.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data19.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... . 423 patterns found. (out of a total of 500 sites) . 70 sites without polymorphism (14.00%). . [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)... . ( 2 sec) [ -23195.5608] [GTR parameters ] . ( 2 sec) [ -22826.5468] [Alpha ][ 0.500960] . ( 2 sec) [ -22336.6482] [ 4154] [depth= 8] . ( 3 sec) [ -22317.2452] [ 4153] [depth= 6] . ( 3 sec) [ -22176.2832] [ 4124] [depth= 4] . ( 3 sec) [ -22106.9510] [ 4100] [depth= 5] . ( 3 sec) [ -21820.1495] [ 4043] [depth= 4] . ( 3 sec) [ -21644.4641] [ 4027] [depth= 6] . ( 3 sec) [ -21615.5985] [ 4010] [depth= 4] . ( 3 sec) [ -21611.8630] [ 4009] [depth= 1] . ( 3 sec) [ -21575.2033] [ 4003] [depth= 5] . ( 3 sec) [ -21468.8141] [ 3957] [depth= 9] . ( 3 sec) [ -17837.7218] [ 3944] [depth= 5] . ( 3 sec) [ -17650.9641] [ 3928] [depth= 2] . ( 3 sec) [ -17440.6457] [ 3813] [depth= 4] . ( 3 sec) [ -17227.7912] [ 3794] [depth= 16] . ( 3 sec) [ -17178.6257] [ 3792] [depth= 3] . ( 3 sec) [ -17159.0736] [ 3786] [depth= 10] . ( 3 sec) [ -16996.8226] [ 3740] [depth= 13] . ( 3 sec) [ -16970.0440] [ 3730] [depth= 1] . ( 3 sec) [ -16900.4145] [ 3699] [depth= 11] . ( 3 sec) [ -16892.8137] [ 3701] [depth= 1] . ( 4 sec) [ -16764.7660] [ 3659] [depth= 11] . ( 4 sec) [ -16585.3698] [ 3612] [depth= 10] . ( 4 sec) [ -16359.1940] [ 3586] [depth= 6] . ( 4 sec) [ -15955.3284] [ 3531] [depth= 1] . ( 4 sec) [ -15873.7470] [ 3494] [depth= 6] . ( 4 sec) [ -15846.8034] [ 3474] [depth= 5] . ( 4 sec) [ -15534.2884] [ 3406] [depth= 1] . ( 4 sec) [ -15308.2486] [ 3316] [depth= 5] . ( 4 sec) [ -15210.6816] [ 3317] [depth= 6] . ( 4 sec) [ -15055.3514] [ 3280] [depth= 14] . ( 5 sec) [ -14845.5076] [ 3203] [depth= 8] . ( 5 sec) [ -14260.1824] [ 3031] [depth= 8] . ( 5 sec) [ -14256.0439] [ 3043] [depth= 1] . ( 5 sec) [ -14099.7940] [ 2982] [depth= 10] . ( 5 sec) [ -13818.4264] [ 2978] [depth= 1] . ( 5 sec) [ -13694.5377] [ 2947] [depth= 13] . ( 5 sec) [ -13679.5967] [ 2940] [depth= 1] . ( 5 sec) [ -12488.3884] [ 2856] [depth= 12] . ( 5 sec) [ -12413.6107] [ 2837] [depth= 5] . ( 5 sec) [ -12219.9011] [ 2706] [depth= 12] . ( 6 sec) [ -12074.5999] [ 2686] [depth= 1] . ( 6 sec) [ -11891.4909] [ 2620] [depth= 14] . ( 6 sec) [ -11721.0225] [ 2624] [depth= 4] . ( 6 sec) [ -11374.6297] [ 2549] [depth= 6] . ( 6 sec) [ -11334.0796] [ 2530] [depth= 1] . ( 6 sec) [ -11323.7342] [ 2540] [depth= 1] . ( 6 sec) [ -11146.5244] [ 2494] [depth= 1] . ( 6 sec) [ -11045.9079] [ 2549] [depth= 3] . ( 6 sec) [ -11028.4971] [ 2551] [depth= 1] . ( 6 sec) [ -10990.3742] [ 2533] [depth= 4] . ( 6 sec) [ -10942.9163] [ 2507] [depth= 3] . ( 6 sec) [ -10865.8075] [ 2447] [depth= 9] . ( 6 sec) [ -10836.5042] [ 2426] [depth= 1] . ( 6 sec) [ -10823.0329] [ 2415] [depth= 1] . ( 7 sec) [ -10793.6512] [ 2391] [depth= 1] . ( 7 sec) [ -10738.9021] [ 2353] [depth= 4] . ( 7 sec) [ -10530.1066] [ 2313] [depth= 5] . ( 7 sec) [ -10497.4042] [ 2315] [depth= 1] . ( 7 sec) [ -10476.0129] [ 2314] [depth= 3] . ( 7 sec) [ -10473.5177] [ 2308] [depth= 1] . ( 7 sec) [ -10377.2815] [ 2276] [depth= 3] . ( 7 sec) [ -10361.6392] [ 2274] [depth= 2] . ( 7 sec) [ -10355.6696] [ 2272] [depth= 1] . ( 7 sec) [ -10355.2572] [ 2277] [depth= 1] . ( 7 sec) [ -10325.9844] [ 2271] [depth= 2] . ( 7 sec) [ -10322.9627] [ 2267] [depth= 1] . ( 7 sec) [ -10314.0880] [ 2252] [depth= 1] . ( 7 sec) [ -10135.4874] [ 2216] [depth= 4] . ( 7 sec) [ -10135.2211] [ 2217] [depth= 1] . ( 7 sec) [ -10056.7206] [ 2200] [depth= 2] . ( 7 sec) [ -10049.1699] [ 2200] [depth= 1] . ( 8 sec) [ -10002.7459] [ 2209] [depth= 1] . ( 8 sec) [ -9929.8453] [ 2184] [depth= 3] . ( 8 sec) [ -9923.5981] [ 2186] [depth= 2] . ( 8 sec) [ -9865.9414] [ 2148] [depth= 2] . ( 8 sec) [ -9858.3398] [ 2115] [depth= 2] . ( 8 sec) [ -9844.3280] [ 2117] [depth= 1] . ( 8 sec) [ -9759.6009] [ 2082] [depth= 3] . ( 8 sec) [ -9485.8297] [ 2046] [depth= 1] . ( 8 sec) [ -9458.4608] [ 2041] [depth= 1] . ( 8 sec) [ -9431.7498] [ 2029] [depth= 2] . ( 8 sec) [ -9411.2322] [ 2036] [depth= 1] . ( 8 sec) [ -9259.2611] [Branch lengths ] . ( 9 sec) [ -9258.4244] [GTR parameters ] . ( 9 sec) [ -9223.4844] [Alpha ][ 0.911887] . ( 9 sec) [ -9223.4631] [ 2041] [depth= 1] . ( 10 sec) [ -9222.6040] [ 2036] [depth= 1] . ( 10 sec) [ -9212.8717] [ 2010] [depth= 2] . ( 10 sec) [ -9200.7883] [ 2007] [depth= 1] . ( 10 sec) [ -9199.2302] [ 2005] [depth= 1] . ( 10 sec) [ -9197.1052] [ 2009] [depth= 1] . ( 10 sec) [ -9166.7781] [ 1996] [depth= 2] . ( 10 sec) [ -9166.2014] [ 1998] [depth= 1] . ( 10 sec) [ -9164.5184] [ 2001] [depth= 1] . ( 10 sec) [ -9163.8003] [ 1998] [depth= 1] . ( 11 sec) [ -9162.0341] [ 2001] [depth= 1] . ( 11 sec) [ -9160.4160] [ 1994] [depth= 1] . ( 11 sec) [ -9142.9005] [ 1996] [depth= 1] . ( 11 sec) [ -9142.3371] [ 1996] [depth= 1] . ( 12 sec) [ -9139.1649] [ 1993] [depth= 1] . ( 12 sec) [ -9135.5358] [ 1989] [depth= 1] . ( 12 sec) [ -9135.2963] [ 1977] [depth= 1] . ( 12 sec) [ -9125.5413] [ 1988] [depth= 1] . ( 12 sec) [ -9125.3727] [ 1997] [depth= 1] . ( 12 sec) [ -9113.5989] [Branch lengths ] . ( 13 sec) [ -9113.4284] [GTR parameters ] . ( 13 sec) [ -9112.9969] [Alpha ][ 0.976102] . ( 14 sec) [ -9112.3460] [ 1996] [depth= 1] . ( 14 sec) [ -9109.7281] [ 1984] [depth= 1] . ( 14 sec) [ -9108.6122] [ 1986] [depth= 1] . ( 15 sec) [ -9108.5958] [ 1988] [depth= 1] . ( 15 sec) [ -9107.9426] [ 1987] [depth= 1] . ( 17 sec) [ -9106.7842] [Branch lengths ] . ( 17 sec) [ -9106.7695] [GTR parameters ] . ( 17 sec) [ -9106.7603] [Alpha ][ 0.986082] . ( 18 sec) [ -9105.9914] [ 1986] [depth= 1] . ( 21 sec) [ -9105.7517] [Branch lengths ] . ( 21 sec) [ -9105.7507] [GTR parameters ] . ( 21 sec) [ -9105.7507] [Alpha ][ 0.986082] . ( 25 sec) [ -9105.7370] [Branch lengths ] . ( 36 sec) [ -9105.5023] [ 1987] [depth= 1] . ( 45 sec) [ -9105.4511] [Branch lengths ] . ( 46 sec) [ -9105.4507] [GTR parameters ] . ( 46 sec) [ -9105.4500] [Alpha ][ 0.988849] . ( 46 sec) [ -9105.4500] [Topology ] . ( 47 sec) [ -9105.4484] [Topology ] . ( 47 sec) [ -9105.4481] [Topology ] . ( 47 sec) [ -9105.4481] [GTR parameters ] . ( 47 sec) [ -9105.4481] [Alpha ][ 0.988849] . ( 48 sec) [ -9105.4481] [Topology ] . ( 48 sec) [ -9105.4480] [Topology ] . ( 48 sec) [ -9105.4480] [GTR parameters ] . ( 48 sec) [ -9105.4480] [Alpha ][ 0.988849] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9105.448039. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -23098.8896] [GTR parameters ] . ( 1 sec) [ -22721.7170] [Alpha ][ 0.500960] . ( 1 sec) [ -22362.4366] [ 4237] [depth= 3] . ( 1 sec) [ -22098.6993] [ 4147] [depth= 10] . ( 1 sec) [ -22033.8502] [ 4119] [depth= 3] . ( 1 sec) [ -22021.3746] [ 4113] [depth= 2] . ( 1 sec) [ -21983.9913] [ 4084] [depth= 1] . ( 1 sec) [ -21882.8819] [ 4072] [depth= 6] . ( 1 sec) [ -21759.8848] [ 4041] [depth= 5] . ( 1 sec) [ -21588.3259] [ 3971] [depth= 1] . ( 1 sec) [ -21332.8567] [ 3925] [depth= 5] . ( 1 sec) [ -21163.1478] [ 3902] [depth= 10] . ( 1 sec) [ -20961.5213] [ 3890] [depth= 4] . ( 1 sec) [ -20877.1201] [ 3882] [depth= 1] . ( 1 sec) [ -20826.7838] [ 3885] [depth= 3] . ( 1 sec) [ -20195.8174] [ 3778] [depth= 3] . ( 1 sec) [ -19921.0528] [ 3709] [depth= 10] . ( 1 sec) [ -19466.1175] [ 3538] [depth= 13] . ( 1 sec) [ -15357.4013] [ 3550] [depth= 1] . ( 1 sec) [ -15256.3680] [ 3534] [depth= 1] . ( 1 sec) [ -15083.2726] [ 3486] [depth= 3] . ( 1 sec) [ -14657.1859] [ 3327] [depth= 9] . ( 1 sec) [ -14414.7346] [ 3257] [depth= 5] . ( 2 sec) [ -14362.0954] [ 3254] [depth= 4] . ( 2 sec) [ -14250.4470] [ 3230] [depth= 5] . ( 2 sec) [ -14079.5785] [ 3154] [depth= 12] . ( 2 sec) [ -13825.3811] [ 3052] [depth= 7] . ( 2 sec) [ -13251.6010] [ 2926] [depth= 12] . ( 2 sec) [ -12926.2029] [ 2881] [depth= 14] . ( 2 sec) [ -12844.1086] [ 2872] [depth= 1] . ( 2 sec) [ -12605.6432] [ 2825] [depth= 4] . ( 2 sec) [ -12328.2957] [ 2811] [depth= 2] . ( 2 sec) [ -12200.0830] [ 2776] [depth= 1] . ( 2 sec) [ -12183.4083] [ 2770] [depth= 2] . ( 2 sec) [ -12109.0157] [ 2770] [depth= 1] . ( 2 sec) [ -12074.5380] [ 2741] [depth= 3] . ( 2 sec) [ -11898.0590] [ 2741] [depth= 1] . ( 2 sec) [ -11895.2751] [ 2713] [depth= 8] . ( 2 sec) [ -11870.5216] [ 2715] [depth= 1] . ( 2 sec) [ -11601.3659] [ 2587] [depth= 13] . ( 2 sec) [ -11586.4866] [ 2585] [depth= 1] . ( 2 sec) [ -11548.5160] [ 2584] [depth= 1] . ( 2 sec) [ -11401.3054] [ 2483] [depth= 10] . ( 3 sec) [ -11163.6121] [ 2436] [depth= 2] . ( 3 sec) [ -10838.8509] [ 2381] [depth= 6] . ( 3 sec) [ -10830.6040] [ 2386] [depth= 3] . ( 3 sec) [ -10830.2203] [ 2356] [depth= 4] . ( 3 sec) [ -10694.4425] [ 2307] [depth= 2] . ( 3 sec) [ -10656.3240] [ 2294] [depth= 1] . ( 3 sec) [ -10517.3710] [ 2253] [depth= 3] . ( 3 sec) [ -10427.7134] [ 2229] [depth= 4] . ( 3 sec) [ -10376.3029] [ 2226] [depth= 1] . ( 3 sec) [ -10287.6823] [ 2205] [depth= 1] . ( 3 sec) [ -10261.3363] [ 2191] [depth= 2] . ( 3 sec) [ -10247.1783] [ 2189] [depth= 1] . ( 3 sec) [ -10238.7580] [ 2193] [depth= 1] . ( 3 sec) [ -10230.7466] [ 2196] [depth= 1] . ( 3 sec) [ -10162.5574] [ 2163] [depth= 10] . ( 3 sec) [ -10133.0035] [ 2127] [depth= 3] . ( 3 sec) [ -9979.2282] [ 2067] [depth= 3] . ( 3 sec) [ -9948.7036] [ 2081] [depth= 1] . ( 3 sec) [ -9927.0000] [ 2067] [depth= 1] . ( 4 sec) [ -9925.5413] [ 2067] [depth= 1] . ( 4 sec) [ -9885.6542] [ 2073] [depth= 1] . ( 4 sec) [ -9865.6371] [ 2085] [depth= 1] . ( 4 sec) [ -9858.7054] [ 2076] [depth= 1] . ( 4 sec) [ -9847.7832] [ 2070] [depth= 1] . ( 4 sec) [ -9845.7542] [ 2070] [depth= 1] . ( 4 sec) [ -9841.6046] [ 2080] [depth= 1] . ( 4 sec) [ -9799.9568] [ 2066] [depth= 1] . ( 4 sec) [ -9737.5554] [ 2062] [depth= 2] . ( 4 sec) [ -9726.3057] [ 2065] [depth= 1] . ( 4 sec) [ -9697.6852] [ 2055] [depth= 1] . ( 4 sec) [ -9689.1086] [ 2058] [depth= 1] . ( 4 sec) [ -9688.3580] [ 2059] [depth= 1] . ( 5 sec) [ -9453.6874] [Branch lengths ] . ( 5 sec) [ -9450.9863] [GTR parameters ] . ( 5 sec) [ -9415.7644] [Alpha ][ 0.882147] . ( 6 sec) [ -9415.6395] [ 2061] [depth= 1] . ( 6 sec) [ -9385.8552] [ 2059] [depth= 1] . ( 6 sec) [ -9284.9348] [ 2012] [depth= 1] . ( 6 sec) [ -9269.5490] [ 2009] [depth= 1] . ( 6 sec) [ -9262.7296] [ 2003] [depth= 2] . ( 6 sec) [ -9259.3395] [ 2006] [depth= 2] . ( 6 sec) [ -9212.9106] [ 2007] [depth= 1] . ( 6 sec) [ -9174.7963] [ 2006] [depth= 1] . ( 6 sec) [ -9172.5347] [ 1993] [depth= 1] . ( 6 sec) [ -9168.2563] [ 1996] [depth= 1] . ( 7 sec) [ -9166.1295] [ 1993] [depth= 1] . ( 7 sec) [ -9165.7961] [ 1990] [depth= 1] . ( 7 sec) [ -9165.6417] [ 1993] [depth= 1] . ( 8 sec) [ -9164.7117] [ 1986] [depth= 1] . ( 8 sec) [ -9162.0814] [ 1992] [depth= 1] . ( 9 sec) [ -9161.7784] [ 1988] [depth= 1] . ( 9 sec) [ -9119.0470] [Branch lengths ] . ( 9 sec) [ -9118.6866] [GTR parameters ] . ( 9 sec) [ -9117.5071] [Alpha ][ 0.985142] . ( 10 sec) [ -9106.8885] [ 1982] [depth= 1] . ( 13 sec) [ -9105.7132] [Branch lengths ] . ( 13 sec) [ -9105.7047] [GTR parameters ] . ( 13 sec) [ -9105.7022] [Alpha ][ 0.990278] . ( 16 sec) [ -9105.5502] [Branch lengths ] . ( 33 sec) [ -9105.5055] [ 1988] [depth= 1] . ( 36 sec) [ -9105.4551] [Branch lengths ] . ( 37 sec) [ -9105.4550] [GTR parameters ] . ( 37 sec) [ -9105.4549] [Alpha ][ 0.989287] . ( 37 sec) [ -9105.4549] [Topology ] . ( 37 sec) [ -9105.4510] [Topology ] . ( 38 sec) [ -9105.4495] [Topology ] . ( 39 sec) [ -9105.4488] [Topology ] . ( 39 sec) [ -9105.4488] [GTR parameters ] . ( 39 sec) [ -9105.4488] [Alpha ][ 0.989287] . ( 39 sec) [ -9105.4488] [Topology ] . ( 40 sec) [ -9105.4485] [Topology ] . ( 40 sec) [ -9105.4485] [GTR parameters ] . ( 40 sec) [ -9105.4485] [Alpha ][ 0.989287] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9105.448492. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23377.8293] [GTR parameters ] . ( 1 sec) [ -22956.1123] [Alpha ][ 0.500960] . ( 1 sec) [ -22577.2802] [ 4380] [depth= 8] . ( 1 sec) [ -22205.0075] [ 4280] [depth= 8] . ( 1 sec) [ -22203.0651] [ 4270] [depth= 2] . ( 1 sec) [ -22162.0820] [ 4264] [depth= 2] . ( 1 sec) [ -22062.9231] [ 4207] [depth= 3] . ( 1 sec) [ -21973.8686] [ 4213] [depth= 1] . ( 1 sec) [ -21411.7612] [ 4113] [depth= 9] . ( 1 sec) [ -21398.6780] [ 4124] [depth= 8] . ( 1 sec) [ -21394.5876] [ 4118] [depth= 7] . ( 1 sec) [ -21177.8072] [ 4043] [depth= 16] . ( 1 sec) [ -20984.0808] [ 3996] [depth= 6] . ( 1 sec) [ -20919.4554] [ 3969] [depth= 6] . ( 1 sec) [ -20810.0887] [ 3966] [depth= 3] . ( 1 sec) [ -20625.0932] [ 3917] [depth= 7] . ( 2 sec) [ -20483.7718] [ 3899] [depth= 1] . ( 2 sec) [ -20293.4566] [ 3880] [depth= 1] . ( 2 sec) [ -20188.3528] [ 3794] [depth= 5] . ( 2 sec) [ -20005.5168] [ 3763] [depth= 10] . ( 2 sec) [ -19770.4666] [ 3762] [depth= 8] . ( 2 sec) [ -19745.4697] [ 3763] [depth= 1] . ( 2 sec) [ -19653.6765] [ 3731] [depth= 6] . ( 2 sec) [ -19192.7639] [ 3692] [depth= 1] . ( 2 sec) [ -18900.6164] [ 3562] [depth= 8] . ( 2 sec) [ -18751.6153] [ 3513] [depth= 1] . ( 2 sec) [ -18542.2451] [ 3414] [depth= 2] . ( 2 sec) [ -18454.7783] [ 3402] [depth= 4] . ( 2 sec) [ -18128.7450] [ 3378] [depth= 8] . ( 2 sec) [ -17898.5089] [ 3271] [depth= 11] . ( 2 sec) [ -17723.9451] [ 3230] [depth= 4] . ( 2 sec) [ -17411.8118] [ 3151] [depth= 10] . ( 2 sec) [ -17364.4595] [ 3140] [depth= 1] . ( 2 sec) [ -17024.8241] [ 3036] [depth= 9] . ( 2 sec) [ -16611.9336] [ 2995] [depth= 4] . ( 2 sec) [ -16375.0986] [ 2913] [depth= 7] . ( 2 sec) [ -16152.4909] [ 2876] [depth= 2] . ( 2 sec) [ -16116.7396] [ 2828] [depth= 1] . ( 3 sec) [ -13297.4195] [ 2809] [depth= 5] . ( 3 sec) [ -13023.9933] [ 2819] [depth= 1] . ( 3 sec) [ -13017.1607] [ 2814] [depth= 1] . ( 3 sec) [ -12973.5316] [ 2790] [depth= 3] . ( 3 sec) [ -12664.5756] [ 2788] [depth= 2] . ( 3 sec) [ -12290.3735] [ 2698] [depth= 6] . ( 3 sec) [ -12205.4932] [ 2635] [depth= 7] . ( 3 sec) [ -12073.9493] [ 2627] [depth= 1] . ( 3 sec) [ -12013.4858] [ 2620] [depth= 2] . ( 3 sec) [ -11919.5377] [ 2620] [depth= 2] . ( 3 sec) [ -11856.7803] [ 2598] [depth= 1] . ( 3 sec) [ -11847.5863] [ 2598] [depth= 1] . ( 3 sec) [ -11839.4138] [ 2591] [depth= 1] . ( 3 sec) [ -11829.6841] [ 2595] [depth= 1] . ( 3 sec) [ -11828.4928] [ 2591] [depth= 1] . ( 3 sec) [ -11800.2195] [ 2568] [depth= 4] . ( 3 sec) [ -11782.2368] [ 2592] [depth= 1] . ( 3 sec) [ -11729.3501] [ 2568] [depth= 1] . ( 3 sec) [ -11540.9482] [ 2489] [depth= 6] . ( 3 sec) [ -11518.8569] [ 2476] [depth= 1] . ( 4 sec) [ -11448.9242] [ 2436] [depth= 5] . ( 4 sec) [ -11441.0057] [ 2442] [depth= 1] . ( 4 sec) [ -11398.1098] [ 2422] [depth= 4] . ( 4 sec) [ -11385.9106] [ 2417] [depth= 1] . ( 4 sec) [ -11364.3311] [ 2378] [depth= 4] . ( 4 sec) [ -10483.3321] [ 2391] [depth= 1] . ( 4 sec) [ -10479.9104] [ 2378] [depth= 1] . ( 4 sec) [ -10428.3344] [ 2324] [depth= 7] . ( 4 sec) [ -10409.1512] [ 2328] [depth= 2] . ( 4 sec) [ -10352.7237] [ 2305] [depth= 1] . ( 4 sec) [ -10296.0806] [ 2309] [depth= 1] . ( 4 sec) [ -10243.2317] [ 2293] [depth= 3] . ( 4 sec) [ -10142.6886] [ 2239] [depth= 5] . ( 4 sec) [ -10050.1417] [ 2228] [depth= 1] . ( 4 sec) [ -10040.5693] [ 2223] [depth= 1] . ( 4 sec) [ -9941.4419] [ 2198] [depth= 1] . ( 4 sec) [ -9872.9817] [ 2170] [depth= 1] . ( 4 sec) [ -9793.1534] [ 2131] [depth= 6] . ( 4 sec) [ -9756.7537] [ 2133] [depth= 2] . ( 5 sec) [ -9755.1221] [ 2134] [depth= 1] . ( 5 sec) [ -9732.4894] [ 2139] [depth= 1] . ( 5 sec) [ -9731.4938] [ 2139] [depth= 1] . ( 5 sec) [ -9707.2444] [ 2117] [depth= 2] . ( 5 sec) [ -9698.2904] [ 2123] [depth= 1] . ( 5 sec) [ -9697.2564] [ 2114] [depth= 1] . ( 5 sec) [ -9436.7020] [Branch lengths ] . ( 6 sec) [ -9432.8285] [GTR parameters ] . ( 6 sec) [ -9397.2841] [Alpha ][ 0.907181] . ( 6 sec) [ -9394.4211] [ 2113] [depth= 1] . ( 6 sec) [ -9392.8525] [ 2116] [depth= 1] . ( 6 sec) [ -9358.8472] [ 2081] [depth= 1] . ( 7 sec) [ -9311.8469] [ 2055] [depth= 1] . ( 7 sec) [ -9298.8935] [ 2053] [depth= 2] . ( 7 sec) [ -9295.8294] [ 2051] [depth= 2] . ( 7 sec) [ -9295.3474] [ 2051] [depth= 1] . ( 7 sec) [ -9276.4790] [ 2035] [depth= 2] . ( 7 sec) [ -9275.8706] [ 2035] [depth= 1] . ( 7 sec) [ -9274.3764] [ 2036] [depth= 1] . ( 8 sec) [ -9260.5592] [ 2039] [depth= 1] . ( 8 sec) [ -9259.5691] [ 2038] [depth= 1] . ( 8 sec) [ -9259.4058] [ 2039] [depth= 1] . ( 8 sec) [ -9247.2681] [ 2039] [depth= 1] . ( 8 sec) [ -9246.2170] [ 2037] [depth= 1] . ( 8 sec) [ -9245.5783] [ 2041] [depth= 1] . ( 8 sec) [ -9209.9347] [ 2019] [depth= 1] . ( 9 sec) [ -9207.6294] [ 2016] [depth= 1] . ( 9 sec) [ -9134.9004] [ 1983] [depth= 2] . ( 9 sec) [ -9134.8066] [ 1985] [depth= 1] . ( 9 sec) [ -9108.8121] [Branch lengths ] . ( 10 sec) [ -9108.7454] [GTR parameters ] . ( 10 sec) [ -9108.1583] [Alpha ][ 0.982687] . ( 10 sec) [ -9107.4266] [ 1983] [depth= 1] . ( 11 sec) [ -9107.3695] [ 1982] [depth= 1] . ( 12 sec) [ -9107.2358] [ 1983] [depth= 1] . ( 13 sec) [ -9106.1764] [Branch lengths ] . ( 14 sec) [ -9106.1752] [GTR parameters ] . ( 14 sec) [ -9106.1748] [Alpha ][ 0.984849] . ( 17 sec) [ -9105.9988] [Branch lengths ] . ( 36 sec) [ -9105.9005] [ 1982] [depth= 1] . ( 36 sec) [ -9105.8546] [ 1988] [depth= 1] . ( 37 sec) [ -9105.7400] [Branch lengths ] . ( 38 sec) [ -9105.7391] [GTR parameters ] . ( 38 sec) [ -9105.7387] [Alpha ][ 0.986906] . ( 38 sec) [ -9105.7387] [Topology ] . ( 39 sec) [ -9105.5668] [Topology ] . ( 39 sec) [ -9105.4725] [Topology ] . ( 40 sec) [ -9105.4569] [Topology ] . ( 41 sec) [ -9105.4520] [Topology ] . ( 42 sec) [ -9105.4502] [Topology ] . ( 42 sec) [ -9105.4496] [Topology ] . ( 43 sec) [ -9105.4491] [GTR parameters ] . ( 43 sec) [ -9105.4487] [Alpha ][ 0.988973] . ( 43 sec) [ -9105.4487] [Topology ] . ( 43 sec) [ -9105.4484] [Topology ] . ( 44 sec) [ -9105.4484] [GTR parameters ] . ( 44 sec) [ -9105.4484] [Alpha ][ 0.988973] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9105.448353. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22908.9545] [GTR parameters ] . ( 0 sec) [ -22508.2036] [Alpha ][ 0.500960] . ( 0 sec) [ -22300.9673] [ 4371] [depth= 8] . ( 0 sec) [ -21931.0697] [ 4230] [depth= 9] . ( 0 sec) [ -21753.0525] [ 4175] [depth= 8] . ( 0 sec) [ -21647.7264] [ 4070] [depth= 1] . ( 1 sec) [ -21547.1288] [ 4040] [depth= 6] . ( 1 sec) [ -21541.8788] [ 4007] [depth= 3] . ( 1 sec) [ -21276.3479] [ 3981] [depth= 5] . ( 1 sec) [ -20879.4249] [ 3824] [depth= 3] . ( 1 sec) [ -20821.6061] [ 3809] [depth= 1] . ( 1 sec) [ -20782.5494] [ 3796] [depth= 2] . ( 1 sec) [ -20774.2871] [ 3799] [depth= 1] . ( 1 sec) [ -20302.6042] [ 3719] [depth= 5] . ( 1 sec) [ -19777.2410] [ 3647] [depth= 7] . ( 1 sec) [ -19638.6428] [ 3626] [depth= 4] . ( 1 sec) [ -19603.6483] [ 3625] [depth= 1] . ( 1 sec) [ -19433.6619] [ 3587] [depth= 13] . ( 1 sec) [ -19203.0737] [ 3519] [depth= 7] . ( 1 sec) [ -18975.4807] [ 3428] [depth= 12] . ( 1 sec) [ -18810.9056] [ 3420] [depth= 1] . ( 1 sec) [ -18745.7367] [ 3390] [depth= 2] . ( 1 sec) [ -18580.0702] [ 3335] [depth= 13] . ( 1 sec) [ -18553.1116] [ 3336] [depth= 1] . ( 1 sec) [ -18460.4273] [ 3290] [depth= 1] . ( 1 sec) [ -18296.8822] [ 3287] [depth= 3] . ( 1 sec) [ -18265.2502] [ 3348] [depth= 4] . ( 1 sec) [ -18142.6461] [ 3324] [depth= 7] . ( 1 sec) [ -18038.3402] [ 3209] [depth= 9] . ( 2 sec) [ -18003.6349] [ 3201] [depth= 2] . ( 2 sec) [ -17886.6951] [ 3149] [depth= 9] . ( 2 sec) [ -17186.2726] [ 2979] [depth= 11] . ( 2 sec) [ -16726.7005] [ 2969] [depth= 2] . ( 2 sec) [ -16681.5258] [ 2961] [depth= 3] . ( 2 sec) [ -16658.6510] [ 2943] [depth= 1] . ( 2 sec) [ -16580.7484] [ 2949] [depth= 9] . ( 2 sec) [ -16272.4926] [ 2833] [depth= 8] . ( 2 sec) [ -12871.6298] [ 2829] [depth= 7] . ( 2 sec) [ -12341.7127] [ 2816] [depth= 2] . ( 2 sec) [ -12099.7006] [ 2755] [depth= 10] . ( 2 sec) [ -11941.6062] [ 2694] [depth= 1] . ( 2 sec) [ -11919.2820] [ 2699] [depth= 1] . ( 2 sec) [ -11499.3321] [ 2635] [depth= 3] . ( 2 sec) [ -11486.5300] [ 2641] [depth= 3] . ( 2 sec) [ -11410.2300] [ 2540] [depth= 8] . ( 2 sec) [ -11331.9442] [ 2541] [depth= 1] . ( 2 sec) [ -11310.3707] [ 2539] [depth= 2] . ( 2 sec) [ -11254.6992] [ 2532] [depth= 2] . ( 3 sec) [ -11193.2961] [ 2505] [depth= 7] . ( 3 sec) [ -11182.3704] [ 2505] [depth= 1] . ( 3 sec) [ -11181.8130] [ 2472] [depth= 4] . ( 3 sec) [ -11180.9238] [ 2476] [depth= 1] . ( 3 sec) [ -11068.3869] [ 2393] [depth= 6] . ( 3 sec) [ -11000.8335] [ 2393] [depth= 2] . ( 3 sec) [ -11000.6667] [ 2394] [depth= 1] . ( 3 sec) [ -10857.2265] [ 2380] [depth= 1] . ( 3 sec) [ -10704.6989] [ 2362] [depth= 5] . ( 3 sec) [ -10526.0668] [ 2331] [depth= 6] . ( 3 sec) [ -10477.0298] [ 2330] [depth= 1] . ( 3 sec) [ -10457.7036] [ 2292] [depth= 1] . ( 3 sec) [ -10442.6078] [ 2301] [depth= 1] . ( 3 sec) [ -10396.2923] [ 2291] [depth= 3] . ( 3 sec) [ -10340.6547] [ 2289] [depth= 1] . ( 3 sec) [ -10315.1236] [ 2279] [depth= 1] . ( 3 sec) [ -10314.5315] [ 2264] [depth= 3] . ( 3 sec) [ -10246.7290] [ 2284] [depth= 1] . ( 3 sec) [ -10229.5089] [ 2260] [depth= 2] . ( 4 sec) [ -10202.0724] [ 2270] [depth= 3] . ( 4 sec) [ -10195.7385] [ 2273] [depth= 1] . ( 4 sec) [ -10189.4915] [ 2274] [depth= 2] . ( 4 sec) [ -10101.8776] [ 2243] [depth= 4] . ( 4 sec) [ -10101.6334] [ 2277] [depth= 2] . ( 4 sec) [ -10080.6574] [ 2273] [depth= 1] . ( 4 sec) [ -10080.2194] [ 2276] [depth= 2] . ( 4 sec) [ -10076.9823] [ 2267] [depth= 1] . ( 4 sec) [ -10074.9565] [ 2270] [depth= 1] . ( 4 sec) [ -10041.1445] [ 2213] [depth= 5] . ( 4 sec) [ -9575.6929] [ 2083] [depth= 5] . ( 4 sec) [ -9376.6396] [Branch lengths ] . ( 5 sec) [ -9373.9413] [GTR parameters ] . ( 5 sec) [ -9344.8831] [Alpha ][ 0.856346] . ( 5 sec) [ -9343.7037] [ 2079] [depth= 1] . ( 5 sec) [ -9343.4101] [ 2081] [depth= 1] . ( 5 sec) [ -9338.7505] [ 2076] [depth= 1] . ( 5 sec) [ -9256.9096] [ 2043] [depth= 1] . ( 5 sec) [ -9252.6678] [ 2047] [depth= 1] . ( 5 sec) [ -9252.5648] [ 2046] [depth= 1] . ( 6 sec) [ -9250.3653] [ 2043] [depth= 1] . ( 6 sec) [ -9237.6184] [ 2038] [depth= 1] . ( 6 sec) [ -9224.5345] [ 2024] [depth= 1] . ( 6 sec) [ -9219.2612] [ 2021] [depth= 1] . ( 6 sec) [ -9207.2317] [ 2007] [depth= 6] . ( 6 sec) [ -9207.1500] [ 2004] [depth= 1] . ( 6 sec) [ -9202.9656] [ 1998] [depth= 1] . ( 6 sec) [ -9196.3467] [ 1998] [depth= 1] . ( 7 sec) [ -9195.5597] [ 1999] [depth= 1] . ( 7 sec) [ -9195.5159] [ 2000] [depth= 1] . ( 7 sec) [ -9188.1324] [ 2006] [depth= 1] . ( 7 sec) [ -9151.1761] [ 1987] [depth= 2] . ( 7 sec) [ -9149.0837] [ 1995] [depth= 2] . ( 7 sec) [ -9148.8583] [ 1995] [depth= 1] . ( 7 sec) [ -9148.7495] [ 1994] [depth= 1] . ( 8 sec) [ -9148.0811] [ 1991] [depth= 1] . ( 8 sec) [ -9125.4855] [ 1976] [depth= 3] . ( 9 sec) [ -9111.2724] [Branch lengths ] . ( 9 sec) [ -9110.9005] [GTR parameters ] . ( 9 sec) [ -9109.5201] [Alpha ][ 0.968634] . ( 9 sec) [ -9109.5015] [ 1980] [depth= 1] . ( 10 sec) [ -9109.4599] [ 1982] [depth= 1] . ( 12 sec) [ -9106.2731] [Branch lengths ] . ( 13 sec) [ -9106.2674] [GTR parameters ] . ( 13 sec) [ -9106.2478] [Alpha ][ 0.983242] . ( 16 sec) [ -9105.6742] [Branch lengths ] . ( 36 sec) [ -9105.5538] [Branch lengths ] . ( 36 sec) [ -9105.5538] [Topology ] . ( 37 sec) [ -9105.5365] [Topology ] . ( 38 sec) [ -9105.5290] [Topology ] . ( 39 sec) [ -9105.5249] [Topology ] . ( 39 sec) [ -9105.5225] [Topology ] . ( 40 sec) [ -9105.5210] [Topology ] . ( 41 sec) [ -9105.5201] [Topology ] . ( 41 sec) [ -9105.5196] [GTR parameters ] . ( 41 sec) [ -9105.5173] [Alpha ][ 0.988234] . ( 41 sec) [ -9105.5173] [Topology ] . ( 42 sec) [ -9105.5166] [Topology ] . ( 42 sec) [ -9105.5166] [GTR parameters ] . ( 42 sec) [ -9105.5166] [Alpha ][ 0.988234] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -9105.4500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -9105.4497] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9105.449742. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24235.9638] [GTR parameters ] . ( 1 sec) [ -23818.0777] [Alpha ][ 0.500960] . ( 1 sec) [ -23338.3063] [ 4424] [depth= 6] . ( 1 sec) [ -23040.8880] [ 4322] [depth= 11] . ( 1 sec) [ -23013.0816] [ 4304] [depth= 2] . ( 1 sec) [ -22984.5028] [ 4287] [depth= 7] . ( 1 sec) [ -22761.1993] [ 4217] [depth= 5] . ( 1 sec) [ -22702.5872] [ 4210] [depth= 1] . ( 1 sec) [ -22481.0601] [ 4180] [depth= 6] . ( 2 sec) [ -22352.8989] [ 4145] [depth= 2] . ( 2 sec) [ -22275.3935] [ 4103] [depth= 7] . ( 2 sec) [ -21971.9897] [ 4021] [depth= 2] . ( 2 sec) [ -21897.3649] [ 3983] [depth= 17] . ( 2 sec) [ -21603.5646] [ 3922] [depth= 8] . ( 2 sec) [ -21412.9928] [ 3919] [depth= 1] . ( 2 sec) [ -21328.7113] [ 3896] [depth= 12] . ( 2 sec) [ -21284.7041] [ 3897] [depth= 1] . ( 2 sec) [ -21246.5721] [ 3884] [depth= 2] . ( 2 sec) [ -21206.3986] [ 3858] [depth= 2] . ( 2 sec) [ -21094.6720] [ 3844] [depth= 3] . ( 2 sec) [ -20891.8443] [ 3782] [depth= 8] . ( 2 sec) [ -20860.6219] [ 3780] [depth= 1] . ( 2 sec) [ -20722.6755] [ 3728] [depth= 9] . ( 2 sec) [ -20718.6653] [ 3728] [depth= 1] . ( 2 sec) [ -20522.2216] [ 3718] [depth= 1] . ( 2 sec) [ -20464.0219] [ 3672] [depth= 2] . ( 2 sec) [ -20456.3439] [ 3677] [depth= 1] . ( 2 sec) [ -19989.7913] [ 3548] [depth= 6] . ( 2 sec) [ -19972.9457] [ 3542] [depth= 1] . ( 2 sec) [ -19776.0597] [ 3445] [depth= 8] . ( 2 sec) [ -19534.7568] [ 3443] [depth= 3] . ( 3 sec) [ -19303.1560] [ 3361] [depth= 7] . ( 3 sec) [ -19193.8525] [ 3378] [depth= 1] . ( 3 sec) [ -18813.3275] [ 3312] [depth= 2] . ( 3 sec) [ -18664.2620] [ 3263] [depth= 7] . ( 3 sec) [ -18242.4122] [ 3139] [depth= 10] . ( 3 sec) [ -18079.0004] [ 3087] [depth= 12] . ( 3 sec) [ -17892.0957] [ 3026] [depth= 1] . ( 3 sec) [ -17864.5749] [ 3013] [depth= 2] . ( 3 sec) [ -17406.9429] [ 2948] [depth= 3] . ( 3 sec) [ -17342.2714] [ 2901] [depth= 1] . ( 3 sec) [ -17197.2506] [ 2859] [depth= 8] . ( 3 sec) [ -16852.7012] [ 2803] [depth= 1] . ( 3 sec) [ -16674.9117] [ 2682] [depth= 4] . ( 3 sec) [ -16587.4760] [ 2683] [depth= 1] . ( 3 sec) [ -16573.5395] [ 2687] [depth= 1] . ( 3 sec) [ -16396.5147] [ 2640] [depth= 1] . ( 3 sec) [ -16064.7027] [ 2568] [depth= 2] . ( 3 sec) [ -15828.5812] [ 2506] [depth= 5] . ( 3 sec) [ -15779.4728] [ 2456] [depth= 6] . ( 4 sec) [ -15366.9507] [ 2454] [depth= 2] . ( 4 sec) [ -15356.5389] [ 2451] [depth= 1] . ( 4 sec) [ -15346.9096] [ 2455] [depth= 1] . ( 4 sec) [ -15112.5880] [ 2416] [depth= 2] . ( 4 sec) [ -15099.6461] [ 2415] [depth= 4] . ( 4 sec) [ -14847.6114] [ 2405] [depth= 1] . ( 4 sec) [ -14815.3934] [ 2392] [depth= 1] . ( 4 sec) [ -14745.7163] [ 2375] [depth= 1] . ( 4 sec) [ -14720.6675] [ 2347] [depth= 1] . ( 4 sec) [ -11305.8023] [ 2316] [depth= 3] . ( 4 sec) [ -11126.2135] [ 2267] [depth= 4] . ( 4 sec) [ -11117.7546] [ 2265] [depth= 1] . ( 4 sec) [ -11020.9933] [ 2258] [depth= 1] . ( 4 sec) [ -11018.5364] [ 2258] [depth= 1] . ( 4 sec) [ -10828.8405] [ 2199] [depth= 4] . ( 4 sec) [ -10626.9226] [ 2140] [depth= 3] . ( 5 sec) [ -10216.3288] [ 2130] [depth= 1] . ( 5 sec) [ -9936.7778] [ 2092] [depth= 3] . ( 5 sec) [ -9933.8856] [ 2084] [depth= 1] . ( 5 sec) [ -9930.4309] [ 2083] [depth= 1] . ( 5 sec) [ -9925.0777] [ 2082] [depth= 1] . ( 5 sec) [ -9862.6321] [ 2054] [depth= 2] . ( 5 sec) [ -9797.6756] [ 2053] [depth= 1] . ( 5 sec) [ -9793.7117] [ 2055] [depth= 1] . ( 5 sec) [ -9696.1867] [ 2067] [depth= 1] . ( 5 sec) [ -9498.2612] [Branch lengths ] . ( 6 sec) [ -9495.7757] [GTR parameters ] . ( 6 sec) [ -9466.1972] [Alpha ][ 0.868618] . ( 6 sec) [ -9462.9809] [ 2070] [depth= 1] . ( 6 sec) [ -9451.2087] [ 2044] [depth= 3] . ( 7 sec) [ -9432.4858] [ 2037] [depth= 2] . ( 7 sec) [ -9420.7112] [ 2039] [depth= 2] . ( 7 sec) [ -9415.0115] [ 2026] [depth= 1] . ( 7 sec) [ -9404.3440] [ 2031] [depth= 1] . ( 7 sec) [ -9403.2714] [ 2029] [depth= 1] . ( 7 sec) [ -9400.4811] [ 2029] [depth= 1] . ( 7 sec) [ -9374.7803] [ 2036] [depth= 3] . ( 7 sec) [ -9370.6305] [ 2026] [depth= 1] . ( 7 sec) [ -9361.7514] [ 2025] [depth= 2] . ( 8 sec) [ -9360.9615] [ 2022] [depth= 1] . ( 8 sec) [ -9358.2436] [ 2024] [depth= 1] . ( 8 sec) [ -9341.5284] [ 2033] [depth= 1] . ( 8 sec) [ -9267.1610] [ 2003] [depth= 2] . ( 8 sec) [ -9248.3634] [ 2047] [depth= 2] . ( 8 sec) [ -9244.9704] [ 2047] [depth= 1] . ( 8 sec) [ -9235.1366] [ 2037] [depth= 1] . ( 8 sec) [ -9234.3978] [ 2037] [depth= 1] . ( 8 sec) [ -9228.2204] [ 2038] [depth= 1] . ( 8 sec) [ -9222.6767] [ 2033] [depth= 3] . ( 9 sec) [ -9215.9417] [ 2034] [depth= 2] . ( 9 sec) [ -9215.7611] [ 2039] [depth= 1] . ( 9 sec) [ -9189.8759] [ 2027] [depth= 1] . ( 9 sec) [ -9189.1107] [ 2030] [depth= 1] . ( 9 sec) [ -9188.5428] [ 2032] [depth= 1] . ( 9 sec) [ -9165.8332] [ 1995] [depth= 1] . ( 9 sec) [ -9165.4065] [ 2002] [depth= 1] . ( 9 sec) [ -9164.9683] [ 1997] [depth= 1] . ( 9 sec) [ -9116.5624] [Branch lengths ] . ( 10 sec) [ -9116.4063] [GTR parameters ] . ( 10 sec) [ -9115.2103] [Alpha ][ 0.973366] . ( 10 sec) [ -9115.0670] [ 1998] [depth= 1] . ( 11 sec) [ -9113.5618] [ 1996] [depth= 1] . ( 12 sec) [ -9112.9954] [ 1995] [depth= 1] . ( 12 sec) [ -9112.2098] [ 1993] [depth= 1] . ( 12 sec) [ -9110.7804] [ 1994] [depth= 1] . ( 13 sec) [ -9109.9870] [ 1987] [depth= 1] . ( 14 sec) [ -9105.9734] [Branch lengths ] . ( 14 sec) [ -9105.9591] [GTR parameters ] . ( 14 sec) [ -9105.9443] [Alpha ][ 0.985986] . ( 17 sec) [ -9105.7560] [Branch lengths ] . ( 38 sec) [ -9105.7396] [Branch lengths ] . ( 38 sec) [ -9105.7396] [Topology ] . ( 38 sec) [ -9105.5627] [Topology ] . ( 39 sec) [ -9105.4693] [Topology ] . ( 40 sec) [ -9105.4559] [Topology ] . ( 41 sec) [ -9105.4519] [Topology ] . ( 41 sec) [ -9105.4505] [Topology ] . ( 42 sec) [ -9105.4501] [Topology ] . ( 42 sec) [ -9105.4496] [GTR parameters ] . ( 42 sec) [ -9105.4488] [Alpha ][ 0.988950] . ( 42 sec) [ -9105.4488] [Topology ] . ( 43 sec) [ -9105.4485] [Topology ] . ( 43 sec) [ -9105.4485] [GTR parameters ] . ( 43 sec) [ -9105.4485] [Alpha ][ 0.988950] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -9105.4482] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9105.448234. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9166.391103 . ( 1 sec) [ -9163.6827] [GTR parameters ] . ( 1 sec) [ -9163.5645] [Alpha ][ 0.962775] . ( 1 sec) [ -9163.5645] [Topology ] . ( 2 sec) [ -9118.6274] [Topology ] . ( 2 sec) [ -9110.9425] [Topology ] . ( 3 sec) [ -9108.0749] [Topology ] . ( 4 sec) [ -9106.8802] [Topology ] . ( 5 sec) [ -9106.2436] [Topology ] . ( 6 sec) [ -9105.8925] [Topology ] . ( 6 sec) [ -9105.7386] [Topology ] . ( 7 sec) [ -9105.6590] [Topology ] . ( 8 sec) [ -9105.6166] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9105.593658 . ( 15 sec) [ -9105.5414] [GTR parameters ] . ( 15 sec) [ -9105.4855] [Alpha ][ 0.986389] . ( 15 sec) [ -9105.4855] [Topology ] . ( 16 sec) [ -9105.4674] [Topology ] . ( 16 sec) [ -9105.4587] [Topology ] . ( 17 sec) [ -9105.4542] [Topology ] . ( 18 sec) [ -9105.4518] [Topology ] . ( 19 sec) [ -9105.4505] [Topology ] . ( 19 sec) [ -9105.4498] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -9105.4495] [Topology ] . Before opt ts/t=1.000000 LK=-9105.449465 . ( 25 sec) [ -9105.4494] [GTR parameters ] . ( 25 sec) [ -9105.4489] [Alpha ][ 0.988775] . ( 25 sec) [ -9105.4489] [Topology ] . ( 26 sec) [ -9105.4484] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9105.448438 . ( 32 sec) [ -9105.4484] [GTR parameters ] . ( 32 sec) [ -9105.4484] [Alpha ][ 0.988775] . ( 32 sec) [ -9105.4484] [Topology ] . ( 33 sec) [ -9105.4482] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -9163.6827] [GTR parameters ] . ( 45 sec) [ -9163.5645] [Alpha ][ 0.962775] . ( 46 sec) [ -9162.0615] [ 1979] [depth= 1] . ( 46 sec) [ -9161.7501] [ 1981] [depth= 1] . ( 46 sec) [ -9159.0573] [ 1980] [depth= 1] . ( 46 sec) [ -9159.0379] [ 1985] [depth= 1] . ( 46 sec) [ -9158.6642] [ 1989] [depth= 1] . ( 47 sec) [ -9157.5898] [ 1984] [depth= 1] . ( 47 sec) [ -9153.8178] [ 1989] [depth= 1] . ( 47 sec) [ -9149.8869] [ 1993] [depth= 1] . ( 47 sec) [ -9149.7471] [ 1992] [depth= 1] . ( 47 sec) [ -9146.2539] [ 1993] [depth= 1] . ( 47 sec) [ -9144.0859] [ 1995] [depth= 1] . ( 47 sec) [ -9138.4448] [ 1991] [depth= 1] . ( 47 sec) [ -9134.7219] [ 1995] [depth= 1] . ( 48 sec) [ -9134.0681] [ 1996] [depth= 1] . ( 48 sec) [ -9133.6594] [ 1994] [depth= 1] . ( 48 sec) [ -9133.1926] [ 1996] [depth= 1] . ( 48 sec) [ -9132.5205] [ 1995] [depth= 1] . ( 49 sec) [ -9110.6705] [Branch lengths ] . ( 49 sec) [ -9110.6132] [GTR parameters ] . ( 49 sec) [ -9110.5887] [Alpha ][ 0.979168] . ( 50 sec) [ -9109.7161] [ 1993] [depth= 1] . ( 50 sec) [ -9109.4972] [ 1988] [depth= 1] . ( 53 sec) [ -9105.8178] [Branch lengths ] . ( 53 sec) [ -9105.8110] [GTR parameters ] . ( 53 sec) [ -9105.8083] [Alpha ][ 0.984572] . ( 57 sec) [ -9105.5127] [Branch lengths ] . ( 77 sec) [ -9105.4612] [Branch lengths ] . ( 77 sec) [ -9105.4612] [Topology ] . ( 78 sec) [ -9105.4552] [Topology ] . ( 78 sec) [ -9105.4529] [Topology ] . ( 79 sec) [ -9105.4517] [Topology ] . ( 80 sec) [ -9105.4511] [Topology ] . ( 80 sec) [ -9105.4508] [GTR parameters ] . ( 80 sec) [ -9105.4492] [Alpha ][ 0.988743] . ( 80 sec) [ -9105.4492] [Topology ] . ( 81 sec) [ -9105.4487] [Topology ] . ( 81 sec) [ -9105.4487] [GTR parameters ] . ( 81 sec) [ -9105.4487] [Alpha ][ 0.988743] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -9105.4484] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9105.448221 . Log likelihood obtained after SPR moves : -9105.448397 . Log likelihood of the current tree: -9105.448221. . Printing the most likely tree in file 'data19.phy_phyml_tree.txt'... . Best log likelihood : -9105.448039 . Time used 0h1m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo