [ -20451.1884] [ 5528] [depth= 6] . ( 1 sec) [ -20352.7411] [ 5469] [depth= 1] . ( 1 sec) [ -20222.7381] [ 5452] [depth= 2] . ( 1 sec) [ -20190.6119] [ 5468] [depth= 1] . ( 1 sec) [ -20075.1802] [ 5433] [depth= 4] . ( 1 sec) [ -19997.1444] [ 5422] [depth= 3] . ( 1 sec) [ -19880.0617] [ 5421] [depth= 1] . ( 1 sec) [ -19870.6451] [ 5411] [depth= 3] . ( 2 sec) [ -19833.2828] [ 5360] [depth= 5] . ( 2 sec) [ -19758.8542] [ 5319] [depth= 3] . ( 2 sec) [ -19388.6567] [ 5187] [depth= 12] . ( 2 sec) [ -19286.7294] [ 5159] [depth= 16] . ( 2 sec) [ -19243.5466] [ 5094] [depth= 1] . ( 2 sec) [ -19242.5247] [ 5083] [depth= 6] . ( 2 sec) [ -18886.7960] [ 4992] [depth= 9] . ( 2 sec) [ -18818.5995] [ 4970] [depth= 1] . ( 2 sec) [ -18757.1597] [ 4964] [depth= 5] . ( 2 sec) [ -18444.3804] [ 4857] [depth= 4] . ( 2 sec) [ -18367.4379] [ 4794] [depth= 1] . ( 2 sec) [ -18196.1323] [ 4804] [depth= 1] . ( 2 sec) [ -18052.8137] [ 4771] [depth= 8] . ( 2 sec) [ -17663.4507] [ 4617] [depth= 7] . ( 2 sec) [ -17414.6691] [ 4453] [depth= 2] . ( 2 sec) [ -17187.7412] [ 4422] [depth= 12] . ( 2 sec) [ -17015.8250] [ 4378] [depth= 4] . ( 2 sec) [ -16628.1209] [ 4272] [depth= 12] . ( 2 sec) [ -16627.7130] [ 4301] [depth= 1] . ( 3 sec) [ -16481.9251] [ 4210] [depth= 6] . ( 3 sec) [ -16404.4208] [ 4212] [depth= 14] . ( 3 sec) [ -16399.7708] [ 4250] [depth= 2] . ( 3 sec) [ -16167.1187] [ 4184] [depth= 1] . ( 3 sec) [ -16072.6702] [ 4148] [depth= 2] . ( 3 sec) [ -15968.6214] [ 4116] [depth= 2] . ( 3 sec) [ -15688.0915] [ 3994] [depth= 11] . ( 3 sec) [ -15629.2774] [ 3998] [depth= 1] . ( 3 sec) [ -15512.3286] [ 3983] [depth= 1] . ( 3 sec) [ -15336.1714] [ 3979] [depth= 2] . ( 3 sec) [ -15197.6422] [ 3897] [depth= 1] . ( 3 sec) [ -15061.1116] [ 3779] [depth= 4] . ( 3 sec) [ -14971.0097] [ 3769] [depth= 1] . ( 3 sec) [ -14879.5808] [ 3763] [depth= 1] . ( 3 sec) [ -14812.1533] [ 3787] [depth= 2] . ( 3 sec) [ -14659.5297] [ 3741] [depth= 3] . ( 3 sec) [ -14260.3348] [ 3606] [depth= 1] . ( 3 sec) [ -14218.7967] [ 3593] [depth= 1] . ( 3 sec) [ -14003.8806] [ 3550] [depth= 8] . ( 3 sec) [ -13970.5394] [ 3551] [depth= 1] . ( 3 sec) [ -13606.0453] [ 3325] [depth= 8] . ( 3 sec) [ -13588.7052] [ 3319] [depth= 1] . ( 4 sec) [ -13404.0488] [ 3266] [depth= 7] . ( 4 sec) [ -13394.6413] [ 3265] [depth= 1] . ( 4 sec) [ -13311.8255] [ 3260] [depth= 1] . ( 4 sec) [ -13039.3193] [ 3169] [depth= 11] . ( 4 sec) [ -12837.0236] [ 3128] [depth= 4] . ( 4 sec) [ -12698.3908] [ 3114] [depth= 2] . ( 4 sec) [ -12532.6052] [ 3046] [depth= 3] . ( 4 sec) [ -12348.8490] [ 3005] [depth= 2] . ( 4 sec) [ -12240.8647] [ 2982] [depth= 2] . ( 4 sec) [ -12040.3533] [ 2853] [depth= 3] . ( 4 sec) [ -12017.2191] [ 2828] [depth= 1] . ( 4 sec) [ -12003.6535] [ 2828] [depth= 1] . ( 4 sec) [ -11842.2367] [ 2743] [depth= 1] . ( 4 sec) [ -11829.3589] [ 2736] [depth= 1] . ( 4 sec) [ -11751.8479] [ 2724] [depth= 2] . ( 4 sec) [ -11742.8578] [ 2708] [depth= 1] . ( 4 sec) [ -11715.1069] [ 2717] [depth= 2] . ( 4 sec) [ -11536.2743] [ 2603] [depth= 3] . ( 4 sec) [ -11482.5424] [ 2599] [depth= 2] . ( 4 sec) [ -11454.9847] [ 2606] [depth= 1] . ( 5 sec) [ -11448.6545] [ 2608] [depth= 1] . ( 5 sec) [ -11438.7291] [ 2618] [depth= 2] . ( 5 sec) [ -11379.6256] [ 2581] [depth= 1] . ( 5 sec) [ -11365.3818] [ 2584] [depth= 1] . ( 5 sec) [ -11316.0222] [ 2575] [depth= 5] . ( 5 sec) [ -11314.3096] [ 2563] [depth= 3] . ( 5 sec) [ -11312.4841] [ 2563] [depth= 1] . ( 5 sec) [ -11302.2360] [ 2560] [depth= 1] . ( 5 sec) [ -11100.4725] [Branch lengths ] . ( 6 sec) [ -11097.0728] [GTR parameters ] . ( 6 sec) [ -11052.9865] [Alpha ][ 0.959768] . ( 6 sec) [ -11051.6680] [ 2559] [depth= 1] . ( 6 sec) [ -11051.4383] [ 2561] [depth= 1] . ( 6 sec) [ -11049.9523] [ 2560] [depth= 1] . ( 6 sec) [ -11002.6753] [ 2528] [depth= 4] . ( 6 sec) [ -10999.0590] [ 2526] [depth= 1] . ( 7 sec) [ -10995.2866] [ 2521] [depth= 1] . ( 7 sec) [ -10984.7146] [ 2514] [depth= 1] . ( 7 sec) [ -10982.3987] [ 2516] [depth= 1] . ( 7 sec) [ -10981.2785] [ 2522] [depth= 2] . ( 7 sec) [ -10978.7201] [ 2564] [depth= 1] . ( 7 sec) [ -10975.8351] [ 2563] [depth= 1] . ( 7 sec) [ -10975.4977] [ 2568] [depth= 1] . ( 7 sec) [ -10975.4469] [ 2527] [depth= 1] . ( 8 sec) [ -10968.2786] [ 2532] [depth= 1] . ( 8 sec) [ -10967.1169] [ 2536] [depth= 1] . ( 9 sec) [ -10964.9189] [ 2532] [depth= 1] . ( 9 sec) [ -10964.3752] [ 2535] [depth= 1] . ( 9 sec) [ -10960.9789] [ 2545] [depth= 1] . ( 10 sec) [ -10940.4220] [Branch lengths ] . ( 10 sec) [ -10940.2736] [GTR parameters ] . ( 10 sec) [ -10938.3412] [Alpha ][ 1.100397] . ( 10 sec) [ -10938.2152] [ 2548] [depth= 1] . ( 11 sec) [ -10938.1875] [ 2548] [depth= 1] . ( 11 sec) [ -10931.4638] [ 2544] [depth= 1] . ( 11 sec) [ -10931.3699] [ 2536] [depth= 1] . ( 12 sec) [ -10931.3023] [ 2535] [depth= 1] . ( 13 sec) [ -10931.2770] [ 2536] [depth= 1] . ( 14 sec) [ -10927.0218] [Branch lengths ] . ( 14 sec) [ -10927.0104] [GTR parameters ] . ( 14 sec) [ -10927.0035] [Alpha ][ 1.109472] . ( 14 sec) [ -10926.9329] [ 2535] [depth= 1] . ( 15 sec) [ -10926.8942] [ 2538] [depth= 1] . ( 16 sec) [ -10926.7711] [ 2538] [depth= 1] . ( 18 sec) [ -10926.1688] [Branch lengths ] . ( 18 sec) [ -10926.1670] [GTR parameters ] . ( 18 sec) [ -10926.1669] [Alpha ][ 1.110589] . ( 21 sec) [ -10926.1482] [ 2542] [depth= 1] . ( 35 sec) [ -10925.3076] [ 2545] [depth= 1] . ( 40 sec) [ -10924.9545] [Branch lengths ] . ( 40 sec) [ -10924.9529] [GTR parameters ] . ( 40 sec) [ -10924.9529] [Alpha ][ 1.110589] . ( 62 sec) [ -10924.9018] [Branch lengths ] . ( 62 sec) [ -10924.9018] [Topology ] . ( 63 sec) [ -10924.8348] [Topology ] . ( 64 sec) [ -10924.8043] [Topology ] . ( 64 sec) [ -10924.7928] [Topology ] . ( 65 sec) [ -10924.7869] [Topology ] . ( 66 sec) [ -10924.7836] [Topology ] . ( 67 sec) [ -10924.7815] [Topology ] . ( 68 sec) [ -10924.7802] [Topology ] . ( 68 sec) [ -10924.7797] [GTR parameters ] . ( 68 sec) [ -10924.7797] [Alpha ][ 1.110589] . ( 68 sec) [ -10924.7797] [Topology ] . ( 69 sec) [ -10924.7788] [Topology ] . ( 69 sec) [ -10924.7788] [GTR parameters ] . ( 69 sec) [ -10924.7788] [Alpha ][ 1.110589] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -10924.3677] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.367657. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23812.8494] [GTR parameters ] . ( 1 sec) [ -23301.4038] [Alpha ][ 0.500960] . ( 1 sec) [ -23034.0694] [ 6062] [depth= 9] . ( 1 sec) [ -22630.9263] [ 5996] [depth= 11] . ( 1 sec) [ -22437.4656] [ 5959] [depth= 4] . ( 1 sec) [ -22361.3635] [ 5944] [depth= 1] . ( 1 sec) [ -22255.2546] [ 5876] [depth= 6] . ( 1 sec) [ -22037.1719] [ 5852] [depth= 5] . ( 1 sec) [ -21760.2066] [ 5835] [depth= 17] . ( 1 sec) [ -21450.3442] [ 5816] [depth= 1] . ( 1 sec) [ -21168.4807] [ 5686] [depth= 21] . ( 1 sec) [ -20865.5861] [ 5537] [depth= 17] . ( 1 sec) [ -20768.8435] [ 5435] [depth= 11] . ( 1 sec) [ -20682.5841] [ 5489] [depth= 3] . ( 1 sec) [ -20329.4478] [ 5391] [depth= 2] . ( 1 sec) [ -20319.4868] [ 5377] [depth= 1] . ( 1 sec) [ -20225.1138] [ 5354] [depth= 2] . ( 1 sec) [ -19945.7271] [ 5305] [depth= 8] . ( 2 sec) [ -19907.5489] [ 5301] [depth= 1] . ( 2 sec) [ -19861.4674] [ 5268] [depth= 1] . ( 2 sec) [ -19850.9128] [ 5262] [depth= 1] . ( 2 sec) [ -19651.5772] [ 5239] [depth= 1] . ( 2 sec) [ -19168.5277] [ 5087] [depth= 9] . ( 2 sec) [ -19000.0873] [ 5051] [depth= 4] . ( 2 sec) [ -18885.8924] [ 5043] [depth= 1] . ( 2 sec) [ -18744.6209] [ 4921] [depth= 12] . ( 2 sec) [ -18590.3402] [ 4871] [depth= 1] . ( 2 sec) [ -17833.3372] [ 4796] [depth= 4] . ( 2 sec) [ -17802.5549] [ 4814] [depth= 1] . ( 2 sec) [ -17390.8099] [ 4736] [depth= 9] . ( 2 sec) [ -17033.7191] [ 4544] [depth= 11] . ( 2 sec) [ -16640.0892] [ 4365] [depth= 2] . ( 2 sec) [ -16557.8382] [ 4323] [depth= 6] . ( 2 sec) [ -16232.0360] [ 4294] [depth= 1] . ( 2 sec) [ -15889.1615] [ 4118] [depth= 8] . ( 2 sec) [ -15603.0055] [ 4036] [depth= 12] . ( 2 sec) [ -15465.3680] [ 3932] [depth= 11] . ( 2 sec) [ -15165.1589] [ 3784] [depth= 7] . ( 3 sec) [ -14987.9579] [ 3757] [depth= 1] . ( 3 sec) [ -14974.6312] [ 3752] [depth= 1] . ( 3 sec) [ -14730.3342] [ 3693] [depth= 1] . ( 3 sec) [ -14370.6015] [ 3607] [depth= 4] . ( 3 sec) [ -14326.5782] [ 3521] [depth= 4] . ( 3 sec) [ -13995.0437] [ 3391] [depth= 10] . ( 3 sec) [ -13825.3135] [ 3336] [depth= 1] . ( 3 sec) [ -13806.3461] [ 3339] [depth= 1] . ( 3 sec) [ -13518.2811] [ 3262] [depth= 3] . ( 3 sec) [ -13244.3150] [ 3198] [depth= 6] . ( 3 sec) [ -13233.1772] [ 3194] [depth= 2] . ( 3 sec) [ -12975.9706] [ 3075] [depth= 3] . ( 3 sec) [ -12957.8623] [ 3071] [depth= 1] . ( 3 sec) [ -12905.8778] [ 3066] [depth= 2] . ( 3 sec) [ -12642.5712] [ 3014] [depth= 2] . ( 3 sec) [ -12641.0514] [ 3013] [depth= 1] . ( 3 sec) [ -12632.4924] [ 3008] [depth= 1] . ( 3 sec) [ -12613.6208] [ 3008] [depth= 1] . ( 4 sec) [ -12233.1319] [ 2976] [depth= 7] . ( 4 sec) [ -12213.0941] [ 2967] [depth= 1] . ( 4 sec) [ -12205.1292] [ 2967] [depth= 1] . ( 4 sec) [ -12204.1727] [ 2967] [depth= 1] . ( 4 sec) [ -12202.0742] [ 2967] [depth= 1] . ( 4 sec) [ -12169.7873] [ 2968] [depth= 2] . ( 4 sec) [ -12145.1278] [ 2918] [depth= 4] . ( 4 sec) [ -12138.4864] [ 2916] [depth= 1] . ( 4 sec) [ -11979.7524] [ 2858] [depth= 1] . ( 4 sec) [ -11915.6587] [ 2803] [depth= 3] . ( 4 sec) [ -11866.8100] [ 2757] [depth= 1] . ( 4 sec) [ -11823.2415] [ 2743] [depth= 1] . ( 4 sec) [ -11776.2653] [ 2689] [depth= 1] . ( 4 sec) [ -11603.6429] [ 2617] [depth= 2] . ( 4 sec) [ -11598.3841] [ 2615] [depth= 1] . ( 4 sec) [ -11541.8314] [ 2604] [depth= 1] . ( 4 sec) [ -11499.8015] [ 2645] [depth= 2] . ( 4 sec) [ -11483.0030] [ 2643] [depth= 1] . ( 4 sec) [ -11469.6568] [ 2641] [depth= 1] . ( 4 sec) [ -11445.9204] [ 2645] [depth= 2] . ( 4 sec) [ -11444.5369] [ 2650] [depth= 2] . ( 5 sec) [ -11425.6772] [ 2648] [depth= 1] . ( 5 sec) [ -11411.5832] [ 2644] [depth= 1] . ( 5 sec) [ -11279.1552] [ 2563] [depth= 2] . ( 5 sec) [ -11269.2972] [ 2561] [depth= 1] . ( 5 sec) [ -11088.2457] [Branch lengths ] . ( 6 sec) [ -11085.1127] [GTR parameters ] . ( 6 sec) [ -11040.8442] [Alpha ][ 0.972540] . ( 6 sec) [ -11040.3692] [ 2559] [depth= 1] . ( 6 sec) [ -11036.4621] [ 2561] [depth= 1] . ( 6 sec) [ -10992.1059] [ 2532] [depth= 1] . ( 6 sec) [ -10988.2352] [ 2532] [depth= 1] . ( 6 sec) [ -10987.1748] [ 2543] [depth= 1] . ( 6 sec) [ -10986.7551] [ 2538] [depth= 2] . ( 6 sec) [ -10986.0480] [ 2539] [depth= 1] . ( 7 sec) [ -10978.1137] [ 2531] [depth= 1] . ( 7 sec) [ -10973.4030] [ 2542] [depth= 1] . ( 7 sec) [ -10973.1882] [ 2543] [depth= 1] . ( 7 sec) [ -10971.5718] [ 2541] [depth= 1] . ( 7 sec) [ -10971.5529] [ 2544] [depth= 1] . ( 8 sec) [ -10970.7676] [ 2541] [depth= 1] . ( 8 sec) [ -10970.4671] [ 2541] [depth= 1] . ( 8 sec) [ -10969.7396] [ 2541] [depth= 1] . ( 8 sec) [ -10956.6880] [ 2522] [depth= 2] . ( 8 sec) [ -10950.4085] [ 2521] [depth= 1] . ( 9 sec) [ -10950.2497] [ 2525] [depth= 1] . ( 9 sec) [ -10949.7479] [ 2521] [depth= 1] . ( 9 sec) [ -10930.5892] [Branch lengths ] . ( 10 sec) [ -10930.4457] [GTR parameters ] . ( 10 sec) [ -10929.0309] [Alpha ][ 1.094521] . ( 10 sec) [ -10928.6648] [ 2522] [depth= 1] . ( 10 sec) [ -10928.6000] [ 2510] [depth= 1] . ( 10 sec) [ -10928.5509] [ 2511] [depth= 1] . ( 11 sec) [ -10928.2914] [ 2514] [depth= 1] . ( 13 sec) [ -10928.1619] [ 2519] [depth= 1] . ( 13 sec) [ -10925.7337] [Branch lengths ] . ( 13 sec) [ -10925.7294] [GTR parameters ] . ( 13 sec) [ -10925.7211] [Alpha ][ 1.104542] . ( 13 sec) [ -10925.6979] [ 2524] [depth= 2] . ( 16 sec) [ -10925.2776] [ 2527] [depth= 1] . ( 16 sec) [ -10925.1858] [ 2513] [depth= 1] . ( 17 sec) [ -10924.4750] [Branch lengths ] . ( 17 sec) [ -10924.4737] [GTR parameters ] . ( 17 sec) [ -10924.4719] [Alpha ][ 1.109174] . ( 21 sec) [ -10924.3463] [Branch lengths ] . ( 42 sec) [ -10924.3187] [Branch lengths ] . ( 42 sec) [ -10924.3187] [Topology ] . ( 43 sec) [ -10924.3147] [Topology ] . ( 44 sec) [ -10924.3129] [Topology ] . ( 45 sec) [ -10924.3118] [Topology ] . ( 46 sec) [ -10924.3112] [Topology ] . ( 46 sec) [ -10924.3109] [GTR parameters ] . ( 46 sec) [ -10924.3108] [Alpha ][ 1.110283] . ( 46 sec) [ -10924.3108] [Topology ] . ( 47 sec) [ -10924.3104] [Topology ] . ( 47 sec) [ -10924.3104] [GTR parameters ] . ( 47 sec) [ -10924.3104] [Alpha ][ 1.110283] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.310406. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11033.487122 . ( 1 sec) [ -11032.9128] [GTR parameters ] . ( 1 sec) [ -11030.8409] [Alpha ][ 1.162653] . ( 1 sec) [ -11030.8409] [Topology ] . ( 2 sec) [ -10949.5341] [Topology ] . ( 3 sec) [ -10930.4633] [Topology ] . ( 4 sec) [ -10926.6486] [Topology ] . ( 4 sec) [ -10925.5193] [Topology ] . ( 5 sec) [ -10925.0495] [Topology ] . ( 6 sec) [ -10924.8277] [Topology ] . ( 7 sec) [ -10924.7164] [Topology ] . ( 8 sec) [ -10924.6577] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.657736 . ( 16 sec) [ -10924.5882] [GTR parameters ] . ( 16 sec) [ -10924.3961] [Alpha ][ 1.113397] . ( 16 sec) [ -10924.3961] [Topology ] . ( 16 sec) [ -10924.3525] [Topology ] . ( 17 sec) [ -10924.3339] [Topology ] . ( 18 sec) [ -10924.3239] [Topology ] . ( 19 sec) [ -10924.3183] [Topology ] . ( 20 sec) [ -10924.3151] [Topology ] . ( 21 sec) [ -10924.3133] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.313310 . ( 28 sec) [ -10924.3131] [GTR parameters ] . ( 28 sec) [ -10924.3124] [Alpha ][ 1.110450] . ( 28 sec) [ -10924.3124] [Topology ] . ( 29 sec) [ -10924.3113] [Topology ] . ( 30 sec) [ -10924.3107] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.310696 . ( 37 sec) [ -10924.3107] [GTR parameters ] . ( 37 sec) [ -10924.3107] [Alpha ][ 1.110450] . ( 37 sec) [ -10924.3107] [Topology ] . ( 38 sec) [ -10924.3103] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -11032.9128] [GTR parameters ] . ( 53 sec) [ -11030.8409] [Alpha ][ 1.162653] . ( 54 sec) [ -11027.8222] [ 2511] [depth= 1] . ( 54 sec) [ -11015.2292] [ 2496] [depth= 1] . ( 54 sec) [ -11013.5463] [ 2501] [depth= 1] . ( 54 sec) [ -10995.1740] [ 2506] [depth= 1] . ( 55 sec) [ -10994.9317] [ 2508] [depth= 1] . ( 55 sec) [ -10992.7866] [ 2506] [depth= 1] . ( 55 sec) [ -10991.4563] [ 2508] [depth= 1] . ( 55 sec) [ -10990.8017] [ 2511] [depth= 1] . ( 55 sec) [ -10988.5056] [ 2515] [depth= 1] . ( 55 sec) [ -10984.9145] [ 2511] [depth= 1] . ( 55 sec) [ -10980.2992] [ 2514] [depth= 2] . ( 56 sec) [ -10980.1407] [ 2514] [depth= 1] . ( 56 sec) [ -10978.5828] [ 2515] [depth= 1] . ( 56 sec) [ -10964.8826] [ 2521] [depth= 2] . ( 57 sec) [ -10932.2004] [Branch lengths ] . ( 57 sec) [ -10932.1336] [GTR parameters ] . ( 57 sec) [ -10931.8741] [Alpha ][ 1.105045] . ( 58 sec) [ -10930.3061] [ 2517] [depth= 1] . ( 58 sec) [ -10929.6557] [ 2514] [depth= 1] . ( 59 sec) [ -10929.3083] [ 2523] [depth= 1] . ( 59 sec) [ -10928.3874] [ 2513] [depth= 2] . ( 60 sec) [ -10924.9659] [Branch lengths ] . ( 60 sec) [ -10924.9621] [GTR parameters ] . ( 61 sec) [ -10924.9610] [Alpha ][ 1.108696] . ( 64 sec) [ -10924.4729] [Branch lengths ] . ( 86 sec) [ -10924.3586] [Branch lengths ] . ( 86 sec) [ -10924.3586] [Topology ] . ( 87 sec) [ -10924.3398] [Topology ] . ( 88 sec) [ -10924.3276] [Topology ] . ( 88 sec) [ -10924.3214] [Topology ] . ( 89 sec) [ -10924.3179] [Topology ] . ( 90 sec) [ -10924.3157] [Topology ] . ( 91 sec) [ -10924.3144] [Topology ] . ( 91 sec) [ -10924.3124] [GTR parameters ] . ( 91 sec) [ -10924.3122] [Alpha ][ 1.110175] . ( 91 sec) [ -10924.3122] [Topology ] . ( 92 sec) [ -10924.3113] [Topology ] . ( 92 sec) [ -10924.3113] [GTR parameters ] . ( 92 sec) [ -10924.3113] [Alpha ][ 1.110175] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10924.310330 . Log likelihood obtained after SPR moves : -10924.311344 . Log likelihood of the current tree: -10924.310330. . Printing the most likely tree in file 'data71.phy_phyml_tree.txt'... . Best log likelihood : -10924.310169 . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo