.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data2.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... . 454 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . [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) [ -24602.8638] [GTR parameters ] . ( 1 sec) [ -24138.8461] [Alpha ][ 0.500960] . ( 1 sec) [ -23326.8313] [ 4909] [depth= 8] . ( 1 sec) [ -22714.1174] [ 4887] [depth= 13] . ( 1 sec) [ -22639.6981] [ 4876] [depth= 1] . ( 1 sec) [ -22415.1234] [ 4857] [depth= 7] . ( 1 sec) [ -21979.5240] [ 4830] [depth= 3] . ( 1 sec) [ -21388.0076] [ 4798] [depth= 10] . ( 1 sec) [ -21202.0151] [ 4756] [depth= 3] . ( 1 sec) [ -21136.3217] [ 4769] [depth= 1] . ( 1 sec) [ -20674.0605] [ 4652] [depth= 6] . ( 1 sec) [ -20143.0257] [ 4529] [depth= 7] . ( 1 sec) [ -19932.6061] [ 4408] [depth= 9] . ( 1 sec) [ -19456.5150] [ 4326] [depth= 13] . ( 2 sec) [ -18990.6262] [ 4252] [depth= 16] . ( 2 sec) [ -18961.3327] [ 4244] [depth= 2] . ( 2 sec) [ -18767.8461] [ 4225] [depth= 4] . ( 2 sec) [ -18711.1381] [ 4217] [depth= 1] . ( 2 sec) [ -18678.3480] [ 4215] [depth= 3] . ( 2 sec) [ -18525.9012] [ 4182] [depth= 3] . ( 2 sec) [ -18352.2029] [ 4195] [depth= 1] . ( 2 sec) [ -17797.2191] [ 4116] [depth= 2] . ( 2 sec) [ -17119.6223] [ 4094] [depth= 2] . ( 2 sec) [ -16976.8537] [ 4065] [depth= 4] . ( 2 sec) [ -16879.8166] [ 4050] [depth= 14] . ( 2 sec) [ -16850.1581] [ 4047] [depth= 3] . ( 2 sec) [ -16496.7472] [ 4039] [depth= 1] . ( 2 sec) [ -16401.2521] [ 4013] [depth= 4] . ( 2 sec) [ -15989.4071] [ 3904] [depth= 17] . ( 2 sec) [ -15556.1091] [ 3908] [depth= 5] . ( 2 sec) [ -15473.7596] [ 3901] [depth= 3] . ( 2 sec) [ -15288.0531] [ 3838] [depth= 5] . ( 2 sec) [ -15282.1013] [ 3828] [depth= 1] . ( 2 sec) [ -15023.9315] [ 3750] [depth= 6] . ( 2 sec) [ -15022.7683] [ 3764] [depth= 8] . ( 2 sec) [ -14831.8750] [ 3726] [depth= 12] . ( 3 sec) [ -14511.5988] [ 3699] [depth= 1] . ( 3 sec) [ -14333.9760] [ 3634] [depth= 2] . ( 3 sec) [ -13747.3772] [ 3498] [depth= 5] . ( 3 sec) [ -13711.3102] [ 3486] [depth= 4] . ( 3 sec) [ -13550.3184] [ 3455] [depth= 2] . ( 3 sec) [ -13430.4190] [ 3431] [depth= 2] . ( 3 sec) [ -13237.7423] [ 3306] [depth= 12] . ( 3 sec) [ -13066.5477] [ 3263] [depth= 8] . ( 3 sec) [ -13048.5523] [ 3250] [depth= 1] . ( 3 sec) [ -12975.8252] [ 3218] [depth= 14] . ( 3 sec) [ -12780.2119] [ 3223] [depth= 1] . ( 3 sec) [ -12674.3205] [ 3218] [depth= 1] . ( 3 sec) [ -12634.4674] [ 3185] [depth= 2] . ( 3 sec) [ -12567.2247] [ 3169] [depth= 10] . ( 3 sec) [ -12540.7975] [ 3160] [depth= 2] . ( 3 sec) [ -12501.5487] [ 3171] [depth= 1] . ( 3 sec) [ -12180.2481] [ 3044] [depth= 9] . ( 3 sec) [ -12097.5998] [ 3039] [depth= 1] . ( 4 sec) [ -11968.8688] [ 3026] [depth= 6] . ( 4 sec) [ -11953.8247] [ 3009] [depth= 7] . ( 4 sec) [ -11865.3690] [ 3022] [depth= 1] . ( 4 sec) [ -11824.0492] [ 3005] [depth= 1] . ( 4 sec) [ -11651.2567] [ 2899] [depth= 1] . ( 4 sec) [ -11206.8738] [ 2733] [depth= 5] . ( 4 sec) [ -11179.8273] [ 2730] [depth= 1] . ( 4 sec) [ -11156.0669] [ 2734] [depth= 1] . ( 4 sec) [ -11101.8833] [ 2737] [depth= 1] . ( 4 sec) [ -11025.9026] [ 2704] [depth= 1] . ( 4 sec) [ -10953.8290] [ 2665] [depth= 5] . ( 4 sec) [ -10917.0448] [ 2651] [depth= 1] . ( 4 sec) [ -10872.6113] [ 2637] [depth= 1] . ( 4 sec) [ -10862.3418] [ 2628] [depth= 2] . ( 4 sec) [ -10840.6885] [ 2600] [depth= 1] . ( 4 sec) [ -10683.8573] [ 2591] [depth= 2] . ( 4 sec) [ -10583.4608] [ 2574] [depth= 2] . ( 4 sec) [ -10560.7762] [ 2535] [depth= 2] . ( 4 sec) [ -10340.4804] [ 2455] [depth= 3] . ( 5 sec) [ -10336.8054] [ 2457] [depth= 1] . ( 5 sec) [ -10323.9757] [ 2457] [depth= 1] . ( 5 sec) [ -10223.5390] [ 2430] [depth= 1] . ( 5 sec) [ -10218.9251] [ 2424] [depth= 1] . ( 5 sec) [ -10217.6100] [ 2424] [depth= 1] . ( 5 sec) [ -10210.6991] [ 2422] [depth= 1] . ( 5 sec) [ -10204.9548] [ 2397] [depth= 4] . ( 5 sec) [ -10203.4833] [ 2398] [depth= 1] . ( 5 sec) [ -10189.5448] [ 2392] [depth= 1] . ( 5 sec) [ -10000.1609] [Branch lengths ] . ( 6 sec) [ -9995.0337] [GTR parameters ] . ( 6 sec) [ -9943.0054] [Alpha ][ 1.000268] . ( 6 sec) [ -9942.7682] [ 2393] [depth= 1] . ( 6 sec) [ -9939.9004] [ 2376] [depth= 2] . ( 6 sec) [ -9837.5034] [ 2315] [depth= 1] . ( 6 sec) [ -9835.7123] [ 2315] [depth= 1] . ( 6 sec) [ -9827.7532] [ 2313] [depth= 1] . ( 6 sec) [ -9806.1087] [ 2288] [depth= 2] . ( 7 sec) [ -9801.1887] [ 2278] [depth= 2] . ( 7 sec) [ -9800.5361] [ 2278] [depth= 1] . ( 7 sec) [ -9797.0390] [ 2283] [depth= 1] . ( 7 sec) [ -9794.4260] [ 2277] [depth= 1] . ( 7 sec) [ -9762.9571] [ 2242] [depth= 1] . ( 7 sec) [ -9760.8432] [ 2237] [depth= 1] . ( 7 sec) [ -9749.9094] [ 2254] [depth= 1] . ( 8 sec) [ -9741.0436] [ 2237] [depth= 1] . ( 9 sec) [ -9740.5519] [ 2242] [depth= 1] . ( 9 sec) [ -9728.0817] [Branch lengths ] . ( 10 sec) [ -9727.7505] [GTR parameters ] . ( 10 sec) [ -9725.4838] [Alpha ][ 1.170408] . ( 12 sec) [ -9724.0644] [Branch lengths ] . ( 33 sec) [ -9723.8980] [Branch lengths ] . ( 33 sec) [ -9723.8980] [Topology ] . ( 34 sec) [ -9723.8819] [Topology ] . ( 35 sec) [ -9723.8766] [Topology ] . ( 36 sec) [ -9723.8742] [Topology ] . ( 37 sec) [ -9723.8730] [Topology ] . ( 38 sec) [ -9723.8724] [Topology ] . ( 38 sec) [ -9723.8711] [GTR parameters ] . ( 38 sec) [ -9723.8614] [Alpha ][ 1.182610] . ( 38 sec) [ -9723.8614] [Topology ] . ( 39 sec) [ -9723.8607] [Topology ] . ( 39 sec) [ -9723.8606] [GTR parameters ] . ( 39 sec) [ -9723.8606] [Alpha ][ 1.182610] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.860646. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23160.5824] [GTR parameters ] . ( 1 sec) [ -22698.5593] [Alpha ][ 0.500960] . ( 1 sec) [ -21818.4205] [ 4957] [depth= 3] . ( 1 sec) [ -21662.5116] [ 4905] [depth= 9] . ( 1 sec) [ -21408.0406] [ 4868] [depth= 4] . ( 1 sec) [ -21290.8901] [ 4848] [depth= 7] . ( 1 sec) [ -21167.3149] [ 4736] [depth= 1] . ( 1 sec) [ -20779.7888] [ 4702] [depth= 2] . ( 1 sec) [ -20716.7059] [ 4667] [depth= 1] . ( 1 sec) [ -20463.3192] [ 4641] [depth= 4] . ( 1 sec) [ -20402.9000] [ 4575] [depth= 1] . ( 1 sec) [ -20306.5532] [ 4538] [depth= 3] . ( 1 sec) [ -19520.5378] [ 4446] [depth= 8] . ( 1 sec) [ -19138.6444] [ 4431] [depth= 3] . ( 1 sec) [ -19030.9072] [ 4343] [depth= 1] . ( 1 sec) [ -18960.2936] [ 4330] [depth= 2] . ( 1 sec) [ -18690.7894] [ 4261] [depth= 9] . ( 2 sec) [ -18346.5008] [ 4162] [depth= 12] . ( 2 sec) [ -18182.1055] [ 4115] [depth= 6] . ( 2 sec) [ -18000.5244] [ 4066] [depth= 3] . ( 2 sec) [ -17372.5974] [ 4052] [depth= 1] . ( 2 sec) [ -16880.9762] [ 4040] [depth= 9] . ( 2 sec) [ -16637.4705] [ 3925] [depth= 3] . ( 2 sec) [ -16347.1759] [ 3900] [depth= 11] . ( 2 sec) [ -16332.1620] [ 3894] [depth= 1] . ( 2 sec) [ -15807.7289] [ 3833] [depth= 11] . ( 2 sec) [ -15263.3329] [ 3689] [depth= 12] . ( 2 sec) [ -15114.6320] [ 3708] [depth= 1] . ( 2 sec) [ -15032.4401] [ 3720] [depth= 1] . ( 2 sec) [ -15007.0746] [ 3695] [depth= 1] . ( 2 sec) [ -14951.6209] [ 3712] [depth= 1] . ( 2 sec) [ -14623.3699] [ 3623] [depth= 7] . ( 2 sec) [ -14616.0573] [ 3609] [depth= 1] . ( 2 sec) [ -14531.1641] [ 3594] [depth= 11] . ( 2 sec) [ -13989.2897] [ 3512] [depth= 3] . ( 2 sec) [ -13703.2356] [ 3394] [depth= 11] . ( 2 sec) [ -13607.3908] [ 3340] [depth= 1] . ( 2 sec) [ -13414.9546] [ 3321] [depth= 2] . ( 3 sec) [ -13092.2569] [ 3251] [depth= 1] . ( 3 sec) [ -12978.2769] [ 3235] [depth= 1] . ( 3 sec) [ -12953.9615] [ 3229] [depth= 2] . ( 3 sec) [ -12905.3901] [ 3194] [depth= 1] . ( 3 sec) [ -12870.3070] [ 3148] [depth= 1] . ( 3 sec) [ -12777.0485] [ 3155] [depth= 1] . ( 3 sec) [ -12578.7568] [ 3070] [depth= 6] . ( 3 sec) [ -12574.5644] [ 3070] [depth= 1] . ( 3 sec) [ -12565.9974] [ 3065] [depth= 1] . ( 3 sec) [ -12497.0835] [ 3053] [depth= 1] . ( 3 sec) [ -12418.8023] [ 2977] [depth= 8] . ( 3 sec) [ -12398.2962] [ 2968] [depth= 2] . ( 3 sec) [ -12384.9164] [ 2965] [depth= 1] . ( 3 sec) [ -12207.4772] [ 2874] [depth= 4] . ( 3 sec) [ -12187.2084] [ 2848] [depth= 1] . ( 3 sec) [ -12141.8545] [ 2830] [depth= 1] . ( 3 sec) [ -12115.1799] [ 2846] [depth= 1] . ( 3 sec) [ -11791.2247] [ 2875] [depth= 1] . ( 3 sec) [ -11772.3435] [ 2879] [depth= 1] . ( 4 sec) [ -11745.5148] [ 2846] [depth= 2] . ( 4 sec) [ -11648.0796] [ 2773] [depth= 5] . ( 4 sec) [ -11559.8846] [ 2753] [depth= 1] . ( 4 sec) [ -11467.2471] [ 2750] [depth= 4] . ( 4 sec) [ -11461.7332] [ 2761] [depth= 2] . ( 4 sec) [ -11445.0244] [ 2761] [depth= 2] . ( 4 sec) [ -11257.5546] [ 2697] [depth= 5] . ( 4 sec) [ -11168.5984] [ 2683] [depth= 7] . ( 4 sec) [ -11163.7136] [ 2681] [depth= 6] . ( 4 sec) [ -11043.4915] [ 2593] [depth= 4] . ( 4 sec) [ -10800.4942] [ 2592] [depth= 1] . ( 4 sec) [ -10778.8659] [ 2557] [depth= 3] . ( 4 sec) [ -10774.2516] [ 2564] [depth= 1] . ( 4 sec) [ -10755.6791] [ 2559] [depth= 1] . ( 4 sec) [ -10698.0994] [ 2527] [depth= 2] . ( 4 sec) [ -10511.5010] [ 2469] [depth= 7] . ( 4 sec) [ -10500.8173] [ 2467] [depth= 1] . ( 5 sec) [ -10375.5727] [ 2413] [depth= 1] . ( 5 sec) [ -10364.9326] [ 2418] [depth= 1] . ( 5 sec) [ -10291.7980] [ 2390] [depth= 6] . ( 5 sec) [ -10283.1893] [ 2406] [depth= 1] . ( 5 sec) [ -10282.5791] [ 2411] [depth= 1] . ( 5 sec) [ -10260.3916] [ 2390] [depth= 3] . ( 5 sec) [ -10100.8234] [ 2273] [depth= 4] . ( 5 sec) [ -9852.7211] [Branch lengths ] . ( 6 sec) [ -9851.2668] [GTR parameters ] . ( 6 sec) [ -9791.8338] [Alpha ][ 1.000679] . ( 6 sec) [ -9767.9416] [ 2258] [depth= 1] . ( 6 sec) [ -9764.8829] [ 2261] [depth= 1] . ( 6 sec) [ -9762.7141] [ 2259] [depth= 1] . ( 7 sec) [ -9762.6330] [ 2259] [depth= 1] . ( 7 sec) [ -9758.4537] [ 2254] [depth= 1] . ( 7 sec) [ -9757.2440] [ 2255] [depth= 1] . ( 7 sec) [ -9756.6666] [ 2258] [depth= 1] . ( 8 sec) [ -9751.5589] [ 2250] [depth= 1] . ( 8 sec) [ -9749.8461] [ 2246] [depth= 1] . ( 8 sec) [ -9748.8123] [ 2245] [depth= 1] . ( 8 sec) [ -9747.9253] [ 2242] [depth= 1] . ( 9 sec) [ -9727.6862] [Branch lengths ] . ( 9 sec) [ -9727.6386] [GTR parameters ] . ( 9 sec) [ -9725.1471] [Alpha ][ 1.179643] . ( 12 sec) [ -9724.0623] [Branch lengths ] . ( 33 sec) [ -9723.9031] [Branch lengths ] . ( 33 sec) [ -9723.9031] [Topology ] . ( 34 sec) [ -9723.8821] [Topology ] . ( 35 sec) [ -9723.8740] [Topology ] . ( 36 sec) [ -9723.8696] [Topology ] . ( 37 sec) [ -9723.8672] [Topology ] . ( 38 sec) [ -9723.8659] [Topology ] . ( 38 sec) [ -9723.8651] [Topology ] . ( 39 sec) [ -9723.8623] [GTR parameters ] . ( 39 sec) [ -9723.8614] [Alpha ][ 1.183197] . ( 39 sec) [ -9723.8614] [Topology ] . ( 39 sec) [ -9723.8610] [Topology ] . ( 40 sec) [ -9723.8610] [GTR parameters ] . ( 40 sec) [ -9723.8610] [Alpha ][ 1.183197] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.860950. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -25320.1311] [GTR parameters ] . ( 1 sec) [ -24829.5614] [Alpha ][ 0.500960] . ( 1 sec) [ -23382.8180] [ 5065] [depth= 8] . ( 1 sec) [ -23121.6688] [ 5027] [depth= 6] . ( 1 sec) [ -22862.2531] [ 5005] [depth= 4] . ( 1 sec) [ -22783.0612] [ 4999] [depth= 2] . ( 1 sec) [ -22735.4660] [ 4925] [depth= 9] . ( 1 sec) [ -22601.7996] [ 4922] [depth= 6] . ( 1 sec) [ -22234.3534] [ 4884] [depth= 16] . ( 2 sec) [ -22062.8359] [ 4840] [depth= 7] . ( 2 sec) [ -22015.6697] [ 4836] [depth= 2] . ( 2 sec) [ -21907.2624] [ 4871] [depth= 1] . ( 2 sec) [ -21613.5715] [ 4733] [depth= 13] . ( 2 sec) [ -21056.1443] [ 4656] [depth= 14] . ( 2 sec) [ -20407.8456] [ 4527] [depth= 3] . ( 2 sec) [ -19721.8278] [ 4516] [depth= 1] . ( 2 sec) [ -19581.2286] [ 4482] [depth= 11] . ( 2 sec) [ -19552.2047] [ 4365] [depth= 2] . ( 2 sec) [ -19526.7333] [ 4354] [depth= 5] . ( 2 sec) [ -19274.3718] [ 4267] [depth= 6] . ( 2 sec) [ -19109.4322] [ 4272] [depth= 1] . ( 2 sec) [ -19087.6010] [ 4257] [depth= 1] . ( 2 sec) [ -18347.8474] [ 4085] [depth= 10] . ( 2 sec) [ -18263.8542] [ 4048] [depth= 1] . ( 2 sec) [ -18146.9292] [ 4019] [depth= 6] . ( 2 sec) [ -18028.2914] [ 3865] [depth= 7] . ( 2 sec) [ -17996.4113] [ 3854] [depth= 2] . ( 2 sec) [ -17898.8759] [ 3841] [depth= 8] . ( 2 sec) [ -17568.1272] [ 3838] [depth= 13] . ( 2 sec) [ -17312.0052] [ 3832] [depth= 2] . ( 3 sec) [ -17307.5934] [ 3835] [depth= 2] . ( 3 sec) [ -17271.9846] [ 3830] [depth= 1] . ( 3 sec) [ -17186.1441] [ 3808] [depth= 3] . ( 3 sec) [ -16610.3502] [ 3706] [depth= 2] . ( 3 sec) [ -16401.4577] [ 3687] [depth= 8] . ( 3 sec) [ -16188.1390] [ 3637] [depth= 4] . ( 3 sec) [ -16052.9824] [ 3652] [depth= 1] . ( 3 sec) [ -16004.0219] [ 3622] [depth= 1] . ( 3 sec) [ -14702.8130] [ 3527] [depth= 8] . ( 3 sec) [ -14651.1319] [ 3530] [depth= 11] . ( 3 sec) [ -14590.7580] [ 3528] [depth= 11] . ( 3 sec) [ -14442.8950] [ 3533] [depth= 1] . ( 3 sec) [ -13929.5746] [ 3398] [depth= 4] . ( 3 sec) [ -13659.9833] [ 3318] [depth= 4] . ( 3 sec) [ -13471.9570] [ 3309] [depth= 1] . ( 3 sec) [ -13461.7132] [ 3317] [depth= 1] . ( 3 sec) [ -13414.8007] [ 3293] [depth= 1] . ( 3 sec) [ -13387.5014] [ 3290] [depth= 2] . ( 3 sec) [ -13327.7993] [ 3251] [depth= 2] . ( 3 sec) [ -12970.1482] [ 3204] [depth= 1] . ( 4 sec) [ -12918.3328] [ 3195] [depth= 5] . ( 4 sec) [ -12854.3259] [ 3167] [depth= 1] . ( 4 sec) [ -12826.1251] [ 3159] [depth= 3] . ( 4 sec) [ -12674.4209] [ 3149] [depth= 1] . ( 4 sec) [ -12477.0032] [ 3066] [depth= 11] . ( 4 sec) [ -12475.5290] [ 3068] [depth= 1] . ( 4 sec) [ -12389.5187] [ 3043] [depth= 4] . ( 4 sec) [ -12355.9849] [ 3023] [depth= 1] . ( 4 sec) [ -12019.1520] [ 2887] [depth= 7] . ( 4 sec) [ -11888.2380] [ 2867] [depth= 5] . ( 4 sec) [ -11784.2365] [ 2857] [depth= 1] . ( 4 sec) [ -11752.3155] [ 2844] [depth= 2] . ( 4 sec) [ -11669.3760] [ 2808] [depth= 1] . ( 4 sec) [ -11660.8115] [ 2809] [depth= 1] . ( 4 sec) [ -11625.9777] [ 2782] [depth= 2] . ( 4 sec) [ -11255.8832] [ 2686] [depth= 6] . ( 4 sec) [ -10950.5322] [ 2660] [depth= 5] . ( 4 sec) [ -10945.4342] [ 2663] [depth= 1] . ( 4 sec) [ -10867.5725] [ 2627] [depth= 3] . ( 5 sec) [ -10824.3422] [ 2557] [depth= 2] . ( 5 sec) [ -10804.1209] [ 2521] [depth= 2] . ( 5 sec) [ -10790.1946] [ 2522] [depth= 1] . ( 5 sec) [ -10779.5243] [ 2519] [depth= 1] . ( 5 sec) [ -10682.2403] [ 2495] [depth= 1] . ( 5 sec) [ -10647.0255] [ 2475] [depth= 1] . ( 5 sec) [ -10639.3985] [ 2468] [depth= 5] . ( 5 sec) [ -10597.1235] [ 2458] [depth= 2] . ( 5 sec) [ -10577.1683] [ 2456] [depth= 2] . ( 5 sec) [ -10444.7923] [ 2436] [depth= 1] . ( 5 sec) [ -10355.5597] [ 2417] [depth= 1] . ( 5 sec) [ -10313.1467] [ 2427] [depth= 1] . ( 5 sec) [ -10199.0218] [ 2342] [depth= 3] . ( 5 sec) [ -10073.7001] [ 2311] [depth= 4] . ( 6 sec) [ -9887.8659] [Branch lengths ] . ( 6 sec) [ -9885.4163] [GTR parameters ] . ( 6 sec) [ -9828.7794] [Alpha ][ 1.000578] . ( 7 sec) [ -9828.6803] [ 2312] [depth= 1] . ( 7 sec) [ -9825.5428] [ 2306] [depth= 1] . ( 7 sec) [ -9824.5089] [ 2299] [depth= 1] . ( 7 sec) [ -9824.4341] [ 2299] [depth= 1] . ( 7 sec) [ -9799.2165] [ 2287] [depth= 1] . ( 7 sec) [ -9786.2286] [ 2284] [depth= 2] . ( 7 sec) [ -9785.4829] [ 2279] [depth= 1] . ( 7 sec) [ -9762.7374] [ 2260] [depth= 1] . ( 7 sec) [ -9762.5669] [ 2258] [depth= 1] . ( 7 sec) [ -9762.4455] [ 2260] [depth= 1] . ( 8 sec) [ -9762.3041] [ 2260] [depth= 1] . ( 8 sec) [ -9761.5401] [ 2263] [depth= 1] . ( 8 sec) [ -9761.5284] [ 2261] [depth= 1] . ( 8 sec) [ -9756.7801] [ 2255] [depth= 1] . ( 8 sec) [ -9755.4484] [ 2260] [depth= 1] . ( 9 sec) [ -9730.8878] [Branch lengths ] . ( 10 sec) [ -9730.7335] [GTR parameters ] . ( 10 sec) [ -9728.4503] [Alpha ][ 1.169704] . ( 10 sec) [ -9728.4129] [ 2261] [depth= 1] . ( 13 sec) [ -9725.3689] [Branch lengths ] . ( 14 sec) [ -9725.3649] [GTR parameters ] . ( 14 sec) [ -9725.3634] [Alpha ][ 1.174440] . ( 17 sec) [ -9725.0315] [Branch lengths ] . ( 37 sec) [ -9724.9990] [Branch lengths ] . ( 37 sec) [ -9724.9990] [Topology ] . ( 38 sec) [ -9724.3494] [Topology ] . ( 39 sec) [ -9724.2132] [Topology ] . ( 40 sec) [ -9724.1962] [Topology ] . ( 41 sec) [ -9724.1920] [Topology ] . ( 41 sec) [ -9724.1907] [Topology ] . ( 42 sec) [ -9724.1903] [Topology ] . ( 42 sec) [ -9724.1885] [GTR parameters ] . ( 42 sec) [ -9724.1880] [Alpha ][ 1.177125] . ( 42 sec) [ -9724.1880] [Topology ] . ( 43 sec) [ -9724.1878] [Topology ] . ( 43 sec) [ -9724.1878] [GTR parameters ] . ( 43 sec) [ -9724.1878] [Alpha ][ 1.177125] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -9723.8645] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.864532. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23878.4293] [GTR parameters ] . ( 1 sec) [ -23448.1569] [Alpha ][ 0.500960] . ( 1 sec) [ -22729.4286] [ 5036] [depth= 8] . ( 1 sec) [ -22462.9285] [ 4955] [depth= 7] . ( 1 sec) [ -22180.4859] [ 4960] [depth= 1] . ( 1 sec) [ -21774.1288] [ 4874] [depth= 7] . ( 1 sec) [ -21634.0299] [ 4810] [depth= 2] . ( 1 sec) [ -21422.6188] [ 4736] [depth= 9] . ( 2 sec) [ -20486.5038] [ 4716] [depth= 3] . ( 2 sec) [ -20106.8228] [ 4699] [depth= 2] . ( 2 sec) [ -20026.2624] [ 4530] [depth= 7] . ( 2 sec) [ -19917.4234] [ 4520] [depth= 5] . ( 2 sec) [ -19884.4217] [ 4390] [depth= 2] . ( 2 sec) [ -19624.2143] [ 4337] [depth= 6] . ( 2 sec) [ -18929.5729] [ 4352] [depth= 11] . ( 2 sec) [ -18457.0852] [ 4335] [depth= 11] . ( 2 sec) [ -17918.1964] [ 4308] [depth= 2] . ( 2 sec) [ -17763.3082] [ 4195] [depth= 3] . ( 2 sec) [ -17612.0425] [ 4185] [depth= 1] . ( 2 sec) [ -17540.0339] [ 4128] [depth= 7] . ( 2 sec) [ -17398.6350] [ 4121] [depth= 1] . ( 2 sec) [ -17002.7457] [ 4123] [depth= 4] . ( 2 sec) [ -16822.4237] [ 3999] [depth= 3] . ( 2 sec) [ -16765.4640] [ 3985] [depth= 1] . ( 2 sec) [ -16485.5527] [ 3984] [depth= 1] . ( 2 sec) [ -16351.3494] [ 3973] [depth= 1] . ( 2 sec) [ -16086.7672] [ 3963] [depth= 3] . ( 2 sec) [ -16049.5322] [ 3957] [depth= 2] . ( 2 sec) [ -15825.0511] [ 3832] [depth= 10] . ( 3 sec) [ -15731.3025] [ 3801] [depth= 1] . ( 3 sec) [ -15693.2086] [ 3766] [depth= 5] . ( 3 sec) [ -15689.7749] [ 3767] [depth= 8] . ( 3 sec) [ -15657.9143] [ 3738] [depth= 1] . ( 3 sec) [ -14967.2602] [ 3756] [depth= 2] . ( 3 sec) [ -14864.4644] [ 3737] [depth= 1] . ( 3 sec) [ -14658.4962] [ 3650] [depth= 5] . ( 3 sec) [ -14654.3503] [ 3641] [depth= 12] . ( 3 sec) [ -14492.1009] [ 3565] [depth= 1] . ( 3 sec) [ -14133.7957] [ 3455] [depth= 3] . ( 3 sec) [ -13763.0172] [ 3304] [depth= 4] . ( 3 sec) [ -13718.0083] [ 3288] [depth= 1] . ( 3 sec) [ -13255.1810] [ 3137] [depth= 3] . ( 3 sec) [ -13241.4821] [ 3147] [depth= 1] . ( 3 sec) [ -13137.0007] [ 3118] [depth= 6] . ( 3 sec) [ -13113.2236] [ 3066] [depth= 5] . ( 3 sec) [ -12916.1271] [ 2980] [depth= 1] . ( 3 sec) [ -12819.7834] [ 2981] [depth= 1] . ( 3 sec) [ -12740.9095] [ 2966] [depth= 6] . ( 4 sec) [ -12712.5083] [ 2958] [depth= 1] . ( 4 sec) [ -12654.9242] [ 2951] [depth= 3] . ( 4 sec) [ -12345.1561] [ 2932] [depth= 3] . ( 4 sec) [ -12262.0162] [ 2902] [depth= 1] . ( 4 sec) [ -12225.9490] [ 2907] [depth= 14] . ( 4 sec) [ -11916.4117] [ 2833] [depth= 13] . ( 4 sec) [ -11856.2403] [ 2812] [depth= 1] . ( 4 sec) [ -11736.1925] [ 2809] [depth= 6] . ( 4 sec) [ -11453.8647] [ 2804] [depth= 2] . ( 4 sec) [ -11072.3015] [ 2758] [depth= 1] . ( 4 sec) [ -11044.4856] [ 2757] [depth= 1] . ( 4 sec) [ -10910.5182] [ 2675] [depth= 4] . ( 4 sec) [ -10899.3183] [ 2664] [depth= 1] . ( 4 sec) [ -10888.0719] [ 2663] [depth= 1] . ( 4 sec) [ -10863.8959] [ 2658] [depth= 2] . ( 4 sec) [ -10828.6879] [ 2586] [depth= 9] . ( 4 sec) [ -10773.5672] [ 2542] [depth= 3] . ( 5 sec) [ -10761.9132] [ 2539] [depth= 1] . ( 5 sec) [ -10654.9250] [ 2515] [depth= 1] . ( 5 sec) [ -10631.7311] [ 2485] [depth= 1] . ( 5 sec) [ -10585.1546] [ 2483] [depth= 1] . ( 5 sec) [ -10584.0717] [ 2484] [depth= 1] . ( 5 sec) [ -10478.2790] [ 2453] [depth= 4] . ( 5 sec) [ -10440.3488] [ 2445] [depth= 1] . ( 5 sec) [ -10409.0269] [ 2440] [depth= 1] . ( 5 sec) [ -10408.8314] [ 2444] [depth= 1] . ( 5 sec) [ -10351.2651] [ 2394] [depth= 4] . ( 5 sec) [ -10341.5286] [ 2394] [depth= 1] . ( 5 sec) [ -10251.7703] [ 2343] [depth= 1] . ( 5 sec) [ -10241.3220] [ 2353] [depth= 1] . ( 5 sec) [ -10238.8841] [ 2351] [depth= 1] . ( 5 sec) [ -10231.0388] [ 2345] [depth= 1] . ( 5 sec) [ -10230.3761] [ 2345] [depth= 1] . ( 5 sec) [ -10229.0003] [ 2346] [depth= 1] . ( 6 sec) [ -9963.3837] [Branch lengths ] . ( 6 sec) [ -9962.5357] [GTR parameters ] . ( 6 sec) [ -9904.6177] [Alpha ][ 1.000449] . ( 6 sec) [ -9898.8895] [ 2351] [depth= 1] . ( 6 sec) [ -9897.9255] [ 2351] [depth= 1] . ( 7 sec) [ -9893.8350] [ 2354] [depth= 1] . ( 7 sec) [ -9878.9937] [ 2339] [depth= 1] . ( 7 sec) [ -9868.9332] [ 2329] [depth= 1] . ( 7 sec) [ -9866.5058] [ 2315] [depth= 1] . ( 8 sec) [ -9865.3613] [ 2307] [depth= 1] . ( 8 sec) [ -9865.3478] [ 2307] [depth= 1] . ( 8 sec) [ -9750.6527] [ 2260] [depth= 5] . ( 8 sec) [ -9750.2053] [ 2264] [depth= 1] . ( 9 sec) [ -9742.1418] [ 2246] [depth= 1] . ( 10 sec) [ -9729.8514] [Branch lengths ] . ( 10 sec) [ -9729.8212] [GTR parameters ] . ( 10 sec) [ -9727.2964] [Alpha ][ 1.176346] . ( 13 sec) [ -9725.0008] [Branch lengths ] . ( 34 sec) [ -9724.7268] [Branch lengths ] . ( 34 sec) [ -9724.7268] [Topology ] . ( 35 sec) [ -9724.0611] [Topology ] . ( 36 sec) [ -9723.9057] [Topology ] . ( 36 sec) [ -9723.8800] [Topology ] . ( 37 sec) [ -9723.8714] [Topology ] . ( 38 sec) [ -9723.8679] [Topology ] . ( 39 sec) [ -9723.8664] [Topology ] . ( 40 sec) [ -9723.8657] [Topology ] . ( 40 sec) [ -9723.8639] [GTR parameters ] . ( 40 sec) [ -9723.8610] [Alpha ][ 1.182983] . ( 40 sec) [ -9723.8610] [Topology ] . ( 41 sec) [ -9723.8606] [Topology ] . ( 41 sec) [ -9723.8606] [GTR parameters ] . ( 41 sec) [ -9723.8606] [Alpha ][ 1.182983] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.860561. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -25284.0308] [GTR parameters ] . ( 0 sec) [ -24779.4897] [Alpha ][ 0.500960] . ( 1 sec) [ -23616.9807] [ 5163] [depth= 6] . ( 1 sec) [ -23206.4624] [ 5098] [depth= 13] . ( 1 sec) [ -22819.3577] [ 5066] [depth= 5] . ( 1 sec) [ -22805.9240] [ 5048] [depth= 1] . ( 1 sec) [ -22465.2432] [ 4908] [depth= 5] . ( 1 sec) [ -22265.6883] [ 4843] [depth= 6] . ( 1 sec) [ -21922.7851] [ 4876] [depth= 1] . ( 1 sec) [ -21336.9314] [ 4779] [depth= 2] . ( 1 sec) [ -20967.2427] [ 4705] [depth= 3] . ( 1 sec) [ -20569.0453] [ 4595] [depth= 7] . ( 1 sec) [ -19968.5175] [ 4503] [depth= 12] . ( 1 sec) [ -19400.8416] [ 4393] [depth= 9] . ( 1 sec) [ -19118.5155] [ 4296] [depth= 5] . ( 1 sec) [ -19047.4492] [ 4293] [depth= 1] . ( 1 sec) [ -18848.8535] [ 4274] [depth= 9] . ( 1 sec) [ -18790.2100] [ 4270] [depth= 3] . ( 1 sec) [ -18544.8820] [ 4166] [depth= 11] . ( 1 sec) [ -18514.9329] [ 4173] [depth= 1] . ( 1 sec) [ -18214.0863] [ 4136] [depth= 10] . ( 1 sec) [ -16924.7021] [ 3949] [depth= 7] . ( 1 sec) [ -16762.3003] [ 3951] [depth= 2] . ( 2 sec) [ -16614.0091] [ 3944] [depth= 1] . ( 2 sec) [ -16123.2997] [ 3914] [depth= 12] . ( 2 sec) [ -16066.8388] [ 3913] [depth= 19] . ( 2 sec) [ -15978.8537] [ 3884] [depth= 2] . ( 2 sec) [ -15862.3456] [ 3821] [depth= 10] . ( 2 sec) [ -15801.5409] [ 3793] [depth= 3] . ( 2 sec) [ -15280.1841] [ 3745] [depth= 10] . ( 2 sec) [ -15076.5994] [ 3716] [depth= 12] . ( 2 sec) [ -14604.6055] [ 3525] [depth= 9] . ( 2 sec) [ -14296.5652] [ 3487] [depth= 11] . ( 2 sec) [ -13979.2079] [ 3359] [depth= 9] . ( 2 sec) [ -13805.6301] [ 3353] [depth= 1] . ( 2 sec) [ -13510.8241] [ 3247] [depth= 2] . ( 2 sec) [ -13408.7498] [ 3173] [depth= 7] . ( 2 sec) [ -13357.9036] [ 3116] [depth= 7] . ( 2 sec) [ -13318.3364] [ 3118] [depth= 1] . ( 2 sec) [ -13274.8684] [ 3135] [depth= 1] . ( 2 sec) [ -13239.1203] [ 3145] [depth= 8] . ( 2 sec) [ -13107.4249] [ 3096] [depth= 6] . ( 2 sec) [ -13014.8177] [ 3055] [depth= 1] . ( 3 sec) [ -12553.7631] [ 3004] [depth= 3] . ( 3 sec) [ -12479.6449] [ 2955] [depth= 10] . ( 3 sec) [ -12460.9355] [ 2952] [depth= 1] . ( 3 sec) [ -12388.3135] [ 2960] [depth= 5] . ( 3 sec) [ -12349.1569] [ 2967] [depth= 1] . ( 3 sec) [ -12271.5893] [ 2968] [depth= 3] . ( 3 sec) [ -12216.3860] [ 2948] [depth= 1] . ( 3 sec) [ -12162.6178] [ 2909] [depth= 14] . ( 3 sec) [ -11854.3258] [ 2892] [depth= 4] . ( 3 sec) [ -11784.0153] [ 2879] [depth= 1] . ( 3 sec) [ -11558.2663] [ 2797] [depth= 1] . ( 3 sec) [ -11477.3948] [ 2755] [depth= 3] . ( 3 sec) [ -11443.7894] [ 2751] [depth= 1] . ( 3 sec) [ -11298.0878] [ 2723] [depth= 2] . ( 3 sec) [ -11203.2138] [ 2680] [depth= 5] . ( 3 sec) [ -11203.0024] [ 2685] [depth= 1] . ( 3 sec) [ -11201.7785] [ 2682] [depth= 2] . ( 3 sec) [ -11008.5539] [ 2619] [depth= 2] . ( 3 sec) [ -10997.4876] [ 2605] [depth= 3] . ( 3 sec) [ -10886.0643] [ 2576] [depth= 5] . ( 4 sec) [ -10879.4118] [ 2574] [depth= 2] . ( 4 sec) [ -10865.5991] [ 2561] [depth= 1] . ( 4 sec) [ -10832.0595] [ 2557] [depth= 1] . ( 4 sec) [ -10815.9308] [ 2552] [depth= 1] . ( 4 sec) [ -10735.7845] [ 2530] [depth= 1] . ( 4 sec) [ -10688.5055] [ 2516] [depth= 2] . ( 4 sec) [ -10676.8119] [ 2539] [depth= 2] . ( 4 sec) [ -10628.8118] [ 2508] [depth= 2] . ( 4 sec) [ -10601.0369] [ 2500] [depth= 1] . ( 4 sec) [ -10578.4079] [ 2500] [depth= 1] . ( 4 sec) [ -10468.2166] [ 2444] [depth= 2] . ( 4 sec) [ -10457.6848] [ 2459] [depth= 2] . ( 4 sec) [ -10314.2799] [ 2412] [depth= 2] . ( 4 sec) [ -10312.0668] [ 2414] [depth= 1] . ( 4 sec) [ -10280.6727] [ 2391] [depth= 2] . ( 4 sec) [ -10262.3283] [ 2396] [depth= 1] . ( 4 sec) [ -10250.2529] [ 2397] [depth= 1] . ( 4 sec) [ -10202.6232] [ 2387] [depth= 1] . ( 4 sec) [ -10133.1868] [ 2372] [depth= 2] . ( 5 sec) [ -10128.7710] [ 2368] [depth= 1] . ( 5 sec) [ -10127.7090] [ 2369] [depth= 1] . ( 5 sec) [ -9947.0520] [Branch lengths ] . ( 5 sec) [ -9946.2118] [GTR parameters ] . ( 6 sec) [ -9897.0070] [Alpha ][ 1.000234] . ( 6 sec) [ -9894.7564] [ 2364] [depth= 1] . ( 6 sec) [ -9889.3816] [ 2358] [depth= 1] . ( 6 sec) [ -9889.1729] [ 2358] [depth= 1] . ( 6 sec) [ -9886.9195] [ 2356] [depth= 1] . ( 6 sec) [ -9861.1492] [ 2340] [depth= 1] . ( 6 sec) [ -9859.7156] [ 2322] [depth= 2] . ( 6 sec) [ -9774.2400] [ 2257] [depth= 1] . ( 6 sec) [ -9770.6909] [ 2265] [depth= 1] . ( 7 sec) [ -9770.3682] [ 2265] [depth= 1] . ( 7 sec) [ -9766.3169] [ 2257] [depth= 1] . ( 7 sec) [ -9761.7302] [ 2244] [depth= 1] . ( 7 sec) [ -9761.6541] [ 2249] [depth= 1] . ( 7 sec) [ -9760.1546] [ 2242] [depth= 1] . ( 7 sec) [ -9758.6744] [ 2239] [depth= 1] . ( 8 sec) [ -9753.8938] [ 2235] [depth= 1] . ( 8 sec) [ -9753.7136] [ 2237] [depth= 1] . ( 8 sec) [ -9751.4447] [ 2241] [depth= 1] . ( 8 sec) [ -9750.9324] [ 2243] [depth= 1] . ( 8 sec) [ -9750.9107] [ 2240] [depth= 1] . ( 9 sec) [ -9730.0032] [Branch lengths ] . ( 9 sec) [ -9729.8097] [GTR parameters ] . ( 9 sec) [ -9727.3727] [Alpha ][ 1.178230] . ( 10 sec) [ -9727.3445] [ 2243] [depth= 1] . ( 12 sec) [ -9727.3340] [ 2240] [depth= 1] . ( 12 sec) [ -9725.3395] [Branch lengths ] . ( 13 sec) [ -9725.3366] [GTR parameters ] . ( 13 sec) [ -9725.3316] [Alpha ][ 1.187099] . ( 15 sec) [ -9724.9294] [Branch lengths ] . ( 36 sec) [ -9724.8461] [Branch lengths ] . ( 36 sec) [ -9724.8461] [Topology ] . ( 37 sec) [ -9724.0622] [Topology ] . ( 38 sec) [ -9723.8933] [Topology ] . ( 39 sec) [ -9723.8731] [Topology ] . ( 39 sec) [ -9723.8677] [Topology ] . ( 40 sec) [ -9723.8659] [Topology ] . ( 41 sec) [ -9723.8651] [Topology ] . ( 41 sec) [ -9723.8622] [GTR parameters ] . ( 41 sec) [ -9723.8614] [Alpha ][ 1.183467] . ( 41 sec) [ -9723.8614] [Topology ] . ( 42 sec) [ -9723.8609] [Topology ] . ( 42 sec) [ -9723.8609] [GTR parameters ] . ( 42 sec) [ -9723.8609] [Alpha ][ 1.183467] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.860911. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9801.144178 . ( 1 sec) [ -9799.9617] [GTR parameters ] . ( 1 sec) [ -9797.1449] [Alpha ][ 1.202689] . ( 1 sec) [ -9797.1449] [Topology ] . ( 1 sec) [ -9743.9815] [Topology ] . ( 2 sec) [ -9735.8535] [Topology ] . ( 3 sec) [ -9733.2210] [Topology ] . ( 4 sec) [ -9732.0913] [Topology ] . ( 5 sec) [ -9731.5407] [Topology ] . ( 6 sec) [ -9731.2519] [Topology ] . ( 7 sec) [ -9730.9560] [Topology ] . ( 7 sec) [ -9729.8822] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9729.882213 . ( 14 sec) [ -9729.8433] [GTR parameters ] . ( 14 sec) [ -9729.8272] [Alpha ][ 1.186224] . ( 14 sec) [ -9729.8272] [Topology ] . ( 15 sec) [ -9726.3677] [Topology ] . ( 16 sec) [ -9724.1515] [Topology ] . ( 17 sec) [ -9723.9354] [Topology ] . ( 18 sec) [ -9723.8862] [Topology ] . ( 18 sec) [ -9723.8718] [Topology ] . ( 19 sec) [ -9723.8666] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.866603 . ( 26 sec) [ -9723.8661] [GTR parameters ] . ( 26 sec) [ -9723.8658] [Alpha ][ 1.183900] . ( 26 sec) [ -9723.8658] [Topology ] . ( 27 sec) [ -9723.8635] [Topology ] . ( 28 sec) [ -9723.8622] [Topology ] . ( 29 sec) [ -9723.8615] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.861484 . ( 35 sec) [ -9723.8615] [GTR parameters ] . ( 35 sec) [ -9723.8615] [Alpha ][ 1.183900] . ( 35 sec) [ -9723.8615] [Topology ] . ( 36 sec) [ -9723.8611] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -9799.9617] [GTR parameters ] . ( 50 sec) [ -9797.1449] [Alpha ][ 1.202689] . ( 50 sec) [ -9795.9543] [ 2238] [depth= 1] . ( 50 sec) [ -9795.3567] [ 2243] [depth= 1] . ( 50 sec) [ -9792.7475] [ 2238] [depth= 1] . ( 51 sec) [ -9791.1715] [ 2241] [depth= 1] . ( 51 sec) [ -9791.1134] [ 2241] [depth= 1] . ( 51 sec) [ -9790.5221] [ 2242] [depth= 1] . ( 51 sec) [ -9789.6051] [ 2241] [depth= 1] . ( 51 sec) [ -9774.3044] [ 2260] [depth= 1] . ( 51 sec) [ -9773.3126] [ 2263] [depth= 1] . ( 52 sec) [ -9771.1987] [ 2267] [depth= 1] . ( 52 sec) [ -9769.3226] [ 2263] [depth= 1] . ( 52 sec) [ -9765.0078] [ 2260] [depth= 1] . ( 53 sec) [ -9735.0402] [Branch lengths ] . ( 53 sec) [ -9735.0094] [GTR parameters ] . ( 53 sec) [ -9734.9747] [Alpha ][ 1.179629] . ( 54 sec) [ -9734.9419] [ 2257] [depth= 1] . ( 54 sec) [ -9734.8060] [ 2260] [depth= 1] . ( 56 sec) [ -9732.0306] [Branch lengths ] . ( 56 sec) [ -9732.0301] [GTR parameters ] . ( 56 sec) [ -9732.0301] [Alpha ][ 1.179629] . ( 57 sec) [ -9732.0105] [ 2257] [depth= 1] . ( 59 sec) [ -9731.4085] [Branch lengths ] . ( 59 sec) [ -9731.4082] [GTR parameters ] . ( 59 sec) [ -9731.4080] [Alpha ][ 1.177616] . ( 62 sec) [ -9731.3620] [ 2264] [depth= 1] . ( 73 sec) [ -9731.2125] [ 2239] [depth= 1] . ( 80 sec) [ -9730.9422] [Branch lengths ] . ( 80 sec) [ -9730.9413] [GTR parameters ] . ( 80 sec) [ -9730.9385] [Alpha ][ 1.184179] . ( 80 sec) [ -9730.9385] [Topology ] . ( 81 sec) [ -9730.9101] [Topology ] . ( 82 sec) [ -9730.8110] [Topology ] . ( 83 sec) [ -9730.1843] [Topology ] . ( 84 sec) [ -9727.6112] [Topology ] . ( 84 sec) [ -9724.2608] [Topology ] . ( 85 sec) [ -9723.9489] [Topology ] . ( 85 sec) [ -9723.9481] [GTR parameters ] . ( 85 sec) [ -9723.9481] [Alpha ][ 1.182995] . ( 85 sec) [ -9723.9481] [Topology ] . ( 86 sec) [ -9723.8817] [Topology ] . ( 87 sec) [ -9723.8659] [Topology ] . ( 88 sec) [ -9723.8618] [Topology ] . ( 89 sec) [ -9723.8608] [Topology ] . ( 90 sec) [ -9723.8605] [Topology ] . ( 90 sec) [ -9723.8605] [GTR parameters ] . ( 90 sec) [ -9723.8605] [Alpha ][ 1.182995] . ( 90 sec) [ -9723.8605] [Topology ] . ( 91 sec) [ -9723.8604] [Topology ] . ( 91 sec) [ -9723.8604] [GTR parameters ] . ( 91 sec) [ -9723.8604] [Alpha ][ 1.182995] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9723.861076 . Log likelihood obtained after SPR moves : -9723.860371 . Log likelihood of the current tree: -9723.860371. . Printing the most likely tree in file 'data2.phy_phyml_tree.txt'... . Best log likelihood : -9723.860371 . Time used 0h1m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo