.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data53.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... . 429 patterns found. (out of a total of 500 sites) . 66 sites without polymorphism (13.20%). . [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) [ -23551.5643] [GTR parameters ] . ( 1 sec) [ -22964.6814] [Alpha ][ 0.500960] . ( 1 sec) [ -21875.7552] [ 5372] [depth= 8] . ( 1 sec) [ -21269.7598] [ 5380] [depth= 6] . ( 1 sec) [ -21177.9302] [ 5344] [depth= 1] . ( 1 sec) [ -20944.2893] [ 5340] [depth= 7] . ( 1 sec) [ -20584.9509] [ 5227] [depth= 5] . ( 1 sec) [ -20422.9671] [ 5213] [depth= 6] . ( 1 sec) [ -20413.1348] [ 5188] [depth= 4] . ( 1 sec) [ -20088.3302] [ 5176] [depth= 1] . ( 1 sec) [ -19771.1840] [ 5080] [depth= 6] . ( 1 sec) [ -19343.6033] [ 4943] [depth= 4] . ( 1 sec) [ -19229.3704] [ 4857] [depth= 15] . ( 1 sec) [ -19156.2182] [ 4851] [depth= 8] . ( 1 sec) [ -18855.3847] [ 4811] [depth= 12] . ( 1 sec) [ -18621.2827] [ 4809] [depth= 2] . ( 2 sec) [ -18307.3281] [ 4786] [depth= 3] . ( 2 sec) [ -17926.8136] [ 4729] [depth= 4] . ( 2 sec) [ -17738.0695] [ 4727] [depth= 5] . ( 2 sec) [ -17690.9541] [ 4711] [depth= 3] . ( 2 sec) [ -17632.6087] [ 4684] [depth= 2] . ( 2 sec) [ -17614.8879] [ 4629] [depth= 1] . ( 2 sec) [ -17454.9344] [ 4624] [depth= 1] . ( 2 sec) [ -17253.5997] [ 4583] [depth= 6] . ( 2 sec) [ -17047.6697] [ 4440] [depth= 2] . ( 2 sec) [ -16846.7986] [ 4437] [depth= 16] . ( 2 sec) [ -16841.6503] [ 4326] [depth= 2] . ( 2 sec) [ -16764.3626] [ 4310] [depth= 1] . ( 2 sec) [ -16383.3980] [ 4245] [depth= 7] . ( 2 sec) [ -16356.9601] [ 4249] [depth= 14] . ( 2 sec) [ -16346.0261] [ 4235] [depth= 2] . ( 2 sec) [ -16148.2814] [ 4211] [depth= 13] . ( 2 sec) [ -16131.8536] [ 4226] [depth= 1] . ( 2 sec) [ -15923.0511] [ 3987] [depth= 5] . ( 2 sec) [ -15807.3317] [ 3982] [depth= 1] . ( 2 sec) [ -15584.2865] [ 3884] [depth= 4] . ( 3 sec) [ -15481.9728] [ 3889] [depth= 1] . ( 3 sec) [ -15332.9224] [ 3715] [depth= 6] . ( 3 sec) [ -14961.3074] [ 3635] [depth= 5] . ( 3 sec) [ -14763.5828] [ 3605] [depth= 7] . ( 3 sec) [ -14507.6635] [ 3448] [depth= 6] . ( 3 sec) [ -14324.6225] [ 3446] [depth= 6] . ( 3 sec) [ -14322.0706] [ 3442] [depth= 1] . ( 3 sec) [ -14058.2064] [ 3363] [depth= 5] . ( 3 sec) [ -14024.3900] [ 3368] [depth= 1] . ( 3 sec) [ -14018.5200] [ 3370] [depth= 2] . ( 3 sec) [ -13865.7440] [ 3364] [depth= 1] . ( 3 sec) [ -13670.9890] [ 3368] [depth= 9] . ( 3 sec) [ -13668.4188] [ 3372] [depth= 1] . ( 3 sec) [ -13638.4177] [ 3374] [depth= 1] . ( 3 sec) [ -13189.0073] [ 3215] [depth= 8] . ( 3 sec) [ -13158.3337] [ 3217] [depth= 1] . ( 3 sec) [ -12975.0087] [ 3208] [depth= 5] . ( 3 sec) [ -12917.0456] [ 3197] [depth= 1] . ( 3 sec) [ -12342.2503] [ 3148] [depth= 2] . ( 3 sec) [ -12280.3277] [ 3067] [depth= 1] . ( 3 sec) [ -12276.0682] [ 3058] [depth= 1] . ( 3 sec) [ -12143.9914] [ 3047] [depth= 1] . ( 3 sec) [ -12118.1402] [ 2996] [depth= 1] . ( 4 sec) [ -11894.5401] [ 2824] [depth= 4] . ( 4 sec) [ -11769.7012] [ 2670] [depth= 2] . ( 4 sec) [ -11762.2359] [ 2671] [depth= 1] . ( 4 sec) [ -11757.0935] [ 2679] [depth= 1] . ( 4 sec) [ -11739.2941] [ 2670] [depth= 2] . ( 4 sec) [ -11734.3019] [ 2651] [depth= 4] . ( 4 sec) [ -11657.1129] [ 2633] [depth= 2] . ( 4 sec) [ -11654.8522] [ 2634] [depth= 1] . ( 4 sec) [ -11484.0007] [ 2539] [depth= 3] . ( 4 sec) [ -11459.2127] [ 2528] [depth= 1] . ( 4 sec) [ -11130.3206] [ 2459] [depth= 2] . ( 4 sec) [ -11093.7970] [ 2460] [depth= 2] . ( 4 sec) [ -11050.6748] [ 2453] [depth= 2] . ( 4 sec) [ -11026.8078] [ 2440] [depth= 1] . ( 4 sec) [ -11021.3879] [ 2444] [depth= 1] . ( 5 sec) [ -10825.0766] [ 2373] [depth= 2] . ( 5 sec) [ -10621.3648] [ 2294] [depth= 2] . ( 5 sec) [ -10519.1366] [ 2298] [depth= 3] . ( 5 sec) [ -10438.2484] [ 2203] [depth= 1] . ( 5 sec) [ -10435.3062] [ 2203] [depth= 1] . ( 5 sec) [ -10422.6478] [ 2315] [depth= 1] . ( 5 sec) [ -10396.6038] [ 2202] [depth= 4] . ( 5 sec) [ -10345.3670] [ 2201] [depth= 1] . ( 5 sec) [ -10339.4478] [ 2199] [depth= 1] . ( 5 sec) [ -10177.7655] [ 2199] [depth= 2] . ( 5 sec) [ -10168.3550] [ 2196] [depth= 1] . ( 5 sec) [ -10158.3426] [ 2193] [depth= 2] . ( 5 sec) [ -10155.6361] [ 2199] [depth= 1] . ( 5 sec) [ -9648.0787] [Branch lengths ] . ( 6 sec) [ -9645.1554] [GTR parameters ] . ( 6 sec) [ -9615.9739] [Alpha ][ 0.862906] . ( 6 sec) [ -9612.1049] [ 2195] [depth= 1] . ( 6 sec) [ -9611.8928] [ 2197] [depth= 1] . ( 6 sec) [ -9607.1667] [ 2192] [depth= 1] . ( 6 sec) [ -9607.1223] [ 2192] [depth= 1] . ( 7 sec) [ -9605.2853] [ 2200] [depth= 2] . ( 7 sec) [ -9591.7016] [ 2193] [depth= 2] . ( 7 sec) [ -9591.4290] [ 2195] [depth= 1] . ( 7 sec) [ -9590.8865] [ 2197] [depth= 1] . ( 7 sec) [ -9589.8693] [ 2197] [depth= 1] . ( 7 sec) [ -9585.2688] [ 2206] [depth= 1] . ( 7 sec) [ -9583.7672] [ 2204] [depth= 1] . ( 7 sec) [ -9583.2054] [ 2203] [depth= 2] . ( 8 sec) [ -9578.2102] [ 2200] [depth= 1] . ( 8 sec) [ -9576.1282] [ 2178] [depth= 1] . ( 8 sec) [ -9576.0531] [ 2179] [depth= 1] . ( 9 sec) [ -9575.8851] [ 2178] [depth= 1] . ( 9 sec) [ -9575.2548] [ 2158] [depth= 1] . ( 9 sec) [ -9575.1556] [ 2158] [depth= 1] . ( 9 sec) [ -9572.0438] [ 2156] [depth= 3] . ( 9 sec) [ -9571.1320] [ 2159] [depth= 1] . ( 9 sec) [ -9570.9697] [ 2157] [depth= 1] . ( 10 sec) [ -9570.1153] [ 2156] [depth= 1] . ( 10 sec) [ -9569.5062] [ 2153] [depth= 1] . ( 10 sec) [ -9550.8260] [Branch lengths ] . ( 11 sec) [ -9550.6611] [GTR parameters ] . ( 11 sec) [ -9550.0926] [Alpha ][ 0.930619] . ( 11 sec) [ -9550.0426] [ 2153] [depth= 1] . ( 11 sec) [ -9549.5179] [ 2144] [depth= 1] . ( 13 sec) [ -9549.0006] [ 2141] [depth= 2] . ( 14 sec) [ -9545.2409] [Branch lengths ] . ( 15 sec) [ -9545.2331] [GTR parameters ] . ( 15 sec) [ -9545.2226] [Alpha ][ 0.940393] . ( 19 sec) [ -9544.3251] [Branch lengths ] . ( 42 sec) [ -9544.1110] [Branch lengths ] . ( 42 sec) [ -9544.1110] [Topology ] . ( 42 sec) [ -9544.0744] [Topology ] . ( 43 sec) [ -9544.0567] [Topology ] . ( 44 sec) [ -9544.0464] [Topology ] . ( 45 sec) [ -9544.0402] [Topology ] . ( 45 sec) [ -9544.0364] [Topology ] . ( 46 sec) [ -9544.0340] [Topology ] . ( 47 sec) [ -9544.0328] [GTR parameters ] . ( 47 sec) [ -9544.0248] [Alpha ][ 0.949091] . ( 47 sec) [ -9544.0248] [Topology ] . ( 47 sec) [ -9544.0225] [Topology ] . ( 48 sec) [ -9544.0214] [Topology ] . ( 49 sec) [ -9544.0207] [Topology ] . ( 49 sec) [ -9544.0207] [GTR parameters ] . ( 49 sec) [ -9544.0207] [Alpha ][ 0.950041] . ( 49 sec) [ -9544.0207] [Topology ] . ( 50 sec) [ -9544.0202] [Topology ] . ( 50 sec) [ -9544.0202] [GTR parameters ] . ( 50 sec) [ -9544.0202] [Alpha ][ 0.950041] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.020233. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23293.9445] [GTR parameters ] . ( 1 sec) [ -22722.1530] [Alpha ][ 0.500960] . ( 1 sec) [ -22003.2946] [ 5489] [depth= 3] . ( 1 sec) [ -21785.4383] [ 5397] [depth= 10] . ( 1 sec) [ -21720.3433] [ 5332] [depth= 3] . ( 1 sec) [ -20878.0348] [ 5298] [depth= 2] . ( 1 sec) [ -20460.2239] [ 5177] [depth= 3] . ( 1 sec) [ -20322.0535] [ 5166] [depth= 6] . ( 1 sec) [ -20200.3883] [ 5162] [depth= 4] . ( 1 sec) [ -20140.8160] [ 5067] [depth= 1] . ( 1 sec) [ -20048.8313] [ 5049] [depth= 3] . ( 1 sec) [ -19823.0545] [ 4928] [depth= 8] . ( 1 sec) [ -19811.8544] [ 4921] [depth= 1] . ( 1 sec) [ -19544.8120] [ 4808] [depth= 3] . ( 1 sec) [ -19497.4256] [ 4805] [depth= 4] . ( 1 sec) [ -18972.5682] [ 4728] [depth= 2] . ( 1 sec) [ -18819.6254] [ 4716] [depth= 4] . ( 1 sec) [ -18552.6965] [ 4623] [depth= 3] . ( 1 sec) [ -18503.2145] [ 4617] [depth= 3] . ( 1 sec) [ -18106.0768] [ 4588] [depth= 6] . ( 1 sec) [ -17689.5737] [ 4580] [depth= 1] . ( 2 sec) [ -16900.2665] [ 4427] [depth= 13] . ( 2 sec) [ -16523.3276] [ 4426] [depth= 8] . ( 2 sec) [ -16496.6824] [ 4334] [depth= 1] . ( 2 sec) [ -16362.3005] [ 4268] [depth= 7] . ( 2 sec) [ -16155.0491] [ 4175] [depth= 1] . ( 2 sec) [ -15509.6404] [ 4162] [depth= 2] . ( 2 sec) [ -15306.0470] [ 4035] [depth= 15] . ( 2 sec) [ -15304.7877] [ 4038] [depth= 19] . ( 2 sec) [ -15113.7111] [ 3990] [depth= 2] . ( 2 sec) [ -14949.9715] [ 3960] [depth= 8] . ( 2 sec) [ -14927.4407] [ 3923] [depth= 15] . ( 2 sec) [ -14823.2914] [ 3893] [depth= 1] . ( 2 sec) [ -14458.1515] [ 3853] [depth= 4] . ( 2 sec) [ -14248.0196] [ 3791] [depth= 2] . ( 2 sec) [ -14157.8807] [ 3640] [depth= 2] . ( 2 sec) [ -14151.5661] [ 3646] [depth= 1] . ( 2 sec) [ -14031.3376] [ 3622] [depth= 1] . ( 2 sec) [ -13911.3972] [ 3597] [depth= 3] . ( 2 sec) [ -13906.9335] [ 3586] [depth= 1] . ( 2 sec) [ -13855.1709] [ 3587] [depth= 5] . ( 3 sec) [ -13738.6427] [ 3591] [depth= 2] . ( 3 sec) [ -13470.8843] [ 3555] [depth= 13] . ( 3 sec) [ -13304.6873] [ 3423] [depth= 11] . ( 3 sec) [ -13235.7911] [ 3411] [depth= 9] . ( 3 sec) [ -13188.8740] [ 3412] [depth= 1] . ( 3 sec) [ -12954.5934] [ 3356] [depth= 6] . ( 3 sec) [ -12597.5558] [ 3130] [depth= 6] . ( 3 sec) [ -12438.6186] [ 3007] [depth= 2] . ( 3 sec) [ -12429.3988] [ 3008] [depth= 1] . ( 3 sec) [ -12413.2406] [ 2944] [depth= 3] . ( 3 sec) [ -12286.3066] [ 2930] [depth= 1] . ( 3 sec) [ -12185.3795] [ 2920] [depth= 1] . ( 3 sec) [ -11875.3897] [ 2909] [depth= 1] . ( 3 sec) [ -11743.0849] [ 2909] [depth= 1] . ( 3 sec) [ -11410.3383] [ 2729] [depth= 4] . ( 3 sec) [ -11398.4961] [ 2719] [depth= 2] . ( 3 sec) [ -11371.3519] [ 2706] [depth= 1] . ( 3 sec) [ -11196.2104] [ 2704] [depth= 2] . ( 3 sec) [ -11183.2063] [ 2703] [depth= 1] . ( 4 sec) [ -11183.1126] [ 2705] [depth= 1] . ( 4 sec) [ -10973.7604] [ 2558] [depth= 5] . ( 4 sec) [ -10943.3701] [ 2540] [depth= 3] . ( 4 sec) [ -10820.4469] [ 2539] [depth= 1] . ( 4 sec) [ -10756.2284] [ 2452] [depth= 8] . ( 4 sec) [ -10568.6995] [ 2449] [depth= 1] . ( 4 sec) [ -10563.3701] [ 2442] [depth= 3] . ( 4 sec) [ -10556.8378] [ 2440] [depth= 1] . ( 4 sec) [ -10556.2894] [ 2446] [depth= 15] . ( 4 sec) [ -10551.3327] [ 2447] [depth= 3] . ( 4 sec) [ -10551.0564] [ 2452] [depth= 2] . ( 4 sec) [ -10550.3995] [ 2452] [depth= 1] . ( 4 sec) [ -10523.7337] [ 2453] [depth= 1] . ( 4 sec) [ -10523.3980] [ 2454] [depth= 1] . ( 4 sec) [ -10520.2708] [ 2454] [depth= 1] . ( 4 sec) [ -10506.1847] [ 2454] [depth= 1] . ( 4 sec) [ -10463.5612] [ 2461] [depth= 1] . ( 4 sec) [ -10415.5213] [ 2451] [depth= 3] . ( 5 sec) [ -10137.1577] [ 2369] [depth= 10] . ( 5 sec) [ -10135.1724] [ 2368] [depth= 1] . ( 5 sec) [ -10134.2836] [ 2365] [depth= 2] . ( 5 sec) [ -10124.9562] [ 2362] [depth= 2] . ( 5 sec) [ -10119.8684] [ 2361] [depth= 1] . ( 5 sec) [ -10077.3478] [ 2356] [depth= 1] . ( 5 sec) [ -10034.1624] [ 2344] [depth= 1] . ( 5 sec) [ -10028.3938] [ 2346] [depth= 1] . ( 5 sec) [ -10027.0549] [ 2349] [depth= 1] . ( 5 sec) [ -9992.8126] [ 2347] [depth= 1] . ( 5 sec) [ -9870.9419] [Branch lengths ] . ( 6 sec) [ -9868.6014] [GTR parameters ] . ( 6 sec) [ -9844.9730] [Alpha ][ 0.797906] . ( 6 sec) [ -9739.7661] [ 2267] [depth= 7] . ( 6 sec) [ -9739.5248] [ 2265] [depth= 1] . ( 6 sec) [ -9729.7412] [ 2262] [depth= 1] . ( 7 sec) [ -9702.4295] [ 2257] [depth= 1] . ( 7 sec) [ -9702.0650] [ 2257] [depth= 1] . ( 7 sec) [ -9697.9742] [ 2237] [depth= 2] . ( 7 sec) [ -9694.2068] [ 2230] [depth= 1] . ( 7 sec) [ -9693.7248] [ 2230] [depth= 1] . ( 7 sec) [ -9640.1046] [ 2232] [depth= 1] . ( 7 sec) [ -9623.2990] [ 2219] [depth= 1] . ( 7 sec) [ -9583.8717] [ 2154] [depth= 4] . ( 7 sec) [ -9582.2204] [ 2144] [depth= 2] . ( 7 sec) [ -9580.0198] [ 2147] [depth= 1] . ( 7 sec) [ -9578.0311] [ 2162] [depth= 1] . ( 7 sec) [ -9575.8044] [ 2173] [depth= 1] . ( 8 sec) [ -9575.4995] [ 2174] [depth= 1] . ( 8 sec) [ -9569.9335] [ 2167] [depth= 3] . ( 8 sec) [ -9566.3384] [ 2153] [depth= 1] . ( 8 sec) [ -9566.1073] [ 2153] [depth= 1] . ( 8 sec) [ -9565.7931] [ 2150] [depth= 1] . ( 9 sec) [ -9565.1635] [ 2148] [depth= 1] . ( 9 sec) [ -9564.6988] [ 2150] [depth= 1] . ( 10 sec) [ -9551.1001] [Branch lengths ] . ( 10 sec) [ -9550.8260] [GTR parameters ] . ( 10 sec) [ -9548.6043] [Alpha ][ 0.925991] . ( 11 sec) [ -9547.9591] [ 2143] [depth= 1] . ( 14 sec) [ -9545.5833] [Branch lengths ] . ( 14 sec) [ -9545.5762] [GTR parameters ] . ( 14 sec) [ -9545.5500] [Alpha ][ 0.941540] . ( 18 sec) [ -9544.3662] [Branch lengths ] . ( 41 sec) [ -9544.1167] [Branch lengths ] . ( 41 sec) [ -9544.1167] [Topology ] . ( 42 sec) [ -9544.0756] [Topology ] . ( 42 sec) [ -9544.0565] [Topology ] . ( 43 sec) [ -9544.0454] [Topology ] . ( 44 sec) [ -9544.0387] [Topology ] . ( 45 sec) [ -9544.0346] [Topology ] . ( 45 sec) [ -9544.0321] [Topology ] . ( 46 sec) [ -9544.0309] [GTR parameters ] . ( 46 sec) [ -9544.0247] [Alpha ][ 0.949167] . ( 46 sec) [ -9544.0247] [Topology ] . ( 47 sec) [ -9544.0224] [Topology ] . ( 47 sec) [ -9544.0213] [Topology ] . ( 48 sec) [ -9544.0206] [Topology ] . ( 48 sec) [ -9544.0206] [GTR parameters ] . ( 48 sec) [ -9544.0206] [Alpha ][ 0.950116] . ( 48 sec) [ -9544.0206] [Topology ] . ( 49 sec) [ -9544.0201] [Topology ] . ( 49 sec) [ -9544.0201] [GTR parameters ] . ( 49 sec) [ -9544.0201] [Alpha ][ 0.950116] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.020145. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24509.8559] [GTR parameters ] . ( 1 sec) [ -23886.1139] [Alpha ][ 0.500960] . ( 1 sec) [ -22993.4007] [ 5701] [depth= 8] . ( 1 sec) [ -22328.8676] [ 5659] [depth= 10] . ( 1 sec) [ -22248.2955] [ 5634] [depth= 4] . ( 1 sec) [ -22167.4092] [ 5629] [depth= 2] . ( 1 sec) [ -21976.6290] [ 5554] [depth= 9] . ( 1 sec) [ -21859.6060] [ 5545] [depth= 3] . ( 1 sec) [ -21415.5462] [ 5401] [depth= 6] . ( 1 sec) [ -20977.4573] [ 5326] [depth= 7] . ( 1 sec) [ -20168.4422] [ 5110] [depth= 10] . ( 1 sec) [ -19625.3916] [ 5111] [depth= 12] . ( 1 sec) [ -19177.7617] [ 4958] [depth= 7] . ( 1 sec) [ -18806.3684] [ 4797] [depth= 10] . ( 1 sec) [ -18600.6805] [ 4766] [depth= 1] . ( 1 sec) [ -18528.6595] [ 4758] [depth= 3] . ( 1 sec) [ -18502.8481] [ 4654] [depth= 5] . ( 1 sec) [ -18381.4859] [ 4629] [depth= 2] . ( 1 sec) [ -17899.9359] [ 4636] [depth= 1] . ( 1 sec) [ -17849.3457] [ 4617] [depth= 7] . ( 2 sec) [ -17422.4711] [ 4482] [depth= 5] . ( 2 sec) [ -16907.7170] [ 4353] [depth= 14] . ( 2 sec) [ -16434.0655] [ 4172] [depth= 14] . ( 2 sec) [ -16088.6384] [ 4026] [depth= 8] . ( 2 sec) [ -15952.7985] [ 3997] [depth= 7] . ( 2 sec) [ -15882.4608] [ 4002] [depth= 1] . ( 2 sec) [ -15867.5659] [ 4002] [depth= 1] . ( 2 sec) [ -15723.1731] [ 3974] [depth= 6] . ( 2 sec) [ -15717.4195] [ 3967] [depth= 1] . ( 2 sec) [ -15707.9951] [ 3968] [depth= 1] . ( 2 sec) [ -15615.5856] [ 3977] [depth= 1] . ( 2 sec) [ -15564.8241] [ 3968] [depth= 1] . ( 2 sec) [ -15558.8832] [ 3980] [depth= 12] . ( 2 sec) [ -15299.9429] [ 3841] [depth= 7] . ( 2 sec) [ -15240.9328] [ 3834] [depth= 1] . ( 2 sec) [ -15061.7163] [ 3836] [depth= 1] . ( 2 sec) [ -14884.6782] [ 3823] [depth= 9] . ( 2 sec) [ -14859.8271] [ 3870] [depth= 1] . ( 2 sec) [ -14709.8640] [ 3758] [depth= 3] . ( 2 sec) [ -14698.2655] [ 3676] [depth= 1] . ( 3 sec) [ -14361.8106] [ 3480] [depth= 7] . ( 3 sec) [ -14177.1402] [ 3457] [depth= 8] . ( 3 sec) [ -14149.4222] [ 3456] [depth= 1] . ( 3 sec) [ -14115.3785] [ 3451] [depth= 4] . ( 3 sec) [ -14105.8532] [ 3445] [depth= 1] . ( 3 sec) [ -13565.7338] [ 3346] [depth= 7] . ( 3 sec) [ -13386.1910] [ 3323] [depth= 3] . ( 3 sec) [ -13078.3263] [ 3183] [depth= 7] . ( 3 sec) [ -13047.7115] [ 3166] [depth= 5] . ( 3 sec) [ -13020.8252] [ 3161] [depth= 1] . ( 3 sec) [ -12783.3161] [ 3056] [depth= 11] . ( 3 sec) [ -12778.2076] [ 3055] [depth= 1] . ( 3 sec) [ -12539.3337] [ 2997] [depth= 1] . ( 3 sec) [ -12383.9562] [ 2954] [depth= 2] . ( 3 sec) [ -12364.9595] [ 2929] [depth= 2] . ( 3 sec) [ -12106.0467] [ 2847] [depth= 1] . ( 3 sec) [ -12094.8670] [ 2849] [depth= 1] . ( 3 sec) [ -12037.9970] [ 2846] [depth= 2] . ( 3 sec) [ -12037.9170] [ 2847] [depth= 1] . ( 4 sec) [ -12010.6396] [ 2844] [depth= 3] . ( 4 sec) [ -12000.3588] [ 2839] [depth= 1] . ( 4 sec) [ -11988.3743] [ 2837] [depth= 1] . ( 4 sec) [ -11727.1050] [ 2745] [depth= 1] . ( 4 sec) [ -11384.2631] [ 2637] [depth= 11] . ( 4 sec) [ -11360.7031] [ 2639] [depth= 1] . ( 4 sec) [ -11187.3928] [ 2582] [depth= 3] . ( 4 sec) [ -10840.8524] [ 2399] [depth= 10] . ( 4 sec) [ -10699.6243] [ 2348] [depth= 2] . ( 4 sec) [ -10694.3059] [ 2330] [depth= 3] . ( 4 sec) [ -10635.0746] [ 2357] [depth= 1] . ( 4 sec) [ -10399.5517] [ 2351] [depth= 1] . ( 4 sec) [ -10359.6047] [ 2354] [depth= 1] . ( 4 sec) [ -10331.8415] [ 2352] [depth= 3] . ( 4 sec) [ -10299.3875] [ 2352] [depth= 2] . ( 4 sec) [ -10230.9783] [ 2338] [depth= 5] . ( 4 sec) [ -10070.5015] [ 2311] [depth= 6] . ( 4 sec) [ -10032.7878] [ 2300] [depth= 1] . ( 4 sec) [ -10027.1753] [ 2299] [depth= 1] . ( 4 sec) [ -10014.0329] [ 2278] [depth= 1] . ( 4 sec) [ -9996.5336] [ 2232] [depth= 2] . ( 5 sec) [ -9977.0128] [ 2237] [depth= 2] . ( 5 sec) [ -9919.9088] [ 2182] [depth= 1] . ( 5 sec) [ -9918.0079] [ 2168] [depth= 1] . ( 5 sec) [ -9909.2953] [ 2164] [depth= 1] . ( 5 sec) [ -9834.3992] [ 2152] [depth= 3] . ( 5 sec) [ -9803.7597] [ 2187] [depth= 1] . ( 5 sec) [ -9765.7646] [ 2186] [depth= 1] . ( 5 sec) [ -9619.5219] [Branch lengths ] . ( 6 sec) [ -9616.7739] [GTR parameters ] . ( 6 sec) [ -9591.6454] [Alpha ][ 0.829762] . ( 6 sec) [ -9590.7016] [ 2184] [depth= 2] . ( 6 sec) [ -9590.6071] [ 2185] [depth= 1] . ( 6 sec) [ -9589.9819] [ 2185] [depth= 1] . ( 6 sec) [ -9589.6969] [ 2183] [depth= 1] . ( 6 sec) [ -9566.4647] [ 2141] [depth= 2] . ( 7 sec) [ -9566.2252] [ 2144] [depth= 1] . ( 7 sec) [ -9566.1957] [ 2144] [depth= 1] . ( 7 sec) [ -9565.3080] [ 2146] [depth= 1] . ( 7 sec) [ -9565.1081] [ 2148] [depth= 1] . ( 8 sec) [ -9564.1648] [ 2148] [depth= 1] . ( 8 sec) [ -9563.8058] [ 2145] [depth= 1] . ( 9 sec) [ -9563.7449] [ 2144] [depth= 1] . ( 9 sec) [ -9563.6442] [ 2143] [depth= 1] . ( 10 sec) [ -9563.1855] [ 2142] [depth= 1] . ( 10 sec) [ -9550.9204] [Branch lengths ] . ( 10 sec) [ -9550.8526] [GTR parameters ] . ( 11 sec) [ -9549.6680] [Alpha ][ 0.927826] . ( 12 sec) [ -9549.5762] [ 2143] [depth= 1] . ( 14 sec) [ -9549.4028] [ 2144] [depth= 1] . ( 14 sec) [ -9549.3700] [ 2143] [depth= 1] . ( 14 sec) [ -9549.3384] [ 2142] [depth= 1] . ( 15 sec) [ -9546.9959] [Branch lengths ] . ( 15 sec) [ -9546.9951] [GTR parameters ] . ( 15 sec) [ -9546.9641] [Alpha ][ 0.945006] . ( 18 sec) [ -9546.9203] [ 2143] [depth= 1] . ( 19 sec) [ -9546.9101] [ 2142] [depth= 1] . ( 19 sec) [ -9545.0048] [Branch lengths ] . ( 19 sec) [ -9545.0035] [GTR parameters ] . ( 19 sec) [ -9545.0007] [Alpha ][ 0.950113] . ( 21 sec) [ -9544.9647] [ 2142] [depth= 1] . ( 22 sec) [ -9544.9480] [ 2142] [depth= 1] . ( 23 sec) [ -9544.0795] [Branch lengths ] . ( 23 sec) [ -9544.0783] [GTR parameters ] . ( 23 sec) [ -9544.0783] [Alpha ][ 0.950113] . ( 46 sec) [ -9544.0240] [Branch lengths ] . ( 46 sec) [ -9544.0240] [Topology ] . ( 47 sec) [ -9544.0212] [Topology ] . ( 47 sec) [ -9544.0203] [Topology ] . ( 48 sec) [ -9544.0203] [GTR parameters ] . ( 48 sec) [ -9544.0203] [Alpha ][ 0.950113] . ( 48 sec) [ -9544.0203] [Topology ] . ( 48 sec) [ -9544.0199] [Topology ] . ( 48 sec) [ -9544.0199] [GTR parameters ] . ( 49 sec) [ -9544.0199] [Alpha ][ 0.950113] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.019871. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23578.3845] [GTR parameters ] . ( 1 sec) [ -23003.1403] [Alpha ][ 0.500960] . ( 1 sec) [ -22039.6126] [ 5496] [depth= 8] . ( 1 sec) [ -21821.2876] [ 5359] [depth= 8] . ( 1 sec) [ -21370.9606] [ 5211] [depth= 8] . ( 1 sec) [ -21346.2729] [ 5194] [depth= 1] . ( 1 sec) [ -20866.6270] [ 5113] [depth= 6] . ( 1 sec) [ -20249.0850] [ 5094] [depth= 2] . ( 1 sec) [ -20162.6958] [ 5097] [depth= 5] . ( 1 sec) [ -20106.3328] [ 4948] [depth= 5] . ( 2 sec) [ -19865.6641] [ 4939] [depth= 6] . ( 2 sec) [ -19661.1751] [ 4933] [depth= 4] . ( 2 sec) [ -19634.9633] [ 4932] [depth= 1] . ( 2 sec) [ -19606.0260] [ 4894] [depth= 2] . ( 2 sec) [ -19497.0714] [ 4823] [depth= 12] . ( 2 sec) [ -19279.0097] [ 4786] [depth= 2] . ( 2 sec) [ -19193.9563] [ 4786] [depth= 1] . ( 2 sec) [ -19159.1163] [ 4746] [depth= 5] . ( 2 sec) [ -18872.8398] [ 4729] [depth= 4] . ( 2 sec) [ -18731.7105] [ 4760] [depth= 7] . ( 2 sec) [ -18291.5462] [ 4572] [depth= 7] . ( 2 sec) [ -17323.6092] [ 4537] [depth= 3] . ( 2 sec) [ -17290.0247] [ 4514] [depth= 5] . ( 2 sec) [ -17006.9442] [ 4483] [depth= 12] . ( 2 sec) [ -16877.7378] [ 4481] [depth= 5] . ( 2 sec) [ -16570.3784] [ 4364] [depth= 4] . ( 2 sec) [ -16490.5331] [ 4360] [depth= 10] . ( 2 sec) [ -16095.7039] [ 4212] [depth= 9] . ( 2 sec) [ -16072.8912] [ 4211] [depth= 1] . ( 2 sec) [ -16060.7864] [ 4210] [depth= 1] . ( 2 sec) [ -15790.2105] [ 4126] [depth= 1] . ( 3 sec) [ -15300.4770] [ 3989] [depth= 12] . ( 3 sec) [ -15262.0123] [ 3992] [depth= 1] . ( 3 sec) [ -15070.4301] [ 3814] [depth= 4] . ( 3 sec) [ -15054.4988] [ 3811] [depth= 1] . ( 3 sec) [ -14919.7768] [ 3775] [depth= 1] . ( 3 sec) [ -14686.4826] [ 3697] [depth= 2] . ( 3 sec) [ -14641.5507] [ 3691] [depth= 2] . ( 3 sec) [ -14633.6625] [ 3696] [depth= 1] . ( 3 sec) [ -14155.0605] [ 3504] [depth= 12] . ( 3 sec) [ -13756.4425] [ 3477] [depth= 9] . ( 3 sec) [ -13700.5732] [ 3486] [depth= 1] . ( 3 sec) [ -13534.6788] [ 3454] [depth= 9] . ( 3 sec) [ -13514.3350] [ 3471] [depth= 1] . ( 3 sec) [ -13341.9006] [ 3353] [depth= 10] . ( 3 sec) [ -13151.7000] [ 3334] [depth= 10] . ( 3 sec) [ -13000.3544] [ 3310] [depth= 6] . ( 3 sec) [ -12992.3796] [ 3310] [depth= 1] . ( 3 sec) [ -12985.0872] [ 3310] [depth= 1] . ( 3 sec) [ -12772.6292] [ 3234] [depth= 7] . ( 3 sec) [ -12721.9788] [ 3234] [depth= 2] . ( 3 sec) [ -12037.0215] [ 3161] [depth= 7] . ( 4 sec) [ -11894.7609] [ 3039] [depth= 8] . ( 4 sec) [ -11783.0579] [ 3012] [depth= 7] . ( 4 sec) [ -11762.3218] [ 3005] [depth= 1] . ( 4 sec) [ -11725.5510] [ 2993] [depth= 1] . ( 4 sec) [ -11718.3853] [ 2995] [depth= 6] . ( 4 sec) [ -11581.3254] [ 2963] [depth= 4] . ( 4 sec) [ -11543.0219] [ 2961] [depth= 1] . ( 4 sec) [ -11542.4539] [ 2962] [depth= 1] . ( 4 sec) [ -11228.2871] [ 2782] [depth= 7] . ( 4 sec) [ -11216.7266] [ 2770] [depth= 2] . ( 4 sec) [ -11206.4653] [ 2769] [depth= 1] . ( 4 sec) [ -11179.6389] [ 2764] [depth= 2] . ( 4 sec) [ -11156.1220] [ 2752] [depth= 1] . ( 4 sec) [ -11112.1110] [ 2749] [depth= 7] . ( 4 sec) [ -11084.6855] [ 2744] [depth= 1] . ( 4 sec) [ -11073.2612] [ 2756] [depth= 1] . ( 4 sec) [ -11044.4013] [ 2779] [depth= 1] . ( 4 sec) [ -11033.2071] [ 2776] [depth= 2] . ( 4 sec) [ -11032.9149] [ 2764] [depth= 1] . ( 4 sec) [ -11027.6688] [ 2763] [depth= 1] . ( 4 sec) [ -11026.5154] [ 2762] [depth= 1] . ( 5 sec) [ -11001.5473] [ 2757] [depth= 3] . ( 5 sec) [ -10881.1368] [ 2707] [depth= 2] . ( 5 sec) [ -10804.2597] [ 2676] [depth= 8] . ( 5 sec) [ -10803.2938] [ 2623] [depth= 1] . ( 5 sec) [ -10786.9187] [ 2620] [depth= 4] . ( 5 sec) [ -10785.2844] [ 2621] [depth= 2] . ( 5 sec) [ -10784.8781] [ 2619] [depth= 1] . ( 5 sec) [ -10779.7331] [ 2620] [depth= 1] . ( 5 sec) [ -10689.3895] [ 2599] [depth= 3] . ( 5 sec) [ -10663.0307] [ 2601] [depth= 3] . ( 5 sec) [ -10520.3015] [ 2577] [depth= 2] . ( 5 sec) [ -10498.7254] [ 2580] [depth= 1] . ( 5 sec) [ -10482.0447] [ 2575] [depth= 2] . ( 5 sec) [ -10355.5820] [ 2517] [depth= 1] . ( 6 sec) [ -10239.3294] [Branch lengths ] . ( 6 sec) [ -10238.1607] [GTR parameters ] . ( 6 sec) [ -10219.2956] [Alpha ][ 0.737280] . ( 6 sec) [ -10202.6249] [ 2506] [depth= 1] . ( 6 sec) [ -10202.5630] [ 2510] [depth= 1] . ( 7 sec) [ -10197.3177] [ 2504] [depth= 1] . ( 7 sec) [ -10165.1351] [ 2423] [depth= 7] . ( 7 sec) [ -10113.7106] [ 2391] [depth= 1] . ( 7 sec) [ -9961.3206] [ 2284] [depth= 9] . ( 7 sec) [ -9957.5282] [ 2284] [depth= 1] . ( 7 sec) [ -9956.4847] [ 2286] [depth= 1] . ( 7 sec) [ -9955.2185] [ 2284] [depth= 2] . ( 7 sec) [ -9954.0752] [ 2285] [depth= 1] . ( 7 sec) [ -9948.4652] [ 2287] [depth= 2] . ( 7 sec) [ -9876.2340] [ 2267] [depth= 3] . ( 7 sec) [ -9847.5783] [ 2268] [depth= 1] . ( 7 sec) [ -9753.9261] [ 2275] [depth= 2] . ( 7 sec) [ -9752.7389] [ 2278] [depth= 1] . ( 7 sec) [ -9750.6387] [ 2269] [depth= 1] . ( 8 sec) [ -9738.9849] [ 2266] [depth= 1] . ( 8 sec) [ -9682.4024] [ 2242] [depth= 1] . ( 8 sec) [ -9675.1141] [ 2237] [depth= 1] . ( 8 sec) [ -9674.9802] [ 2236] [depth= 1] . ( 8 sec) [ -9674.6825] [ 2237] [depth= 1] . ( 8 sec) [ -9674.0719] [ 2237] [depth= 1] . ( 8 sec) [ -9672.3684] [ 2233] [depth= 1] . ( 8 sec) [ -9672.2053] [ 2232] [depth= 1] . ( 8 sec) [ -9672.1154] [ 2231] [depth= 1] . ( 8 sec) [ -9670.8650] [ 2232] [depth= 1] . ( 8 sec) [ -9665.5749] [ 2236] [depth= 1] . ( 8 sec) [ -9651.6367] [ 2238] [depth= 3] . ( 9 sec) [ -9646.0939] [ 2238] [depth= 1] . ( 9 sec) [ -9646.0684] [ 2238] [depth= 1] . ( 9 sec) [ -9646.0578] [ 2237] [depth= 1] . ( 9 sec) [ -9638.0681] [ 2233] [depth= 1] . ( 9 sec) [ -9635.5236] [ 2234] [depth= 1] . ( 9 sec) [ -9635.1621] [ 2243] [depth= 1] . ( 9 sec) [ -9606.7587] [ 2195] [depth= 5] . ( 9 sec) [ -9604.3682] [ 2200] [depth= 2] . ( 10 sec) [ -9582.4543] [Branch lengths ] . ( 11 sec) [ -9581.9488] [GTR parameters ] . ( 11 sec) [ -9577.5220] [Alpha ][ 0.905960] . ( 11 sec) [ -9577.2758] [ 2198] [depth= 1] . ( 11 sec) [ -9550.3453] [ 2147] [depth= 4] . ( 12 sec) [ -9549.0025] [ 2146] [depth= 2] . ( 12 sec) [ -9548.8380] [ 2146] [depth= 1] . ( 13 sec) [ -9548.8268] [ 2147] [depth= 1] . ( 14 sec) [ -9548.4955] [ 2144] [depth= 1] . ( 15 sec) [ -9545.5440] [Branch lengths ] . ( 15 sec) [ -9545.5028] [GTR parameters ] . ( 15 sec) [ -9545.2732] [Alpha ][ 0.950755] . ( 19 sec) [ -9544.8415] [Branch lengths ] . ( 39 sec) [ -9544.4590] [ 2142] [depth= 1] . ( 41 sec) [ -9544.0636] [Branch lengths ] . ( 42 sec) [ -9544.0561] [GTR parameters ] . ( 42 sec) [ -9544.0561] [Alpha ][ 0.950755] . ( 42 sec) [ -9544.0561] [Topology ] . ( 42 sec) [ -9544.0390] [Topology ] . ( 43 sec) [ -9544.0321] [Topology ] . ( 44 sec) [ -9544.0279] [Topology ] . ( 45 sec) [ -9544.0253] [Topology ] . ( 46 sec) [ -9544.0235] [Topology ] . ( 46 sec) [ -9544.0223] [Topology ] . ( 47 sec) [ -9544.0223] [GTR parameters ] . ( 47 sec) [ -9544.0222] [Alpha ][ 0.949804] . ( 47 sec) [ -9544.0222] [Topology ] . ( 48 sec) [ -9544.0214] [Topology ] . ( 48 sec) [ -9544.0214] [GTR parameters ] . ( 48 sec) [ -9544.0214] [Alpha ][ 0.949804] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.021373. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -24984.0349] [GTR parameters ] . ( 0 sec) [ -24351.1778] [Alpha ][ 0.500960] . ( 0 sec) [ -22782.0633] [ 5720] [depth= 6] . ( 0 sec) [ -22486.1928] [ 5600] [depth= 9] . ( 0 sec) [ -22326.4829] [ 5570] [depth= 3] . ( 0 sec) [ -22317.5121] [ 5565] [depth= 1] . ( 1 sec) [ -22113.7614] [ 5512] [depth= 6] . ( 1 sec) [ -21926.5240] [ 5496] [depth= 6] . ( 1 sec) [ -21823.9170] [ 5425] [depth= 1] . ( 1 sec) [ -21394.0555] [ 5330] [depth= 7] . ( 1 sec) [ -20858.6036] [ 5233] [depth= 3] . ( 1 sec) [ -20724.6382] [ 5180] [depth= 1] . ( 1 sec) [ -20298.7473] [ 5078] [depth= 13] . ( 1 sec) [ -20215.0727] [ 5058] [depth= 7] . ( 1 sec) [ -20211.8633] [ 5050] [depth= 1] . ( 1 sec) [ -20001.1546] [ 5011] [depth= 5] . ( 1 sec) [ -19869.7011] [ 5006] [depth= 2] . ( 1 sec) [ -19698.2283] [ 4908] [depth= 6] . ( 1 sec) [ -19457.3193] [ 4902] [depth= 3] . ( 1 sec) [ -18815.9846] [ 4876] [depth= 11] . ( 1 sec) [ -18319.0539] [ 4731] [depth= 7] . ( 1 sec) [ -17950.7954] [ 4725] [depth= 9] . ( 1 sec) [ -17330.6510] [ 4590] [depth= 8] . ( 1 sec) [ -16893.7953] [ 4460] [depth= 2] . ( 1 sec) [ -16570.1283] [ 4345] [depth= 16] . ( 1 sec) [ -16001.6214] [ 4274] [depth= 15] . ( 1 sec) [ -15982.1440] [ 4275] [depth= 1] . ( 1 sec) [ -15763.0966] [ 4235] [depth= 8] . ( 2 sec) [ -15601.3050] [ 4226] [depth= 4] . ( 2 sec) [ -15590.2138] [ 4223] [depth= 1] . ( 2 sec) [ -15560.9585] [ 4185] [depth= 10] . ( 2 sec) [ -15343.2936] [ 3965] [depth= 7] . ( 2 sec) [ -15317.4910] [ 3966] [depth= 1] . ( 2 sec) [ -15180.3653] [ 3971] [depth= 4] . ( 2 sec) [ -14795.3898] [ 3921] [depth= 1] . ( 2 sec) [ -14718.8718] [ 3914] [depth= 1] . ( 2 sec) [ -14462.9608] [ 3807] [depth= 9] . ( 2 sec) [ -14261.8614] [ 3695] [depth= 7] . ( 2 sec) [ -14084.7003] [ 3637] [depth= 1] . ( 2 sec) [ -14079.4011] [ 3637] [depth= 1] . ( 2 sec) [ -14075.5746] [ 3638] [depth= 1] . ( 2 sec) [ -14056.2293] [ 3637] [depth= 2] . ( 2 sec) [ -14025.1519] [ 3630] [depth= 2] . ( 2 sec) [ -13908.8200] [ 3593] [depth= 1] . ( 2 sec) [ -13831.9764] [ 3574] [depth= 7] . ( 2 sec) [ -13592.5134] [ 3556] [depth= 9] . ( 2 sec) [ -13425.4174] [ 3519] [depth= 1] . ( 2 sec) [ -13275.2662] [ 3492] [depth= 5] . ( 2 sec) [ -13166.6457] [ 3493] [depth= 4] . ( 3 sec) [ -13077.9636] [ 3463] [depth= 7] . ( 3 sec) [ -12934.1445] [ 3463] [depth= 3] . ( 3 sec) [ -12429.0116] [ 3256] [depth= 11] . ( 3 sec) [ -12357.1829] [ 3240] [depth= 1] . ( 3 sec) [ -12329.2907] [ 3236] [depth= 2] . ( 3 sec) [ -12318.4122] [ 3231] [depth= 1] . ( 3 sec) [ -12279.4448] [ 3232] [depth= 1] . ( 3 sec) [ -12277.5488] [ 3234] [depth= 1] . ( 3 sec) [ -12261.6008] [ 3240] [depth= 1] . ( 3 sec) [ -12244.5455] [ 3227] [depth= 2] . ( 3 sec) [ -12235.6394] [ 3212] [depth= 1] . ( 3 sec) [ -11975.6242] [ 3206] [depth= 5] . ( 3 sec) [ -11967.2609] [ 3210] [depth= 1] . ( 4 sec) [ -11919.6855] [ 3089] [depth= 3] . ( 4 sec) [ -11911.5679] [ 3083] [depth= 1] . ( 4 sec) [ -11619.3391] [ 2949] [depth= 2] . ( 4 sec) [ -11578.4493] [ 2932] [depth= 2] . ( 4 sec) [ -11566.0744] [ 2933] [depth= 1] . ( 4 sec) [ -11470.7212] [ 2901] [depth= 3] . ( 4 sec) [ -11455.0536] [ 2890] [depth= 1] . ( 4 sec) [ -11433.2206] [ 2841] [depth= 4] . ( 4 sec) [ -11224.4920] [ 2840] [depth= 1] . ( 4 sec) [ -11206.1647] [ 2816] [depth= 1] . ( 4 sec) [ -11096.4030] [ 2706] [depth= 3] . ( 4 sec) [ -10910.4024] [ 2692] [depth= 3] . ( 4 sec) [ -10907.9065] [ 2688] [depth= 1] . ( 4 sec) [ -10762.9430] [ 2647] [depth= 2] . ( 4 sec) [ -10762.4225] [ 2649] [depth= 1] . ( 4 sec) [ -10626.0375] [ 2667] [depth= 7] . ( 4 sec) [ -10575.1481] [ 2666] [depth= 1] . ( 4 sec) [ -10573.7528] [ 2665] [depth= 1] . ( 4 sec) [ -10563.8152] [ 2677] [depth= 1] . ( 5 sec) [ -10561.3415] [ 2681] [depth= 1] . ( 5 sec) [ -10533.9484] [ 2643] [depth= 2] . ( 5 sec) [ -10442.7847] [ 2627] [depth= 1] . ( 5 sec) [ -10442.5156] [ 2615] [depth= 1] . ( 5 sec) [ -10265.2165] [Branch lengths ] . ( 6 sec) [ -10263.6336] [GTR parameters ] . ( 6 sec) [ -10252.3833] [Alpha ][ 0.680957] . ( 6 sec) [ -10208.1262] [ 2537] [depth= 3] . ( 6 sec) [ -10203.4717] [ 2537] [depth= 1] . ( 6 sec) [ -10183.3981] [ 2533] [depth= 1] . ( 6 sec) [ -10180.4300] [ 2532] [depth= 1] . ( 6 sec) [ -10178.9388] [ 2529] [depth= 1] . ( 6 sec) [ -10146.4726] [ 2521] [depth= 1] . ( 6 sec) [ -10143.0606] [ 2451] [depth= 1] . ( 6 sec) [ -10141.9822] [ 2455] [depth= 3] . ( 6 sec) [ -10141.3854] [ 2456] [depth= 1] . ( 6 sec) [ -10139.4236] [ 2461] [depth= 3] . ( 6 sec) [ -10136.4079] [ 2455] [depth= 5] . ( 7 sec) [ -10135.9962] [ 2454] [depth= 1] . ( 7 sec) [ -9986.1171] [ 2433] [depth= 3] . ( 7 sec) [ -9985.5355] [ 2434] [depth= 1] . ( 7 sec) [ -9984.8854] [ 2433] [depth= 2] . ( 7 sec) [ -9984.5714] [ 2437] [depth= 1] . ( 7 sec) [ -9664.7705] [ 2226] [depth= 14] . ( 7 sec) [ -9664.1630] [ 2227] [depth= 1] . ( 7 sec) [ -9663.5590] [ 2229] [depth= 1] . ( 7 sec) [ -9663.2668] [ 2231] [depth= 1] . ( 7 sec) [ -9626.4843] [ 2165] [depth= 5] . ( 7 sec) [ -9615.4115] [ 2169] [depth= 1] . ( 8 sec) [ -9614.9682] [ 2168] [depth= 1] . ( 8 sec) [ -9613.7867] [ 2169] [depth= 2] . ( 8 sec) [ -9613.6414] [ 2165] [depth= 1] . ( 8 sec) [ -9613.2912] [ 2165] [depth= 1] . ( 8 sec) [ -9607.2866] [ 2159] [depth= 1] . ( 8 sec) [ -9607.1540] [ 2158] [depth= 1] . ( 9 sec) [ -9602.6043] [ 2153] [depth= 1] . ( 9 sec) [ -9598.9945] [ 2157] [depth= 1] . ( 9 sec) [ -9572.8990] [Branch lengths ] . ( 10 sec) [ -9572.5398] [GTR parameters ] . ( 10 sec) [ -9564.8456] [Alpha ][ 0.896639] . ( 10 sec) [ -9562.3226] [ 2153] [depth= 1] . ( 10 sec) [ -9562.2710] [ 2153] [depth= 1] . ( 10 sec) [ -9553.6708] [ 2142] [depth= 3] . ( 11 sec) [ -9553.6602] [ 2142] [depth= 1] . ( 11 sec) [ -9552.3652] [ 2144] [depth= 2] . ( 11 sec) [ -9551.9583] [ 2146] [depth= 1] . ( 11 sec) [ -9551.9371] [ 2145] [depth= 1] . ( 12 sec) [ -9551.7408] [ 2148] [depth= 1] . ( 13 sec) [ -9551.5447] [ 2150] [depth= 1] . ( 13 sec) [ -9551.3490] [ 2148] [depth= 1] . ( 13 sec) [ -9546.7193] [Branch lengths ] . ( 14 sec) [ -9546.6954] [GTR parameters ] . ( 14 sec) [ -9546.4113] [Alpha ][ 0.946181] . ( 14 sec) [ -9546.2301] [ 2147] [depth= 1] . ( 16 sec) [ -9546.2026] [ 2145] [depth= 1] . ( 16 sec) [ -9545.9040] [ 2142] [depth= 1] . ( 17 sec) [ -9545.8739] [ 2144] [depth= 1] . ( 17 sec) [ -9544.8552] [Branch lengths ] . ( 18 sec) [ -9544.8497] [GTR parameters ] . ( 18 sec) [ -9544.8457] [Alpha ][ 0.952332] . ( 19 sec) [ -9544.8308] [ 2142] [depth= 1] . ( 22 sec) [ -9544.1473] [Branch lengths ] . ( 22 sec) [ -9544.1461] [GTR parameters ] . ( 22 sec) [ -9544.1461] [Alpha ][ 0.952332] . ( 44 sec) [ -9544.0660] [Branch lengths ] . ( 45 sec) [ -9544.0660] [Topology ] . ( 45 sec) [ -9544.0482] [Topology ] . ( 46 sec) [ -9544.0387] [Topology ] . ( 47 sec) [ -9544.0327] [Topology ] . ( 48 sec) [ -9544.0287] [Topology ] . ( 48 sec) [ -9544.0260] [Topology ] . ( 49 sec) [ -9544.0242] [Topology ] . ( 49 sec) [ -9544.0241] [GTR parameters ] . ( 49 sec) [ -9544.0237] [Alpha ][ 0.950317] . ( 49 sec) [ -9544.0237] [Topology ] . ( 50 sec) [ -9544.0224] [Topology ] . ( 51 sec) [ -9544.0215] [Topology ] . ( 51 sec) [ -9544.0215] [GTR parameters ] . ( 51 sec) [ -9544.0215] [Alpha ][ 0.950317] . ( 51 sec) [ -9544.0215] [Topology ] . ( 52 sec) [ -9544.0208] [Topology ] . ( 52 sec) [ -9544.0208] [GTR parameters ] . ( 52 sec) [ -9544.0208] [Alpha ][ 0.950317] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.020840. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9648.148083 . ( 0 sec) [ -9645.7865] [GTR parameters ] . ( 1 sec) [ -9645.7819] [Alpha ][ 0.992321] . ( 1 sec) [ -9645.7819] [Topology ] . ( 1 sec) [ -9563.6932] [Topology ] . ( 2 sec) [ -9549.6521] [Topology ] . ( 3 sec) [ -9546.6529] [Topology ] . ( 4 sec) [ -9545.4735] [Topology ] . ( 5 sec) [ -9544.9102] [Topology ] . ( 5 sec) [ -9544.6138] [Topology ] . ( 6 sec) [ -9544.4490] [Topology ] . ( 7 sec) [ -9544.3556] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.355619 . ( 14 sec) [ -9544.3056] [GTR parameters ] . ( 14 sec) [ -9544.1564] [Alpha ][ 0.953985] . ( 14 sec) [ -9544.1564] [Topology ] . ( 15 sec) [ -9544.0946] [Topology ] . ( 15 sec) [ -9544.0660] [Topology ] . ( 16 sec) [ -9544.0497] [Topology ] . ( 17 sec) [ -9544.0399] [Topology ] . ( 18 sec) [ -9544.0336] [Topology ] . ( 19 sec) [ -9544.0296] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.029640 . ( 25 sec) [ -9544.0293] [GTR parameters ] . ( 25 sec) [ -9544.0281] [Alpha ][ 0.950438] . ( 25 sec) [ -9544.0281] [Topology ] . ( 26 sec) [ -9544.0253] [Topology ] . ( 27 sec) [ -9544.0235] [Topology ] . ( 27 sec) [ -9544.0223] [Topology ] . ( 28 sec) [ -9544.0215] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.021461 . ( 35 sec) [ -9544.0215] [GTR parameters ] . ( 35 sec) [ -9544.0215] [Alpha ][ 0.950438] . ( 35 sec) [ -9544.0215] [Topology ] . ( 36 sec) [ -9544.0209] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -9645.7865] [GTR parameters ] . ( 49 sec) [ -9645.7819] [Alpha ][ 0.992321] . ( 49 sec) [ -9644.2995] [ 2152] [depth= 1] . ( 49 sec) [ -9641.9088] [ 2151] [depth= 1] . ( 49 sec) [ -9641.3366] [ 2152] [depth= 1] . ( 49 sec) [ -9639.9005] [ 2147] [depth= 1] . ( 49 sec) [ -9637.0774] [ 2146] [depth= 1] . ( 49 sec) [ -9636.7170] [ 2148] [depth= 1] . ( 50 sec) [ -9635.4102] [ 2152] [depth= 1] . ( 50 sec) [ -9633.6675] [ 2157] [depth= 3] . ( 50 sec) [ -9632.4627] [ 2148] [depth= 2] . ( 50 sec) [ -9629.2827] [ 2144] [depth= 2] . ( 50 sec) [ -9627.6369] [ 2147] [depth= 2] . ( 50 sec) [ -9615.3235] [ 2153] [depth= 1] . ( 50 sec) [ -9614.1674] [ 2152] [depth= 1] . ( 50 sec) [ -9597.7284] [ 2149] [depth= 1] . ( 50 sec) [ -9595.1914] [ 2154] [depth= 1] . ( 51 sec) [ -9589.5348] [ 2149] [depth= 1] . ( 51 sec) [ -9589.3482] [ 2141] [depth= 1] . ( 51 sec) [ -9587.8988] [ 2142] [depth= 1] . ( 51 sec) [ -9586.6129] [ 2147] [depth= 1] . ( 51 sec) [ -9585.4572] [ 2142] [depth= 1] . ( 51 sec) [ -9584.8741] [ 2145] [depth= 1] . ( 52 sec) [ -9583.8484] [ 2150] [depth= 1] . ( 52 sec) [ -9583.3635] [ 2145] [depth= 1] . ( 52 sec) [ -9581.6305] [ 2145] [depth= 1] . ( 52 sec) [ -9580.4756] [ 2145] [depth= 2] . ( 52 sec) [ -9580.2402] [ 2144] [depth= 1] . ( 53 sec) [ -9549.4316] [Branch lengths ] . ( 53 sec) [ -9549.3204] [GTR parameters ] . ( 53 sec) [ -9549.1981] [Alpha ][ 0.957325] . ( 53 sec) [ -9549.1577] [ 2143] [depth= 1] . ( 54 sec) [ -9549.1475] [ 2143] [depth= 1] . ( 54 sec) [ -9546.9076] [ 2142] [depth= 3] . ( 56 sec) [ -9546.5598] [ 2140] [depth= 1] . ( 57 sec) [ -9545.1529] [Branch lengths ] . ( 57 sec) [ -9545.1391] [GTR parameters ] . ( 57 sec) [ -9545.1372] [Alpha ][ 0.952957] . ( 58 sec) [ -9544.9224] [ 2144] [depth= 1] . ( 61 sec) [ -9544.4231] [Branch lengths ] . ( 62 sec) [ -9544.4205] [GTR parameters ] . ( 62 sec) [ -9544.4198] [Alpha ][ 0.950249] . ( 64 sec) [ -9544.1385] [ 2141] [depth= 1] . ( 84 sec) [ -9544.0258] [Branch lengths ] . ( 84 sec) [ -9544.0249] [GTR parameters ] . ( 84 sec) [ -9544.0249] [Alpha ][ 0.950249] . ( 84 sec) [ -9544.0249] [Topology ] . ( 85 sec) [ -9544.0211] [Topology ] . ( 86 sec) [ -9544.0203] [Topology ] . ( 86 sec) [ -9544.0203] [GTR parameters ] . ( 86 sec) [ -9544.0203] [Alpha ][ 0.950249] . ( 86 sec) [ -9544.0203] [Topology ] . ( 87 sec) [ -9544.0200] [Topology ] . ( 87 sec) [ -9544.0200] [GTR parameters ] . ( 87 sec) [ -9544.0200] [Alpha ][ 0.950249] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9544.020887 . Log likelihood obtained after SPR moves : -9544.019989 . Log likelihood of the current tree: -9544.019989. . Printing the most likely tree in file 'data53.phy_phyml_tree.txt'... . Best log likelihood : -9544.019871 . Time used 0h1m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo