.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data23.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... . 442 patterns found. (out of a total of 500 sites) . 57 sites without polymorphism (11.40%). . [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)... . ( 2 sec) [ -22589.4359] [GTR parameters ] . ( 2 sec) [ -22160.0756] [Alpha ][ 0.500960] . ( 2 sec) [ -21865.7701] [ 5231] [depth= 7] . ( 2 sec) [ -21803.2257] [ 5237] [depth= 1] . ( 2 sec) [ -21522.6396] [ 5134] [depth= 5] . ( 2 sec) [ -21420.7800] [ 5108] [depth= 1] . ( 2 sec) [ -21250.1161] [ 5087] [depth= 7] . ( 2 sec) [ -20787.2115] [ 4966] [depth= 5] . ( 2 sec) [ -20574.9201] [ 4908] [depth= 5] . ( 2 sec) [ -20452.8477] [ 4901] [depth= 1] . ( 2 sec) [ -20381.0086] [ 4884] [depth= 2] . ( 2 sec) [ -20149.2684] [ 4838] [depth= 12] . ( 2 sec) [ -20075.7703] [ 4793] [depth= 1] . ( 2 sec) [ -19818.1577] [ 4731] [depth= 10] . ( 2 sec) [ -19655.7076] [ 4611] [depth= 10] . ( 2 sec) [ -19565.3282] [ 4608] [depth= 1] . ( 2 sec) [ -19516.0467] [ 4580] [depth= 4] . ( 2 sec) [ -19074.3534] [ 4465] [depth= 3] . ( 3 sec) [ -18848.9619] [ 4451] [depth= 3] . ( 3 sec) [ -18847.4609] [ 4454] [depth= 1] . ( 3 sec) [ -18748.1957] [ 4405] [depth= 6] . ( 3 sec) [ -18398.2566] [ 4313] [depth= 3] . ( 3 sec) [ -18010.7356] [ 4203] [depth= 5] . ( 3 sec) [ -17040.4084] [ 4065] [depth= 10] . ( 3 sec) [ -16755.4835] [ 4079] [depth= 12] . ( 3 sec) [ -16650.9055] [ 4059] [depth= 1] . ( 3 sec) [ -16262.6505] [ 4062] [depth= 13] . ( 3 sec) [ -16194.5299] [ 4098] [depth= 15] . ( 3 sec) [ -15808.6766] [ 3968] [depth= 5] . ( 3 sec) [ -15750.1037] [ 3957] [depth= 2] . ( 3 sec) [ -15707.0412] [ 3935] [depth= 1] . ( 3 sec) [ -15615.8036] [ 3940] [depth= 18] . ( 3 sec) [ -15456.7273] [ 3903] [depth= 13] . ( 3 sec) [ -15207.2408] [ 3894] [depth= 3] . ( 3 sec) [ -14905.5866] [ 3826] [depth= 4] . ( 3 sec) [ -14842.6457] [ 3851] [depth= 1] . ( 3 sec) [ -14748.6029] [ 3827] [depth= 4] . ( 3 sec) [ -14659.6037] [ 3801] [depth= 1] . ( 3 sec) [ -14549.2521] [ 3710] [depth= 5] . ( 4 sec) [ -14385.6334] [ 3700] [depth= 2] . ( 4 sec) [ -14268.7278] [ 3635] [depth= 14] . ( 4 sec) [ -14132.5344] [ 3576] [depth= 2] . ( 4 sec) [ -13979.5863] [ 3501] [depth= 2] . ( 4 sec) [ -13750.0912] [ 3436] [depth= 5] . ( 4 sec) [ -13553.2103] [ 3326] [depth= 10] . ( 4 sec) [ -13275.1115] [ 3322] [depth= 1] . ( 4 sec) [ -13055.1792] [ 3281] [depth= 4] . ( 4 sec) [ -13043.4892] [ 3284] [depth= 1] . ( 4 sec) [ -12968.1214] [ 3272] [depth= 1] . ( 4 sec) [ -12948.5224] [ 3264] [depth= 1] . ( 4 sec) [ -12927.2058] [ 3261] [depth= 11] . ( 4 sec) [ -12886.7268] [ 3248] [depth= 11] . ( 4 sec) [ -12627.1340] [ 3082] [depth= 8] . ( 4 sec) [ -12226.3992] [ 3024] [depth= 3] . ( 4 sec) [ -12219.7619] [ 3015] [depth= 1] . ( 4 sec) [ -12180.5929] [ 3031] [depth= 1] . ( 4 sec) [ -12051.5244] [ 2934] [depth= 5] . ( 5 sec) [ -12050.8450] [ 2933] [depth= 2] . ( 5 sec) [ -11997.7106] [ 2885] [depth= 1] . ( 5 sec) [ -11937.5301] [ 2875] [depth= 3] . ( 5 sec) [ -11929.9231] [ 2872] [depth= 1] . ( 5 sec) [ -11904.4907] [ 2828] [depth= 1] . ( 5 sec) [ -11855.5558] [ 2813] [depth= 5] . ( 5 sec) [ -11851.3258] [ 2812] [depth= 1] . ( 5 sec) [ -11844.1971] [ 2793] [depth= 1] . ( 5 sec) [ -11827.2616] [ 2788] [depth= 3] . ( 5 sec) [ -11717.8232] [ 2713] [depth= 2] . ( 5 sec) [ -11639.1479] [ 2677] [depth= 2] . ( 5 sec) [ -11636.1572] [ 2678] [depth= 1] . ( 5 sec) [ -11543.7147] [ 2632] [depth= 4] . ( 5 sec) [ -11531.3262] [ 2644] [depth= 1] . ( 5 sec) [ -11510.2794] [ 2627] [depth= 2] . ( 5 sec) [ -11506.0367] [ 2626] [depth= 1] . ( 5 sec) [ -11502.3941] [ 2625] [depth= 1] . ( 5 sec) [ -11455.1874] [ 2627] [depth= 1] . ( 5 sec) [ -11398.4611] [ 2579] [depth= 1] . ( 6 sec) [ -11174.1003] [Branch lengths ] . ( 6 sec) [ -11172.4674] [GTR parameters ] . ( 6 sec) [ -11138.0897] [Alpha ][ 0.876464] . ( 6 sec) [ -11136.0481] [ 2590] [depth= 1] . ( 6 sec) [ -11134.1850] [ 2584] [depth= 1] . ( 7 sec) [ -11127.9301] [ 2584] [depth= 2] . ( 7 sec) [ -11108.2400] [ 2569] [depth= 2] . ( 7 sec) [ -11106.3676] [ 2570] [depth= 1] . ( 7 sec) [ -11104.9537] [ 2561] [depth= 1] . ( 7 sec) [ -11103.1046] [ 2561] [depth= 1] . ( 7 sec) [ -11100.3624] [ 2566] [depth= 1] . ( 7 sec) [ -11092.6726] [ 2549] [depth= 4] . ( 8 sec) [ -11083.6896] [ 2543] [depth= 1] . ( 8 sec) [ -11082.5149] [ 2546] [depth= 1] . ( 8 sec) [ -11081.1378] [ 2546] [depth= 1] . ( 8 sec) [ -11078.5141] [ 2547] [depth= 1] . ( 9 sec) [ -11076.5693] [ 2551] [depth= 1] . ( 9 sec) [ -11075.4711] [ 2554] [depth= 1] . ( 9 sec) [ -11075.4357] [ 2550] [depth= 1] . ( 9 sec) [ -11074.4411] [ 2552] [depth= 1] . ( 9 sec) [ -11062.8930] [Branch lengths ] . ( 9 sec) [ -11062.8567] [GTR parameters ] . ( 10 sec) [ -11062.4340] [Alpha ][ 0.933528] . ( 10 sec) [ -11061.4032] [ 2551] [depth= 2] . ( 10 sec) [ -11059.7088] [ 2555] [depth= 1] . ( 10 sec) [ -11059.5882] [ 2554] [depth= 1] . ( 11 sec) [ -11059.3624] [ 2550] [depth= 1] . ( 12 sec) [ -11058.8855] [ 2554] [depth= 1] . ( 13 sec) [ -11057.6543] [Branch lengths ] . ( 13 sec) [ -11057.6444] [GTR parameters ] . ( 13 sec) [ -11057.6391] [Alpha ][ 0.940231] . ( 16 sec) [ -11057.6184] [ 2550] [depth= 1] . ( 16 sec) [ -11057.4187] [Branch lengths ] . ( 17 sec) [ -11057.4185] [GTR parameters ] . ( 17 sec) [ -11057.4182] [Alpha ][ 0.941605] . ( 37 sec) [ -11057.4004] [Branch lengths ] . ( 37 sec) [ -11057.4004] [Topology ] . ( 38 sec) [ -11057.3980] [Topology ] . ( 39 sec) [ -11057.3972] [Topology ] . ( 39 sec) [ -11057.3972] [GTR parameters ] . ( 39 sec) [ -11057.3970] [Alpha ][ 0.942798] . ( 39 sec) [ -11057.3970] [Topology ] . ( 40 sec) [ -11057.3966] [Topology ] . ( 40 sec) [ -11057.3966] [GTR parameters ] . ( 40 sec) [ -11057.3966] [Alpha ][ 0.942798] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -11057.2690] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -11057.2669] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11057.266913. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22026.4273] [GTR parameters ] . ( 1 sec) [ -21632.2633] [Alpha ][ 0.500960] . ( 1 sec) [ -21351.9558] [ 5214] [depth= 3] . ( 1 sec) [ -20844.3202] [ 5129] [depth= 3] . ( 1 sec) [ -20516.6954] [ 5047] [depth= 4] . ( 1 sec) [ -20395.3567] [ 5030] [depth= 7] . ( 1 sec) [ -20362.6634] [ 4936] [depth= 5] . ( 1 sec) [ -20110.5368] [ 4947] [depth= 10] . ( 1 sec) [ -19927.3434] [ 4933] [depth= 4] . ( 1 sec) [ -19869.8458] [ 4866] [depth= 2] . ( 1 sec) [ -19678.1891] [ 4868] [depth= 4] . ( 1 sec) [ -19510.0119] [ 4822] [depth= 3] . ( 1 sec) [ -19330.4196] [ 4799] [depth= 5] . ( 1 sec) [ -19080.1734] [ 4699] [depth= 2] . ( 1 sec) [ -18980.8137] [ 4679] [depth= 2] . ( 1 sec) [ -18546.1201] [ 4556] [depth= 10] . ( 1 sec) [ -17586.9016] [ 4452] [depth= 7] . ( 1 sec) [ -17241.6700] [ 4362] [depth= 6] . ( 1 sec) [ -17114.3513] [ 4325] [depth= 7] . ( 2 sec) [ -16822.2501] [ 4235] [depth= 8] . ( 2 sec) [ -16616.1049] [ 4151] [depth= 8] . ( 2 sec) [ -16489.9102] [ 4159] [depth= 9] . ( 2 sec) [ -16183.7935] [ 4087] [depth= 3] . ( 2 sec) [ -16052.7832] [ 4129] [depth= 1] . ( 2 sec) [ -15753.4940] [ 4051] [depth= 7] . ( 2 sec) [ -15564.1896] [ 3951] [depth= 6] . ( 2 sec) [ -15533.9892] [ 3948] [depth= 1] . ( 2 sec) [ -15098.6394] [ 3927] [depth= 9] . ( 2 sec) [ -15067.7270] [ 3879] [depth= 1] . ( 2 sec) [ -15055.3506] [ 3868] [depth= 3] . ( 2 sec) [ -14818.0904] [ 3769] [depth= 4] . ( 2 sec) [ -14621.7244] [ 3628] [depth= 9] . ( 2 sec) [ -14552.5953] [ 3590] [depth= 4] . ( 2 sec) [ -14453.4030] [ 3583] [depth= 1] . ( 2 sec) [ -14333.3109] [ 3573] [depth= 8] . ( 2 sec) [ -14196.8329] [ 3495] [depth= 5] . ( 2 sec) [ -14048.6507] [ 3402] [depth= 8] . ( 2 sec) [ -14038.7079] [ 3405] [depth= 2] . ( 3 sec) [ -13949.6491] [ 3357] [depth= 1] . ( 3 sec) [ -13848.3267] [ 3334] [depth= 1] . ( 3 sec) [ -13780.7043] [ 3304] [depth= 4] . ( 3 sec) [ -13664.9077] [ 3240] [depth= 2] . ( 3 sec) [ -13483.3343] [ 3231] [depth= 2] . ( 3 sec) [ -13358.5357] [ 3165] [depth= 2] . ( 3 sec) [ -13323.9681] [ 3175] [depth= 13] . ( 3 sec) [ -13037.6272] [ 3103] [depth= 1] . ( 3 sec) [ -12844.0776] [ 3097] [depth= 1] . ( 3 sec) [ -12773.1248] [ 3087] [depth= 10] . ( 3 sec) [ -12703.5476] [ 3079] [depth= 2] . ( 3 sec) [ -12611.9849] [ 3074] [depth= 1] . ( 3 sec) [ -12604.0028] [ 3092] [depth= 1] . ( 3 sec) [ -12511.3228] [ 3074] [depth= 1] . ( 3 sec) [ -12423.4391] [ 3046] [depth= 2] . ( 3 sec) [ -12402.1913] [ 3011] [depth= 1] . ( 3 sec) [ -12363.1125] [ 3002] [depth= 1] . ( 3 sec) [ -11995.2290] [ 2880] [depth= 11] . ( 4 sec) [ -11853.2069] [ 2768] [depth= 6] . ( 4 sec) [ -11844.3112] [ 2771] [depth= 1] . ( 4 sec) [ -11820.9078] [ 2768] [depth= 1] . ( 4 sec) [ -11743.8349] [ 2723] [depth= 6] . ( 4 sec) [ -11743.7162] [ 2722] [depth= 1] . ( 4 sec) [ -11742.7527] [ 2725] [depth= 1] . ( 4 sec) [ -11658.9925] [ 2713] [depth= 1] . ( 4 sec) [ -11581.6514] [ 2665] [depth= 4] . ( 4 sec) [ -11465.6961] [ 2615] [depth= 1] . ( 4 sec) [ -11398.5301] [ 2573] [depth= 3] . ( 4 sec) [ -11395.8442] [ 2567] [depth= 1] . ( 4 sec) [ -11386.1760] [ 2569] [depth= 1] . ( 4 sec) [ -11362.7785] [ 2573] [depth= 1] . ( 4 sec) [ -11347.7888] [ 2577] [depth= 1] . ( 4 sec) [ -11329.9687] [ 2565] [depth= 1] . ( 4 sec) [ -11316.7128] [ 2558] [depth= 2] . ( 5 sec) [ -11296.2263] [ 2553] [depth= 1] . ( 5 sec) [ -11285.0590] [ 2562] [depth= 1] . ( 5 sec) [ -11116.9927] [Branch lengths ] . ( 6 sec) [ -11115.1997] [GTR parameters ] . ( 6 sec) [ -11081.8787] [Alpha ][ 0.877891] . ( 6 sec) [ -11081.5846] [ 2566] [depth= 1] . ( 6 sec) [ -11081.0042] [ 2565] [depth= 1] . ( 6 sec) [ -11077.5303] [ 2561] [depth= 1] . ( 6 sec) [ -11075.1508] [ 2565] [depth= 1] . ( 7 sec) [ -11075.1049] [ 2553] [depth= 1] . ( 7 sec) [ -11074.6641] [ 2548] [depth= 1] . ( 8 sec) [ -11074.3232] [ 2549] [depth= 1] . ( 9 sec) [ -11059.7484] [Branch lengths ] . ( 9 sec) [ -11059.7143] [GTR parameters ] . ( 9 sec) [ -11059.2525] [Alpha ][ 0.937705] . ( 12 sec) [ -11057.7379] [Branch lengths ] . ( 13 sec) [ -11057.6871] [ 2560] [depth= 1] . ( 31 sec) [ -11057.6116] [Branch lengths ] . ( 31 sec) [ -11057.6109] [GTR parameters ] . ( 31 sec) [ -11057.6095] [Alpha ][ 0.941126] . ( 31 sec) [ -11057.6095] [Topology ] . ( 32 sec) [ -11057.3804] [Topology ] . ( 33 sec) [ -11057.2910] [Topology ] . ( 34 sec) [ -11057.2651] [Topology ] . ( 34 sec) [ -11057.2545] [Topology ] . ( 35 sec) [ -11057.2500] [Topology ] . ( 36 sec) [ -11057.2480] [Topology ] . ( 37 sec) [ -11057.2471] [Topology ] . ( 37 sec) [ -11057.2452] [GTR parameters ] . ( 37 sec) [ -11057.2449] [Alpha ][ 0.942690] . ( 37 sec) [ -11057.2449] [Topology ] . ( 38 sec) [ -11057.2444] [Topology ] . ( 38 sec) [ -11057.2444] [GTR parameters ] . ( 38 sec) [ -11057.2444] [Alpha ][ 0.942690] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -11057.2277] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11057.227732. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22239.5023] [GTR parameters ] . ( 1 sec) [ -21800.7874] [Alpha ][ 0.500960] . ( 1 sec) [ -21638.4371] [ 5380] [depth= 8] . ( 1 sec) [ -21306.3877] [ 5290] [depth= 8] . ( 1 sec) [ -21284.6878] [ 5263] [depth= 3] . ( 1 sec) [ -21096.1378] [ 5251] [depth= 3] . ( 1 sec) [ -20873.5212] [ 5163] [depth= 8] . ( 1 sec) [ -20830.1009] [ 5157] [depth= 1] . ( 1 sec) [ -20485.4501] [ 5036] [depth= 14] . ( 2 sec) [ -20382.4076] [ 4973] [depth= 6] . ( 2 sec) [ -19806.9776] [ 4773] [depth= 15] . ( 2 sec) [ -19511.3122] [ 4731] [depth= 10] . ( 2 sec) [ -19184.4655] [ 4639] [depth= 14] . ( 2 sec) [ -19006.4478] [ 4624] [depth= 1] . ( 2 sec) [ -18969.3855] [ 4619] [depth= 2] . ( 2 sec) [ -18852.1357] [ 4577] [depth= 1] . ( 2 sec) [ -18758.4153] [ 4563] [depth= 1] . ( 2 sec) [ -18486.3577] [ 4479] [depth= 1] . ( 2 sec) [ -17868.9637] [ 4459] [depth= 2] . ( 2 sec) [ -17631.1777] [ 4398] [depth= 5] . ( 2 sec) [ -17105.9163] [ 4254] [depth= 6] . ( 2 sec) [ -17044.9361] [ 4200] [depth= 1] . ( 2 sec) [ -16868.1117] [ 4124] [depth= 10] . ( 2 sec) [ -16843.7817] [ 4140] [depth= 1] . ( 2 sec) [ -16675.0002] [ 4051] [depth= 9] . ( 2 sec) [ -16611.8254] [ 4037] [depth= 1] . ( 2 sec) [ -16597.4934] [ 4037] [depth= 1] . ( 2 sec) [ -16579.6290] [ 4037] [depth= 1] . ( 2 sec) [ -16405.6361] [ 3938] [depth= 11] . ( 3 sec) [ -15916.9633] [ 3890] [depth= 7] . ( 3 sec) [ -15893.5036] [ 3864] [depth= 1] . ( 3 sec) [ -15830.5074] [ 3827] [depth= 6] . ( 3 sec) [ -15173.8920] [ 3721] [depth= 6] . ( 3 sec) [ -14846.4516] [ 3604] [depth= 11] . ( 3 sec) [ -14766.7807] [ 3591] [depth= 1] . ( 3 sec) [ -14717.2840] [ 3596] [depth= 2] . ( 3 sec) [ -14646.4684] [ 3572] [depth= 1] . ( 3 sec) [ -14421.7945] [ 3465] [depth= 3] . ( 3 sec) [ -14045.2867] [ 3334] [depth= 12] . ( 3 sec) [ -13971.3582] [ 3343] [depth= 6] . ( 3 sec) [ -13682.6047] [ 3298] [depth= 6] . ( 3 sec) [ -13427.8954] [ 3234] [depth= 5] . ( 3 sec) [ -13424.2621] [ 3229] [depth= 2] . ( 3 sec) [ -13367.4032] [ 3211] [depth= 2] . ( 3 sec) [ -13137.4151] [ 3127] [depth= 3] . ( 3 sec) [ -13050.6577] [ 3114] [depth= 1] . ( 3 sec) [ -12850.3219] [ 3047] [depth= 6] . ( 3 sec) [ -12795.9038] [ 3048] [depth= 1] . ( 3 sec) [ -12789.3437] [ 3047] [depth= 1] . ( 4 sec) [ -12693.8254] [ 3034] [depth= 5] . ( 4 sec) [ -12653.6444] [ 3029] [depth= 1] . ( 4 sec) [ -12549.7592] [ 2968] [depth= 6] . ( 4 sec) [ -12479.2811] [ 2970] [depth= 1] . ( 4 sec) [ -12304.4104] [ 2931] [depth= 6] . ( 4 sec) [ -12300.5345] [ 2929] [depth= 1] . ( 4 sec) [ -12252.5919] [ 2923] [depth= 5] . ( 4 sec) [ -12097.8566] [ 2901] [depth= 1] . ( 4 sec) [ -12040.5493] [ 2915] [depth= 1] . ( 4 sec) [ -12017.4236] [ 2922] [depth= 1] . ( 4 sec) [ -11946.4116] [ 2889] [depth= 1] . ( 4 sec) [ -11926.3138] [ 2841] [depth= 4] . ( 4 sec) [ -11865.0094] [ 2780] [depth= 1] . ( 4 sec) [ -11845.1325] [ 2766] [depth= 2] . ( 4 sec) [ -11811.3423] [ 2748] [depth= 1] . ( 4 sec) [ -11777.5451] [ 2741] [depth= 1] . ( 4 sec) [ -11699.8322] [ 2718] [depth= 3] . ( 4 sec) [ -11669.4326] [ 2710] [depth= 1] . ( 5 sec) [ -11646.4539] [ 2711] [depth= 1] . ( 5 sec) [ -11643.3443] [ 2710] [depth= 1] . ( 5 sec) [ -11488.8279] [ 2650] [depth= 2] . ( 5 sec) [ -11483.0972] [ 2647] [depth= 1] . ( 5 sec) [ -11477.3214] [ 2630] [depth= 1] . ( 5 sec) [ -11442.9335] [ 2623] [depth= 3] . ( 5 sec) [ -11435.2004] [ 2625] [depth= 1] . ( 5 sec) [ -11432.6974] [ 2632] [depth= 1] . ( 5 sec) [ -11429.6305] [ 2629] [depth= 3] . ( 5 sec) [ -11424.5623] [ 2624] [depth= 1] . ( 5 sec) [ -11409.8183] [ 2629] [depth= 2] . ( 5 sec) [ -11398.6742] [ 2626] [depth= 3] . ( 5 sec) [ -11237.5788] [Branch lengths ] . ( 6 sec) [ -11236.1542] [GTR parameters ] . ( 6 sec) [ -11200.9470] [Alpha ][ 0.883289] . ( 6 sec) [ -11200.1451] [ 2631] [depth= 2] . ( 6 sec) [ -11199.3398] [ 2632] [depth= 1] . ( 6 sec) [ -11198.7274] [ 2631] [depth= 1] . ( 7 sec) [ -11188.5379] [ 2614] [depth= 3] . ( 7 sec) [ -11187.0653] [ 2607] [depth= 1] . ( 7 sec) [ -11186.4433] [ 2562] [depth= 2] . ( 7 sec) [ -11175.3679] [ 2548] [depth= 1] . ( 7 sec) [ -11101.7402] [ 2551] [depth= 1] . ( 7 sec) [ -11097.1897] [ 2555] [depth= 1] . ( 7 sec) [ -11095.6116] [ 2559] [depth= 1] . ( 7 sec) [ -11095.3490] [ 2563] [depth= 1] . ( 8 sec) [ -11094.9634] [ 2567] [depth= 1] . ( 8 sec) [ -11089.9766] [ 2566] [depth= 2] . ( 8 sec) [ -11086.2888] [ 2568] [depth= 1] . ( 8 sec) [ -11079.1960] [ 2569] [depth= 1] . ( 9 sec) [ -11078.0838] [ 2568] [depth= 1] . ( 9 sec) [ -11077.5442] [ 2564] [depth= 1] . ( 9 sec) [ -11063.3998] [Branch lengths ] . ( 9 sec) [ -11063.2296] [GTR parameters ] . ( 10 sec) [ -11062.9576] [Alpha ][ 0.928702] . ( 10 sec) [ -11062.0489] [ 2553] [depth= 2] . ( 10 sec) [ -11061.0223] [ 2554] [depth= 1] . ( 10 sec) [ -11060.7737] [ 2553] [depth= 1] . ( 11 sec) [ -11060.6882] [ 2553] [depth= 1] . ( 13 sec) [ -11057.9731] [Branch lengths ] . ( 13 sec) [ -11057.9677] [GTR parameters ] . ( 13 sec) [ -11057.9537] [Alpha ][ 0.939621] . ( 16 sec) [ -11057.7944] [Branch lengths ] . ( 35 sec) [ -11057.7726] [Branch lengths ] . ( 35 sec) [ -11057.7726] [Topology ] . ( 36 sec) [ -11057.5327] [Topology ] . ( 37 sec) [ -11057.3117] [Topology ] . ( 38 sec) [ -11057.2694] [Topology ] . ( 39 sec) [ -11057.2558] [Topology ] . ( 40 sec) [ -11057.2505] [Topology ] . ( 40 sec) [ -11057.2483] [Topology ] . ( 41 sec) [ -11057.2474] [Topology ] . ( 41 sec) [ -11057.2460] [GTR parameters ] . ( 41 sec) [ -11057.2448] [Alpha ][ 0.942703] . ( 41 sec) [ -11057.2448] [Topology ] . ( 42 sec) [ -11057.2444] [Topology ] . ( 42 sec) [ -11057.2444] [GTR parameters ] . ( 43 sec) [ -11057.2444] [Alpha ][ 0.942703] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11057.2442] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11057.244207. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21675.2930] [GTR parameters ] . ( 1 sec) [ -21293.9614] [Alpha ][ 0.500960] . ( 1 sec) [ -21032.2637] [ 5146] [depth= 8] . ( 1 sec) [ -20506.7072] [ 5065] [depth= 9] . ( 1 sec) [ -20288.3677] [ 5022] [depth= 8] . ( 1 sec) [ -20185.9667] [ 4989] [depth= 1] . ( 1 sec) [ -19875.9128] [ 4924] [depth= 9] . ( 1 sec) [ -19851.3016] [ 4902] [depth= 3] . ( 1 sec) [ -19750.4080] [ 4884] [depth= 5] . ( 1 sec) [ -19540.3078] [ 4767] [depth= 6] . ( 1 sec) [ -19523.3571] [ 4764] [depth= 8] . ( 2 sec) [ -19377.4608] [ 4725] [depth= 7] . ( 2 sec) [ -19074.0989] [ 4748] [depth= 3] . ( 2 sec) [ -18712.5793] [ 4646] [depth= 4] . ( 2 sec) [ -18331.3516] [ 4547] [depth= 4] . ( 2 sec) [ -18204.6496] [ 4539] [depth= 2] . ( 2 sec) [ -17966.3537] [ 4498] [depth= 8] . ( 2 sec) [ -17819.8697] [ 4490] [depth= 2] . ( 2 sec) [ -17787.1295] [ 4429] [depth= 1] . ( 2 sec) [ -17352.5818] [ 4305] [depth= 5] . ( 2 sec) [ -17318.5328] [ 4302] [depth= 1] . ( 2 sec) [ -17201.2634] [ 4283] [depth= 10] . ( 2 sec) [ -17195.2012] [ 4258] [depth= 2] . ( 2 sec) [ -17106.2440] [ 4265] [depth= 4] . ( 2 sec) [ -16507.3822] [ 4305] [depth= 18] . ( 2 sec) [ -16173.5133] [ 4174] [depth= 9] . ( 2 sec) [ -16049.6355] [ 4109] [depth= 1] . ( 2 sec) [ -15939.0330] [ 4096] [depth= 7] . ( 2 sec) [ -15937.9151] [ 4115] [depth= 1] . ( 3 sec) [ -15660.9517] [ 4013] [depth= 6] . ( 3 sec) [ -15523.7612] [ 3982] [depth= 1] . ( 3 sec) [ -15422.4573] [ 3943] [depth= 2] . ( 3 sec) [ -15306.7381] [ 3907] [depth= 1] . ( 3 sec) [ -15192.2927] [ 3843] [depth= 1] . ( 3 sec) [ -14886.7205] [ 3766] [depth= 13] . ( 3 sec) [ -14847.2976] [ 3753] [depth= 1] . ( 3 sec) [ -14843.6465] [ 3752] [depth= 1] . ( 3 sec) [ -14718.8147] [ 3708] [depth= 1] . ( 3 sec) [ -14582.4859] [ 3665] [depth= 15] . ( 3 sec) [ -14460.7964] [ 3644] [depth= 1] . ( 3 sec) [ -14349.8201] [ 3627] [depth= 1] . ( 3 sec) [ -14175.4526] [ 3573] [depth= 4] . ( 3 sec) [ -14147.3105] [ 3578] [depth= 1] . ( 3 sec) [ -13901.3484] [ 3470] [depth= 8] . ( 3 sec) [ -13795.5811] [ 3473] [depth= 3] . ( 3 sec) [ -13623.0640] [ 3434] [depth= 13] . ( 3 sec) [ -13456.8780] [ 3333] [depth= 12] . ( 3 sec) [ -13366.8054] [ 3293] [depth= 1] . ( 3 sec) [ -13363.5963] [ 3300] [depth= 2] . ( 4 sec) [ -13150.2847] [ 3271] [depth= 3] . ( 4 sec) [ -13136.3323] [ 3272] [depth= 1] . ( 4 sec) [ -13118.9544] [ 3269] [depth= 2] . ( 4 sec) [ -13024.5723] [ 3204] [depth= 7] . ( 4 sec) [ -12900.0535] [ 3176] [depth= 2] . ( 4 sec) [ -12885.2799] [ 3161] [depth= 1] . ( 4 sec) [ -12839.4738] [ 3150] [depth= 1] . ( 4 sec) [ -12736.8332] [ 3104] [depth= 2] . ( 4 sec) [ -12657.6409] [ 3071] [depth= 3] . ( 4 sec) [ -12593.9077] [ 3031] [depth= 5] . ( 4 sec) [ -12119.6630] [ 2860] [depth= 5] . ( 4 sec) [ -12085.7073] [ 2862] [depth= 1] . ( 4 sec) [ -12043.4843] [ 2823] [depth= 3] . ( 4 sec) [ -12026.1818] [ 2806] [depth= 1] . ( 4 sec) [ -12021.9670] [ 2809] [depth= 1] . ( 4 sec) [ -11876.9956] [ 2796] [depth= 1] . ( 4 sec) [ -11791.5365] [ 2751] [depth= 1] . ( 5 sec) [ -11791.3924] [ 2759] [depth= 1] . ( 5 sec) [ -11665.8675] [ 2716] [depth= 1] . ( 5 sec) [ -11656.6277] [ 2727] [depth= 1] . ( 5 sec) [ -11477.4507] [ 2637] [depth= 3] . ( 5 sec) [ -11453.2685] [ 2647] [depth= 2] . ( 5 sec) [ -11449.0131] [ 2638] [depth= 2] . ( 5 sec) [ -11440.8233] [ 2631] [depth= 1] . ( 5 sec) [ -11413.3414] [ 2622] [depth= 3] . ( 5 sec) [ -11379.4253] [ 2606] [depth= 1] . ( 5 sec) [ -11354.7265] [ 2589] [depth= 1] . ( 5 sec) [ -11350.2871] [ 2588] [depth= 1] . ( 5 sec) [ -11343.5800] [ 2585] [depth= 1] . ( 5 sec) [ -11315.5272] [ 2574] [depth= 1] . ( 5 sec) [ -11306.5334] [ 2572] [depth= 2] . ( 5 sec) [ -11303.8636] [ 2569] [depth= 1] . ( 5 sec) [ -11299.3759] [ 2590] [depth= 1] . ( 6 sec) [ -11269.5571] [ 2578] [depth= 1] . ( 6 sec) [ -11264.0064] [ 2578] [depth= 1] . ( 6 sec) [ -11255.7527] [ 2600] [depth= 1] . ( 6 sec) [ -11246.9671] [ 2604] [depth= 1] . ( 6 sec) [ -11153.8469] [Branch lengths ] . ( 7 sec) [ -11153.2160] [GTR parameters ] . ( 7 sec) [ -11122.1301] [Alpha ][ 0.857029] . ( 7 sec) [ -11103.4556] [ 2582] [depth= 1] . ( 7 sec) [ -11100.0973] [ 2583] [depth= 1] . ( 7 sec) [ -11097.1489] [ 2580] [depth= 1] . ( 7 sec) [ -11096.5062] [ 2581] [depth= 1] . ( 7 sec) [ -11096.1887] [ 2580] [depth= 1] . ( 8 sec) [ -11093.5953] [ 2579] [depth= 2] . ( 8 sec) [ -11082.6879] [ 2558] [depth= 1] . ( 9 sec) [ -11080.8271] [ 2555] [depth= 1] . ( 9 sec) [ -11078.6309] [ 2556] [depth= 1] . ( 9 sec) [ -11078.4960] [ 2555] [depth= 1] . ( 9 sec) [ -11077.2725] [ 2556] [depth= 1] . ( 10 sec) [ -11062.0097] [Branch lengths ] . ( 10 sec) [ -11061.8970] [GTR parameters ] . ( 10 sec) [ -11061.3107] [Alpha ][ 0.923316] . ( 11 sec) [ -11061.2676] [ 2558] [depth= 1] . ( 11 sec) [ -11061.1539] [ 2558] [depth= 1] . ( 11 sec) [ -11060.9953] [ 2558] [depth= 1] . ( 12 sec) [ -11060.4118] [ 2555] [depth= 1] . ( 12 sec) [ -11060.3916] [ 2554] [depth= 1] . ( 13 sec) [ -11057.8791] [Branch lengths ] . ( 14 sec) [ -11057.8762] [GTR parameters ] . ( 14 sec) [ -11057.8517] [Alpha ][ 0.937718] . ( 17 sec) [ -11057.6783] [Branch lengths ] . ( 34 sec) [ -11057.6274] [ 2561] [depth= 1] . ( 36 sec) [ -11057.6045] [Branch lengths ] . ( 36 sec) [ -11057.6041] [GTR parameters ] . ( 36 sec) [ -11057.6025] [Alpha ][ 0.941377] . ( 36 sec) [ -11057.6025] [Topology ] . ( 37 sec) [ -11057.3790] [Topology ] . ( 38 sec) [ -11057.2911] [Topology ] . ( 39 sec) [ -11057.2653] [Topology ] . ( 39 sec) [ -11057.2546] [Topology ] . ( 40 sec) [ -11057.2499] [Topology ] . ( 41 sec) [ -11057.2478] [Topology ] . ( 42 sec) [ -11057.2469] [Topology ] . ( 42 sec) [ -11057.2452] [GTR parameters ] . ( 42 sec) [ -11057.2450] [Alpha ][ 0.942736] . ( 42 sec) [ -11057.2450] [Topology ] . ( 43 sec) [ -11057.2445] [Topology ] . ( 43 sec) [ -11057.2445] [GTR parameters ] . ( 43 sec) [ -11057.2445] [Alpha ][ 0.942736] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -11057.2278] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11057.227833. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22007.3231] [GTR parameters ] . ( 1 sec) [ -21564.2054] [Alpha ][ 0.500960] . ( 1 sec) [ -21108.4184] [ 5335] [depth= 6] . ( 1 sec) [ -20480.3322] [ 5227] [depth= 11] . ( 1 sec) [ -20345.9463] [ 5185] [depth= 3] . ( 1 sec) [ -20193.9560] [ 5185] [depth= 1] . ( 1 sec) [ -20080.5821] [ 5118] [depth= 2] . ( 1 sec) [ -19972.4746] [ 5087] [depth= 6] . ( 1 sec) [ -19964.9361] [ 5117] [depth= 1] . ( 1 sec) [ -19435.7380] [ 5033] [depth= 5] . ( 1 sec) [ -18997.5568] [ 4936] [depth= 3] . ( 1 sec) [ -18822.0810] [ 4841] [depth= 10] . ( 2 sec) [ -18357.3795] [ 4720] [depth= 18] . ( 2 sec) [ -18112.3040] [ 4642] [depth= 10] . ( 2 sec) [ -17975.6680] [ 4605] [depth= 3] . ( 2 sec) [ -17905.7370] [ 4593] [depth= 3] . ( 2 sec) [ -17824.5336] [ 4591] [depth= 1] . ( 2 sec) [ -17644.3080] [ 4542] [depth= 8] . ( 2 sec) [ -17494.7158] [ 4468] [depth= 3] . ( 2 sec) [ -17265.8451] [ 4436] [depth= 5] . ( 2 sec) [ -17198.1815] [ 4426] [depth= 1] . ( 2 sec) [ -16848.2523] [ 4408] [depth= 6] . ( 2 sec) [ -16467.0636] [ 4253] [depth= 6] . ( 2 sec) [ -16238.0454] [ 4221] [depth= 2] . ( 2 sec) [ -16078.3171] [ 4141] [depth= 5] . ( 2 sec) [ -16039.1707] [ 4144] [depth= 1] . ( 2 sec) [ -16010.0633] [ 4146] [depth= 1] . ( 2 sec) [ -15860.3157] [ 4062] [depth= 6] . ( 2 sec) [ -15771.9440] [ 4022] [depth= 5] . ( 2 sec) [ -15751.2381] [ 4020] [depth= 1] . ( 2 sec) [ -15747.7561] [ 4028] [depth= 1] . ( 2 sec) [ -15639.1038] [ 3998] [depth= 12] . ( 2 sec) [ -15248.0810] [ 3870] [depth= 6] . ( 2 sec) [ -15238.9862] [ 3871] [depth= 1] . ( 2 sec) [ -15180.0190] [ 3840] [depth= 2] . ( 3 sec) [ -15124.3512] [ 3836] [depth= 2] . ( 3 sec) [ -14915.7336] [ 3801] [depth= 8] . ( 3 sec) [ -14835.8075] [ 3735] [depth= 1] . ( 3 sec) [ -14780.7163] [ 3713] [depth= 8] . ( 3 sec) [ -14768.3630] [ 3706] [depth= 1] . ( 3 sec) [ -14657.9770] [ 3775] [depth= 1] . ( 3 sec) [ -14435.2209] [ 3677] [depth= 5] . ( 3 sec) [ -14430.2273] [ 3681] [depth= 1] . ( 3 sec) [ -14347.3557] [ 3625] [depth= 4] . ( 3 sec) [ -14038.3462] [ 3443] [depth= 16] . ( 3 sec) [ -14015.6264] [ 3461] [depth= 1] . ( 3 sec) [ -13762.6213] [ 3407] [depth= 11] . ( 3 sec) [ -13599.8244] [ 3349] [depth= 12] . ( 3 sec) [ -13400.4635] [ 3273] [depth= 4] . ( 3 sec) [ -13389.7159] [ 3281] [depth= 4] . ( 3 sec) [ -13003.1420] [ 3197] [depth= 2] . ( 3 sec) [ -13000.8600] [ 3208] [depth= 1] . ( 3 sec) [ -12959.7859] [ 3205] [depth= 1] . ( 3 sec) [ -12914.5971] [ 3177] [depth= 3] . ( 4 sec) [ -12784.7730] [ 3123] [depth= 1] . ( 4 sec) [ -12630.3024] [ 3105] [depth= 4] . ( 4 sec) [ -12542.1406] [ 3076] [depth= 4] . ( 4 sec) [ -12522.8263] [ 3047] [depth= 2] . ( 4 sec) [ -12511.5736] [ 3046] [depth= 9] . ( 4 sec) [ -12506.7362] [ 3045] [depth= 1] . ( 4 sec) [ -12432.9514] [ 3041] [depth= 4] . ( 4 sec) [ -12363.6658] [ 3020] [depth= 1] . ( 4 sec) [ -12361.0809] [ 3010] [depth= 1] . ( 4 sec) [ -12300.3529] [ 2992] [depth= 5] . ( 4 sec) [ -12152.8312] [ 2896] [depth= 7] . ( 4 sec) [ -12021.3699] [ 2899] [depth= 1] . ( 4 sec) [ -12015.7711] [ 2900] [depth= 1] . ( 4 sec) [ -11978.8748] [ 2894] [depth= 2] . ( 4 sec) [ -11953.8205] [ 2876] [depth= 2] . ( 4 sec) [ -11872.4569] [ 2858] [depth= 1] . ( 5 sec) [ -11816.6866] [ 2820] [depth= 3] . ( 5 sec) [ -11813.1062] [ 2810] [depth= 2] . ( 5 sec) [ -11757.6733] [ 2824] [depth= 1] . ( 5 sec) [ -11705.2455] [ 2796] [depth= 1] . ( 5 sec) [ -11649.2590] [ 2779] [depth= 7] . ( 5 sec) [ -11621.2994] [ 2781] [depth= 1] . ( 5 sec) [ -11494.5440] [Branch lengths ] . ( 6 sec) [ -11493.8100] [GTR parameters ] . ( 6 sec) [ -11469.3209] [Alpha ][ 0.807428] . ( 6 sec) [ -11469.1798] [ 2778] [depth= 1] . ( 6 sec) [ -11348.9689] [ 2694] [depth= 4] . ( 6 sec) [ -11338.4461] [ 2692] [depth= 4] . ( 6 sec) [ -11336.0599] [ 2691] [depth= 1] . ( 6 sec) [ -11241.5213] [ 2649] [depth= 4] . ( 7 sec) [ -11230.5509] [ 2643] [depth= 3] . ( 7 sec) [ -11229.8576] [ 2645] [depth= 1] . ( 7 sec) [ -11227.2535] [ 2604] [depth= 1] . ( 7 sec) [ -11226.2959] [ 2567] [depth= 1] . ( 7 sec) [ -11225.9761] [ 2568] [depth= 1] . ( 7 sec) [ -11221.6855] [ 2568] [depth= 1] . ( 7 sec) [ -11203.6653] [ 2560] [depth= 3] . ( 7 sec) [ -11194.8003] [ 2565] [depth= 1] . ( 8 sec) [ -11193.8700] [ 2564] [depth= 2] . ( 8 sec) [ -11193.6853] [ 2569] [depth= 1] . ( 8 sec) [ -11165.1081] [ 2561] [depth= 2] . ( 8 sec) [ -11163.3637] [ 2561] [depth= 1] . ( 8 sec) [ -11139.1709] [ 2564] [depth= 3] . ( 8 sec) [ -11123.6406] [ 2564] [depth= 2] . ( 8 sec) [ -11115.1284] [ 2560] [depth= 1] . ( 8 sec) [ -11108.2612] [ 2554] [depth= 1] . ( 9 sec) [ -11107.8114] [ 2550] [depth= 1] . ( 9 sec) [ -11106.2701] [ 2558] [depth= 1] . ( 9 sec) [ -11105.1022] [ 2561] [depth= 1] . ( 9 sec) [ -11068.3381] [Branch lengths ] . ( 10 sec) [ -11068.2691] [GTR parameters ] . ( 10 sec) [ -11066.8426] [Alpha ][ 0.907628] . ( 10 sec) [ -11066.0577] [ 2556] [depth= 1] . ( 10 sec) [ -11066.0146] [ 2560] [depth= 1] . ( 11 sec) [ -11063.3493] [ 2552] [depth= 1] . ( 12 sec) [ -11062.2587] [ 2557] [depth= 1] . ( 13 sec) [ -11058.6212] [Branch lengths ] . ( 13 sec) [ -11058.6173] [GTR parameters ] . ( 13 sec) [ -11058.5521] [Alpha ][ 0.930096] . ( 16 sec) [ -11057.9147] [Branch lengths ] . ( 36 sec) [ -11057.8051] [Branch lengths ] . ( 36 sec) [ -11057.8051] [Topology ] . ( 37 sec) [ -11057.5609] [Topology ] . ( 38 sec) [ -11057.4666] [Topology ] . ( 39 sec) [ -11057.4389] [Topology ] . ( 40 sec) [ -11057.4275] [Topology ] . ( 40 sec) [ -11057.4227] [Topology ] . ( 41 sec) [ -11057.4206] [Topology ] . ( 42 sec) [ -11057.4196] [Topology ] . ( 42 sec) [ -11057.4166] [GTR parameters ] . ( 42 sec) [ -11057.3981] [Alpha ][ 0.942620] . ( 42 sec) [ -11057.3981] [Topology ] . ( 43 sec) [ -11057.3967] [Topology ] . ( 44 sec) [ -11057.3964] [Topology ] . ( 44 sec) [ -11057.3964] [GTR parameters ] . ( 44 sec) [ -11057.3964] [Alpha ][ 0.942620] . ( 44 sec) [ -11057.3964] [Topology ] . ( 45 sec) [ -11057.3962] [Topology ] . ( 45 sec) [ -11057.3962] [GTR parameters ] . ( 45 sec) [ -11057.3962] [Alpha ][ 0.942620] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -11057.2686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -11057.2664] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11057.266372. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11139.762588 . ( 1 sec) [ -11134.8438] [GTR parameters ] . ( 1 sec) [ -11133.7157] [Alpha ][ 0.897560] . ( 1 sec) [ -11133.7157] [Topology ] . ( 2 sec) [ -11071.6927] [Topology ] . ( 3 sec) [ -11062.4220] [Topology ] . ( 4 sec) [ -11059.6633] [Topology ] . ( 5 sec) [ -11058.5159] [Topology ] . ( 5 sec) [ -11057.9695] [Topology ] . ( 6 sec) [ -11057.7608] [Topology ] . ( 7 sec) [ -11057.6626] [Topology ] . ( 8 sec) [ -11057.6133] [Topology ] . ( 9 sec) [ -11057.5878] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.574544 . ( 17 sec) [ -11057.4909] [GTR parameters ] . ( 17 sec) [ -11057.2749] [Alpha ][ 0.939065] . ( 17 sec) [ -11057.2749] [Topology ] . ( 18 sec) [ -11057.2482] [Topology ] . ( 19 sec) [ -11057.2386] [Topology ] . ( 19 sec) [ -11057.2339] [Topology ] . ( 20 sec) [ -11057.2316] [Topology ] . ( 21 sec) [ -11057.2304] [Topology ] . ( 22 sec) [ -11057.2297] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.229712 . ( 29 sec) [ -11057.2296] [GTR parameters ] . ( 29 sec) [ -11057.2280] [Alpha ][ 0.942620] . ( 29 sec) [ -11057.2280] [Topology ] . ( 30 sec) [ -11057.2275] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.227516 . ( 37 sec) [ -11057.2275] [GTR parameters ] . ( 37 sec) [ -11057.2275] [Alpha ][ 0.942620] . ( 37 sec) [ -11057.2275] [Topology ] . ( 37 sec) [ -11057.2273] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -11134.8438] [GTR parameters ] . ( 52 sec) [ -11133.7157] [Alpha ][ 0.897560] . ( 52 sec) [ -11125.5894] [ 2561] [depth= 1] . ( 53 sec) [ -11123.1740] [ 2569] [depth= 1] . ( 53 sec) [ -11123.0787] [ 2573] [depth= 1] . ( 53 sec) [ -11120.7119] [ 2569] [depth= 1] . ( 53 sec) [ -11119.8083] [ 2574] [depth= 1] . ( 53 sec) [ -11113.5648] [ 2569] [depth= 1] . ( 53 sec) [ -11113.0493] [ 2567] [depth= 1] . ( 53 sec) [ -11111.2409] [ 2566] [depth= 1] . ( 54 sec) [ -11111.1637] [ 2570] [depth= 1] . ( 54 sec) [ -11103.3330] [ 2575] [depth= 1] . ( 54 sec) [ -11102.3404] [ 2575] [depth= 1] . ( 54 sec) [ -11096.4944] [ 2580] [depth= 1] . ( 54 sec) [ -11095.2693] [ 2581] [depth= 1] . ( 54 sec) [ -11094.8994] [ 2582] [depth= 1] . ( 55 sec) [ -11091.3796] [ 2584] [depth= 1] . ( 55 sec) [ -11090.2215] [ 2587] [depth= 1] . ( 55 sec) [ -11090.0575] [ 2592] [depth= 1] . ( 55 sec) [ -11067.7339] [Branch lengths ] . ( 56 sec) [ -11067.5809] [GTR parameters ] . ( 56 sec) [ -11067.4411] [Alpha ][ 0.930639] . ( 56 sec) [ -11066.6179] [ 2582] [depth= 1] . ( 57 sec) [ -11066.2286] [ 2578] [depth= 1] . ( 58 sec) [ -11066.0335] [ 2573] [depth= 1] . ( 58 sec) [ -11065.9066] [ 2572] [depth= 1] . ( 58 sec) [ -11065.8336] [ 2565] [depth= 1] . ( 59 sec) [ -11065.6937] [ 2560] [depth= 1] . ( 59 sec) [ -11065.2189] [ 2563] [depth= 1] . ( 59 sec) [ -11058.9520] [Branch lengths ] . ( 59 sec) [ -11058.9407] [GTR parameters ] . ( 59 sec) [ -11058.9340] [Alpha ][ 0.938137] . ( 63 sec) [ -11058.2824] [Branch lengths ] . ( 83 sec) [ -11058.2307] [Branch lengths ] . ( 83 sec) [ -11058.2307] [Topology ] . ( 83 sec) [ -11057.7048] [Topology ] . ( 84 sec) [ -11057.4067] [Topology ] . ( 85 sec) [ -11057.3452] [Topology ] . ( 86 sec) [ -11057.3231] [Topology ] . ( 87 sec) [ -11057.3145] [Topology ] . ( 87 sec) [ -11057.3110] [Topology ] . ( 88 sec) [ -11057.3095] [Topology ] . ( 88 sec) [ -11057.3075] [GTR parameters ] . ( 88 sec) [ -11057.3051] [Alpha ][ 0.942669] . ( 88 sec) [ -11057.3051] [Topology ] . ( 89 sec) [ -11057.3043] [Topology ] . ( 89 sec) [ -11057.3043] [GTR parameters ] . ( 89 sec) [ -11057.3043] [Alpha ][ 0.942669] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -11057.2458] [Topology ] . Checking for NNIs, optimizing five branches... . ( 103 sec) [ -11057.2456] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11057.227268 . Log likelihood obtained after SPR moves : -11057.245610 . Log likelihood of the current tree: -11057.227268. . Printing the most likely tree in file 'data23.phy_phyml_tree.txt'... . Best log likelihood : -11057.227268 . Time used 0h1m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo