.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data99.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... . 435 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22882.5860] [GTR parameters ] . ( 0 sec) [ -22452.5277] [Alpha ][ 0.500960] . ( 0 sec) [ -21829.9944] [ 4462] [depth= 8] . ( 0 sec) [ -21330.9717] [ 4466] [depth= 6] . ( 0 sec) [ -21143.9264] [ 4442] [depth= 1] . ( 0 sec) [ -20604.8237] [ 4436] [depth= 7] . ( 1 sec) [ -20434.5269] [ 4392] [depth= 5] . ( 1 sec) [ -20003.3927] [ 4372] [depth= 8] . ( 1 sec) [ -19922.2713] [ 4325] [depth= 4] . ( 1 sec) [ -19876.4433] [ 4322] [depth= 1] . ( 1 sec) [ -19654.8892] [ 4282] [depth= 1] . ( 1 sec) [ -19306.8700] [ 4284] [depth= 6] . ( 1 sec) [ -19112.9630] [ 4214] [depth= 3] . ( 1 sec) [ -18544.7094] [ 4091] [depth= 4] . ( 1 sec) [ -18341.2291] [ 4082] [depth= 1] . ( 1 sec) [ -18325.7283] [ 4097] [depth= 1] . ( 1 sec) [ -18255.5614] [ 4092] [depth= 1] . ( 1 sec) [ -16010.9229] [ 4083] [depth= 4] . ( 1 sec) [ -15870.7830] [ 4062] [depth= 3] . ( 1 sec) [ -15814.1449] [ 4058] [depth= 3] . ( 1 sec) [ -15573.1824] [ 4032] [depth= 3] . ( 1 sec) [ -15324.5285] [ 3933] [depth= 6] . ( 1 sec) [ -15125.7890] [ 3904] [depth= 8] . ( 1 sec) [ -15065.5978] [ 3897] [depth= 1] . ( 1 sec) [ -14857.1211] [ 3871] [depth= 10] . ( 1 sec) [ -14538.7562] [ 3743] [depth= 9] . ( 1 sec) [ -14487.6189] [ 3733] [depth= 3] . ( 1 sec) [ -14343.0633] [ 3655] [depth= 1] . ( 1 sec) [ -14229.3915] [ 3642] [depth= 15] . ( 1 sec) [ -14176.3667] [ 3614] [depth= 3] . ( 2 sec) [ -14078.0373] [ 3618] [depth= 1] . ( 2 sec) [ -14019.5006] [ 3598] [depth= 4] . ( 2 sec) [ -14002.4791] [ 3594] [depth= 2] . ( 2 sec) [ -13917.0050] [ 3575] [depth= 12] . ( 2 sec) [ -13817.6550] [ 3543] [depth= 1] . ( 2 sec) [ -13636.7251] [ 3454] [depth= 3] . ( 2 sec) [ -13509.0096] [ 3382] [depth= 8] . ( 2 sec) [ -13322.2876] [ 3334] [depth= 3] . ( 2 sec) [ -13186.3654] [ 3261] [depth= 4] . ( 2 sec) [ -13166.6607] [ 3262] [depth= 1] . ( 2 sec) [ -12888.7773] [ 3230] [depth= 2] . ( 2 sec) [ -12815.5397] [ 3220] [depth= 11] . ( 2 sec) [ -12774.8631] [ 3211] [depth= 1] . ( 2 sec) [ -12773.1884] [ 3215] [depth= 1] . ( 2 sec) [ -12465.2671] [ 3147] [depth= 9] . ( 2 sec) [ -12445.1161] [ 3146] [depth= 1] . ( 2 sec) [ -12287.9750] [ 3100] [depth= 7] . ( 2 sec) [ -12242.3075] [ 3067] [depth= 1] . ( 2 sec) [ -12194.5644] [ 3063] [depth= 1] . ( 2 sec) [ -12193.8968] [ 3067] [depth= 3] . ( 2 sec) [ -12092.3987] [ 3053] [depth= 6] . ( 3 sec) [ -11770.5775] [ 2859] [depth= 10] . ( 3 sec) [ -11763.8794] [ 2858] [depth= 1] . ( 3 sec) [ -11730.7619] [ 2861] [depth= 9] . ( 3 sec) [ -11716.6691] [ 2858] [depth= 2] . ( 3 sec) [ -11647.3209] [ 2843] [depth= 13] . ( 3 sec) [ -11625.6076] [ 2830] [depth= 1] . ( 3 sec) [ -11559.9676] [ 2775] [depth= 12] . ( 3 sec) [ -11457.7087] [ 2726] [depth= 2] . ( 3 sec) [ -11302.7914] [ 2671] [depth= 1] . ( 3 sec) [ -11043.9968] [ 2582] [depth= 5] . ( 3 sec) [ -10933.4242] [ 2531] [depth= 5] . ( 3 sec) [ -10742.0953] [ 2500] [depth= 4] . ( 3 sec) [ -10571.8114] [ 2458] [depth= 5] . ( 3 sec) [ -10551.3938] [ 2488] [depth= 7] . ( 3 sec) [ -10445.6113] [ 2391] [depth= 8] . ( 3 sec) [ -10444.3992] [ 2392] [depth= 1] . ( 3 sec) [ -10416.5539] [ 2389] [depth= 3] . ( 3 sec) [ -10413.9229] [ 2392] [depth= 1] . ( 4 sec) [ -10350.6982] [ 2393] [depth= 2] . ( 4 sec) [ -10303.6984] [ 2392] [depth= 1] . ( 4 sec) [ -10287.8964] [ 2384] [depth= 2] . ( 4 sec) [ -10287.2364] [ 2381] [depth= 2] . ( 4 sec) [ -10286.0610] [ 2383] [depth= 1] . ( 4 sec) [ -10284.5372] [ 2382] [depth= 1] . ( 4 sec) [ -10275.2438] [ 2383] [depth= 1] . ( 4 sec) [ -10119.7826] [ 2297] [depth= 2] . ( 4 sec) [ -10077.3696] [ 2292] [depth= 1] . ( 4 sec) [ -10005.3617] [ 2320] [depth= 1] . ( 4 sec) [ -9867.6752] [ 2260] [depth= 5] . ( 4 sec) [ -9862.4833] [ 2256] [depth= 1] . ( 4 sec) [ -9815.3414] [ 2247] [depth= 2] . ( 4 sec) [ -9813.1830] [ 2257] [depth= 3] . ( 5 sec) [ -9562.8141] [Branch lengths ] . ( 5 sec) [ -9558.2491] [GTR parameters ] . ( 5 sec) [ -9523.8074] [Alpha ][ 0.878455] . ( 5 sec) [ -9521.5010] [ 2236] [depth= 2] . ( 6 sec) [ -9521.0929] [ 2234] [depth= 1] . ( 6 sec) [ -9433.5624] [ 2161] [depth= 5] . ( 6 sec) [ -9433.3526] [ 2163] [depth= 1] . ( 6 sec) [ -9433.2376] [ 2166] [depth= 1] . ( 6 sec) [ -9433.1138] [ 2166] [depth= 1] . ( 6 sec) [ -9432.3562] [ 2150] [depth= 2] . ( 6 sec) [ -9409.4405] [ 2145] [depth= 1] . ( 6 sec) [ -9397.0228] [ 2149] [depth= 1] . ( 7 sec) [ -9396.8882] [ 2149] [depth= 1] . ( 7 sec) [ -9377.3322] [ 2132] [depth= 3] . ( 7 sec) [ -9372.9705] [ 2134] [depth= 1] . ( 7 sec) [ -9366.6131] [ 2122] [depth= 2] . ( 7 sec) [ -9362.4407] [ 2121] [depth= 1] . ( 7 sec) [ -9359.8522] [ 2125] [depth= 1] . ( 7 sec) [ -9359.8011] [ 2128] [depth= 1] . ( 7 sec) [ -9341.3422] [ 2109] [depth= 3] . ( 8 sec) [ -9341.2467] [ 2106] [depth= 1] . ( 9 sec) [ -9298.9155] [Branch lengths ] . ( 9 sec) [ -9298.5968] [GTR parameters ] . ( 9 sec) [ -9297.2813] [Alpha ][ 0.987234] . ( 10 sec) [ -9297.2698] [ 2107] [depth= 1] . ( 11 sec) [ -9297.2380] [ 2104] [depth= 1] . ( 12 sec) [ -9297.2266] [ 2104] [depth= 1] . ( 13 sec) [ -9282.9142] [Branch lengths ] . ( 13 sec) [ -9282.9104] [GTR parameters ] . ( 13 sec) [ -9282.9097] [Alpha ][ 0.989937] . ( 16 sec) [ -9282.0430] [Branch lengths ] . ( 36 sec) [ -9278.0329] [Branch lengths ] . ( 36 sec) [ -9278.0329] [Topology ] . ( 37 sec) [ -9273.1600] [Topology ] . ( 38 sec) [ -9271.1724] [Topology ] . ( 39 sec) [ -9270.4546] [Topology ] . ( 39 sec) [ -9270.1824] [Topology ] . ( 40 sec) [ -9270.0821] [Topology ] . ( 41 sec) [ -9270.0453] [Topology ] . ( 41 sec) [ -9270.0360] [GTR parameters ] . ( 41 sec) [ -9270.0348] [Alpha ][ 0.993465] . ( 41 sec) [ -9270.0348] [Topology ] . ( 42 sec) [ -9270.0203] [Topology ] . ( 43 sec) [ -9270.0148] [Topology ] . ( 43 sec) [ -9270.0126] [Topology ] . ( 44 sec) [ -9270.0117] [Topology ] . ( 44 sec) [ -9270.0117] [GTR parameters ] . ( 44 sec) [ -9270.0117] [Alpha ][ 0.993465] . ( 44 sec) [ -9270.0117] [Topology ] . ( 45 sec) [ -9270.0113] [Topology ] . ( 45 sec) [ -9270.0113] [GTR parameters ] . ( 45 sec) [ -9270.0113] [Alpha ][ 0.993465] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -9270.0102] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9270.010238. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26252.8048] [GTR parameters ] . ( 1 sec) [ -25816.2541] [Alpha ][ 0.500960] . ( 1 sec) [ -25402.0490] [ 4508] [depth= 3] . ( 1 sec) [ -25178.6754] [ 4407] [depth= 10] . ( 1 sec) [ -24764.3119] [ 4379] [depth= 4] . ( 1 sec) [ -24647.0065] [ 4363] [depth= 5] . ( 1 sec) [ -24447.5909] [ 4325] [depth= 1] . ( 2 sec) [ -24168.7226] [ 4313] [depth= 2] . ( 2 sec) [ -23501.5491] [ 4321] [depth= 1] . ( 2 sec) [ -23268.3393] [ 4279] [depth= 4] . ( 2 sec) [ -23172.4822] [ 4194] [depth= 2] . ( 2 sec) [ -22999.1192] [ 4177] [depth= 3] . ( 2 sec) [ -22803.1631] [ 4136] [depth= 7] . ( 2 sec) [ -22630.7384] [ 4126] [depth= 1] . ( 2 sec) [ -22440.6947] [ 3974] [depth= 12] . ( 2 sec) [ -22201.3098] [ 3973] [depth= 3] . ( 2 sec) [ -21820.0140] [ 3877] [depth= 4] . ( 2 sec) [ -21469.3577] [ 3878] [depth= 4] . ( 2 sec) [ -21092.9111] [ 3765] [depth= 15] . ( 2 sec) [ -20809.6886] [ 3725] [depth= 3] . ( 2 sec) [ -16576.4798] [ 3713] [depth= 3] . ( 2 sec) [ -16555.7057] [ 3695] [depth= 1] . ( 2 sec) [ -16319.6159] [ 3555] [depth= 4] . ( 2 sec) [ -16235.8676] [ 3495] [depth= 1] . ( 2 sec) [ -15664.6756] [ 3496] [depth= 19] . ( 2 sec) [ -15572.4948] [ 3443] [depth= 3] . ( 2 sec) [ -14249.1190] [ 3299] [depth= 18] . ( 3 sec) [ -14122.8637] [ 3271] [depth= 1] . ( 3 sec) [ -14067.7944] [ 3192] [depth= 2] . ( 3 sec) [ -13957.9879] [ 3199] [depth= 1] . ( 3 sec) [ -13577.4625] [ 3117] [depth= 13] . ( 3 sec) [ -13433.2746] [ 3046] [depth= 1] . ( 3 sec) [ -13431.3302] [ 3047] [depth= 1] . ( 3 sec) [ -13428.3088] [ 3046] [depth= 1] . ( 3 sec) [ -13421.3555] [ 3051] [depth= 1] . ( 3 sec) [ -13148.6531] [ 3033] [depth= 3] . ( 3 sec) [ -13082.4872] [ 2995] [depth= 1] . ( 3 sec) [ -12588.9707] [ 2955] [depth= 3] . ( 3 sec) [ -12349.3955] [ 2941] [depth= 7] . ( 3 sec) [ -12174.7272] [ 2864] [depth= 7] . ( 3 sec) [ -12065.6954] [ 2823] [depth= 4] . ( 3 sec) [ -12053.8239] [ 2819] [depth= 1] . ( 3 sec) [ -11953.9580] [ 2817] [depth= 1] . ( 3 sec) [ -11850.8876] [ 2754] [depth= 5] . ( 4 sec) [ -11848.5002] [ 2757] [depth= 6] . ( 4 sec) [ -11836.9438] [ 2757] [depth= 1] . ( 4 sec) [ -11577.2365] [ 2615] [depth= 5] . ( 4 sec) [ -11388.4313] [ 2607] [depth= 5] . ( 4 sec) [ -11369.1070] [ 2608] [depth= 1] . ( 4 sec) [ -11362.6904] [ 2607] [depth= 1] . ( 4 sec) [ -11176.2531] [ 2576] [depth= 1] . ( 4 sec) [ -11040.2356] [ 2560] [depth= 2] . ( 4 sec) [ -10776.2843] [ 2488] [depth= 3] . ( 4 sec) [ -10652.3612] [ 2457] [depth= 3] . ( 4 sec) [ -10513.8536] [ 2446] [depth= 2] . ( 4 sec) [ -10457.3862] [ 2397] [depth= 2] . ( 4 sec) [ -10374.3513] [ 2334] [depth= 3] . ( 4 sec) [ -10364.4868] [ 2334] [depth= 1] . ( 4 sec) [ -10304.1768] [ 2311] [depth= 1] . ( 4 sec) [ -10281.4116] [ 2281] [depth= 3] . ( 4 sec) [ -10279.4309] [ 2250] [depth= 1] . ( 4 sec) [ -10272.8693] [ 2243] [depth= 6] . ( 4 sec) [ -10211.0688] [ 2216] [depth= 4] . ( 5 sec) [ -10201.3563] [ 2219] [depth= 2] . ( 5 sec) [ -10183.3878] [ 2219] [depth= 1] . ( 5 sec) [ -10161.1431] [ 2230] [depth= 1] . ( 5 sec) [ -9997.2352] [ 2216] [depth= 4] . ( 5 sec) [ -9988.0932] [ 2223] [depth= 1] . ( 5 sec) [ -9986.3168] [ 2219] [depth= 1] . ( 5 sec) [ -9890.8585] [ 2183] [depth= 3] . ( 5 sec) [ -9841.7501] [ 2191] [depth= 1] . ( 5 sec) [ -9829.0388] [ 2189] [depth= 1] . ( 5 sec) [ -9808.5050] [ 2184] [depth= 2] . ( 5 sec) [ -9805.4115] [ 2181] [depth= 1] . ( 5 sec) [ -9746.1459] [ 2163] [depth= 1] . ( 5 sec) [ -9741.5327] [ 2163] [depth= 1] . ( 5 sec) [ -9740.5051] [ 2163] [depth= 1] . ( 5 sec) [ -9731.1865] [ 2158] [depth= 1] . ( 5 sec) [ -9721.1300] [ 2158] [depth= 1] . ( 5 sec) [ -9716.4650] [ 2158] [depth= 1] . ( 5 sec) [ -9697.0184] [ 2156] [depth= 2] . ( 5 sec) [ -9659.8126] [ 2140] [depth= 1] . ( 6 sec) [ -9631.5207] [ 2121] [depth= 1] . ( 6 sec) [ -9620.1905] [ 2121] [depth= 1] . ( 6 sec) [ -9395.8544] [Branch lengths ] . ( 7 sec) [ -9393.1285] [GTR parameters ] . ( 7 sec) [ -9352.9015] [Alpha ][ 0.957558] . ( 7 sec) [ -9351.8949] [ 2123] [depth= 1] . ( 7 sec) [ -9351.2578] [ 2122] [depth= 1] . ( 7 sec) [ -9350.9873] [ 2122] [depth= 1] . ( 7 sec) [ -9350.9729] [ 2122] [depth= 1] . ( 7 sec) [ -9349.7197] [ 2119] [depth= 1] . ( 7 sec) [ -9341.9846] [ 2108] [depth= 1] . ( 7 sec) [ -9341.5971] [ 2109] [depth= 1] . ( 7 sec) [ -9341.5303] [ 2108] [depth= 1] . ( 8 sec) [ -9340.6163] [ 2107] [depth= 1] . ( 8 sec) [ -9340.4235] [ 2107] [depth= 1] . ( 8 sec) [ -9334.3284] [ 2102] [depth= 1] . ( 9 sec) [ -9332.9463] [ 2107] [depth= 2] . ( 9 sec) [ -9332.8254] [ 2106] [depth= 1] . ( 9 sec) [ -9332.6905] [ 2108] [depth= 1] . ( 9 sec) [ -9332.6308] [ 2108] [depth= 1] . ( 10 sec) [ -9332.4830] [ 2108] [depth= 1] . ( 10 sec) [ -9321.7316] [Branch lengths ] . ( 10 sec) [ -9321.6880] [GTR parameters ] . ( 10 sec) [ -9321.5596] [Alpha ][ 0.993820] . ( 11 sec) [ -9321.5353] [ 2107] [depth= 1] . ( 13 sec) [ -9321.4895] [ 2103] [depth= 1] . ( 14 sec) [ -9320.4288] [Branch lengths ] . ( 14 sec) [ -9320.4279] [GTR parameters ] . ( 14 sec) [ -9320.4251] [Alpha ][ 0.999302] . ( 18 sec) [ -9319.0913] [Branch lengths ] . ( 39 sec) [ -9309.4572] [Branch lengths ] . ( 39 sec) [ -9309.4572] [Topology ] . ( 40 sec) [ -9286.3264] [Topology ] . ( 40 sec) [ -9274.6024] [Topology ] . ( 41 sec) [ -9271.4933] [Topology ] . ( 42 sec) [ -9270.6764] [Topology ] . ( 42 sec) [ -9270.4373] [Topology ] . ( 43 sec) [ -9270.3587] [Topology ] . ( 44 sec) [ -9270.3289] [GTR parameters ] . ( 44 sec) [ -9270.3262] [Alpha ][ 0.993835] . ( 44 sec) [ -9270.3262] [Topology ] . ( 45 sec) [ -9270.2971] [Topology ] . ( 45 sec) [ -9270.2508] [Topology ] . ( 46 sec) [ -9270.0989] [Topology ] . ( 47 sec) [ -9270.0447] [Topology ] . ( 47 sec) [ -9270.0247] [Topology ] . ( 48 sec) [ -9270.0167] [Topology ] . ( 49 sec) [ -9270.0134] [Topology ] . ( 50 sec) [ -9270.0121] [Topology ] . ( 50 sec) [ -9270.0119] [GTR parameters ] . ( 50 sec) [ -9270.0119] [Alpha ][ 0.993835] . ( 50 sec) [ -9270.0119] [Topology ] . ( 51 sec) [ -9270.0114] [Topology ] . ( 51 sec) [ -9270.0114] [GTR parameters ] . ( 51 sec) [ -9270.0114] [Alpha ][ 0.993835] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -9270.0112] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9270.011236. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26235.9415] [GTR parameters ] . ( 1 sec) [ -25796.8283] [Alpha ][ 0.500960] . ( 1 sec) [ -25522.3870] [ 4564] [depth= 8] . ( 1 sec) [ -25222.0627] [ 4475] [depth= 10] . ( 1 sec) [ -25182.2699] [ 4468] [depth= 2] . ( 1 sec) [ -25038.0377] [ 4466] [depth= 6] . ( 1 sec) [ -24900.0130] [ 4440] [depth= 8] . ( 2 sec) [ -21574.4256] [ 4437] [depth= 4] . ( 2 sec) [ -21078.4919] [ 4318] [depth= 13] . ( 2 sec) [ -20771.6561] [ 4275] [depth= 15] . ( 2 sec) [ -19542.2295] [ 4212] [depth= 1] . ( 2 sec) [ -19419.8483] [ 4137] [depth= 9] . ( 2 sec) [ -19048.6254] [ 4025] [depth= 7] . ( 2 sec) [ -18813.8936] [ 3979] [depth= 7] . ( 2 sec) [ -18703.2647] [ 3984] [depth= 1] . ( 2 sec) [ -18479.1960] [ 3940] [depth= 9] . ( 2 sec) [ -18157.3324] [ 3860] [depth= 2] . ( 2 sec) [ -18098.0477] [ 3859] [depth= 4] . ( 2 sec) [ -17636.8200] [ 3818] [depth= 3] . ( 2 sec) [ -17535.8570] [ 3821] [depth= 1] . ( 2 sec) [ -17465.4384] [ 3806] [depth= 1] . ( 2 sec) [ -16857.4870] [ 3660] [depth= 7] . ( 2 sec) [ -16801.1320] [ 3643] [depth= 1] . ( 3 sec) [ -15607.4050] [ 3544] [depth= 11] . ( 3 sec) [ -15600.5806] [ 3549] [depth= 1] . ( 3 sec) [ -15555.8241] [ 3508] [depth= 6] . ( 3 sec) [ -14787.9091] [ 3570] [depth= 2] . ( 3 sec) [ -14658.3219] [ 3482] [depth= 1] . ( 3 sec) [ -14292.1211] [ 3410] [depth= 2] . ( 3 sec) [ -14128.1331] [ 3329] [depth= 10] . ( 3 sec) [ -14092.1357] [ 3324] [depth= 7] . ( 3 sec) [ -14090.4095] [ 3319] [depth= 1] . ( 3 sec) [ -13833.5469] [ 3230] [depth= 2] . ( 3 sec) [ -13722.0738] [ 3208] [depth= 9] . ( 3 sec) [ -12991.4042] [ 3177] [depth= 8] . ( 3 sec) [ -12786.7214] [ 3103] [depth= 2] . ( 3 sec) [ -12634.8379] [ 3103] [depth= 1] . ( 3 sec) [ -12634.0826] [ 3103] [depth= 1] . ( 3 sec) [ -12582.7143] [ 3041] [depth= 6] . ( 3 sec) [ -12574.1988] [ 3049] [depth= 1] . ( 3 sec) [ -12261.7185] [ 2951] [depth= 3] . ( 3 sec) [ -12183.8313] [ 2916] [depth= 1] . ( 3 sec) [ -12071.1092] [ 2910] [depth= 8] . ( 3 sec) [ -12067.0178] [ 2910] [depth= 1] . ( 3 sec) [ -11884.9275] [ 2866] [depth= 6] . ( 4 sec) [ -11723.4642] [ 2802] [depth= 2] . ( 4 sec) [ -11465.5261] [ 2692] [depth= 1] . ( 4 sec) [ -11306.9145] [ 2663] [depth= 6] . ( 4 sec) [ -11246.1934] [ 2660] [depth= 1] . ( 4 sec) [ -11093.5353] [ 2602] [depth= 2] . ( 4 sec) [ -11051.2713] [ 2593] [depth= 1] . ( 4 sec) [ -11015.4920] [ 2585] [depth= 1] . ( 4 sec) [ -10912.4519] [ 2574] [depth= 1] . ( 4 sec) [ -10891.2680] [ 2563] [depth= 1] . ( 4 sec) [ -10825.1841] [ 2536] [depth= 1] . ( 4 sec) [ -10819.9535] [ 2527] [depth= 2] . ( 4 sec) [ -10788.8032] [ 2497] [depth= 1] . ( 4 sec) [ -10755.1441] [ 2472] [depth= 4] . ( 4 sec) [ -10719.0780] [ 2467] [depth= 1] . ( 4 sec) [ -10694.4082] [ 2450] [depth= 1] . ( 4 sec) [ -10662.7329] [ 2445] [depth= 1] . ( 4 sec) [ -10650.4930] [ 2445] [depth= 5] . ( 4 sec) [ -10629.1508] [ 2444] [depth= 1] . ( 5 sec) [ -10484.1027] [ 2400] [depth= 5] . ( 5 sec) [ -10482.5758] [ 2400] [depth= 1] . ( 5 sec) [ -10482.5355] [ 2400] [depth= 1] . ( 5 sec) [ -10433.5618] [ 2397] [depth= 4] . ( 5 sec) [ -10336.0540] [ 2372] [depth= 1] . ( 5 sec) [ -10252.4326] [ 2308] [depth= 5] . ( 5 sec) [ -10249.8200] [ 2308] [depth= 1] . ( 5 sec) [ -10243.8610] [ 2310] [depth= 1] . ( 5 sec) [ -10237.7833] [ 2310] [depth= 2] . ( 5 sec) [ -10233.9572] [ 2309] [depth= 1] . ( 5 sec) [ -10226.4954] [ 2317] [depth= 1] . ( 5 sec) [ -10129.6118] [ 2247] [depth= 5] . ( 5 sec) [ -10095.6126] [ 2220] [depth= 1] . ( 5 sec) [ -10093.5809] [ 2224] [depth= 1] . ( 5 sec) [ -9997.7450] [ 2204] [depth= 1] . ( 5 sec) [ -9994.3973] [ 2208] [depth= 2] . ( 5 sec) [ -9838.0324] [ 2170] [depth= 1] . ( 5 sec) [ -9837.8736] [ 2170] [depth= 1] . ( 6 sec) [ -9836.4857] [ 2171] [depth= 1] . ( 6 sec) [ -9836.4518] [ 2171] [depth= 1] . ( 6 sec) [ -9836.1618] [ 2171] [depth= 1] . ( 6 sec) [ -9768.1614] [ 2149] [depth= 1] . ( 6 sec) [ -9760.7961] [ 2157] [depth= 1] . ( 6 sec) [ -9745.1817] [ 2158] [depth= 1] . ( 6 sec) [ -9729.0026] [ 2165] [depth= 1] . ( 6 sec) [ -9720.8915] [ 2188] [depth= 1] . ( 6 sec) [ -9517.5152] [Branch lengths ] . ( 7 sec) [ -9516.0647] [GTR parameters ] . ( 7 sec) [ -9480.8713] [Alpha ][ 0.897663] . ( 7 sec) [ -9471.4023] [ 2193] [depth= 2] . ( 7 sec) [ -9471.3871] [ 2197] [depth= 2] . ( 7 sec) [ -9426.0683] [ 2182] [depth= 1] . ( 7 sec) [ -9400.9794] [ 2173] [depth= 1] . ( 7 sec) [ -9395.0840] [ 2182] [depth= 1] . ( 7 sec) [ -9395.0392] [ 2182] [depth= 1] . ( 7 sec) [ -9392.1270] [ 2203] [depth= 3] . ( 8 sec) [ -9371.8992] [ 2183] [depth= 2] . ( 8 sec) [ -9371.8871] [ 2181] [depth= 1] . ( 8 sec) [ -9367.8677] [ 2156] [depth= 2] . ( 8 sec) [ -9328.5578] [ 2137] [depth= 2] . ( 8 sec) [ -9311.6491] [ 2107] [depth= 1] . ( 8 sec) [ -9311.0555] [ 2107] [depth= 1] . ( 8 sec) [ -9309.4957] [ 2107] [depth= 1] . ( 9 sec) [ -9309.4841] [ 2108] [depth= 1] . ( 9 sec) [ -9309.4465] [ 2111] [depth= 1] . ( 9 sec) [ -9309.4105] [ 2111] [depth= 1] . ( 9 sec) [ -9307.3675] [ 2110] [depth= 2] . ( 9 sec) [ -9299.9962] [ 2108] [depth= 1] . ( 9 sec) [ -9299.9375] [ 2107] [depth= 2] . ( 10 sec) [ -9297.7234] [ 2107] [depth= 1] . ( 10 sec) [ -9277.5198] [Branch lengths ] . ( 11 sec) [ -9277.4211] [GTR parameters ] . ( 11 sec) [ -9276.6398] [Alpha ][ 0.981962] . ( 13 sec) [ -9276.5576] [ 2107] [depth= 1] . ( 15 sec) [ -9275.4022] [Branch lengths ] . ( 15 sec) [ -9275.4012] [GTR parameters ] . ( 15 sec) [ -9275.4011] [Alpha ][ 0.980980] . ( 19 sec) [ -9275.3348] [Branch lengths ] . ( 40 sec) [ -9275.3310] [Branch lengths ] . ( 40 sec) [ -9275.3310] [Topology ] . ( 40 sec) [ -9275.3305] [Topology ] . ( 41 sec) [ -9275.3305] [GTR parameters ] . ( 41 sec) [ -9275.3305] [Alpha ][ 0.981961] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9275.330454. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -24605.0633] [GTR parameters ] . ( 1 sec) [ -24225.9567] [Alpha ][ 0.500960] . ( 1 sec) [ -23678.7516] [ 4545] [depth= 8] . ( 1 sec) [ -23105.9076] [ 4431] [depth= 9] . ( 1 sec) [ -22725.1941] [ 4355] [depth= 2] . ( 1 sec) [ -21786.5976] [ 4296] [depth= 1] . ( 1 sec) [ -21637.1891] [ 4193] [depth= 9] . ( 1 sec) [ -21505.7125] [ 4150] [depth= 3] . ( 1 sec) [ -21381.1898] [ 4144] [depth= 5] . ( 1 sec) [ -21232.4709] [ 4082] [depth= 2] . ( 1 sec) [ -21090.0975] [ 4069] [depth= 3] . ( 1 sec) [ -20811.2084] [ 4035] [depth= 9] . ( 1 sec) [ -20802.8170] [ 4032] [depth= 1] . ( 1 sec) [ -19882.9982] [ 3988] [depth= 11] . ( 1 sec) [ -19872.1731] [ 3987] [depth= 1] . ( 1 sec) [ -19814.2730] [ 3966] [depth= 11] . ( 1 sec) [ -19808.4678] [ 3948] [depth= 2] . ( 1 sec) [ -19780.8125] [ 3936] [depth= 2] . ( 1 sec) [ -19611.3869] [ 3938] [depth= 1] . ( 1 sec) [ -19386.1008] [ 3820] [depth= 6] . ( 1 sec) [ -18956.7953] [ 3774] [depth= 4] . ( 1 sec) [ -18797.1511] [ 3731] [depth= 10] . ( 1 sec) [ -18574.0372] [ 3673] [depth= 9] . ( 2 sec) [ -18407.0641] [ 3631] [depth= 2] . ( 2 sec) [ -18036.9313] [ 3524] [depth= 15] . ( 2 sec) [ -17584.0679] [ 3470] [depth= 3] . ( 2 sec) [ -14660.0614] [ 3490] [depth= 11] . ( 2 sec) [ -14576.6321] [ 3423] [depth= 12] . ( 2 sec) [ -14575.8221] [ 3428] [depth= 2] . ( 2 sec) [ -14462.3019] [ 3394] [depth= 1] . ( 2 sec) [ -14412.1845] [ 3365] [depth= 1] . ( 2 sec) [ -14341.9262] [ 3327] [depth= 3] . ( 2 sec) [ -14211.6486] [ 3256] [depth= 10] . ( 2 sec) [ -14200.8340] [ 3257] [depth= 1] . ( 2 sec) [ -14139.4098] [ 3223] [depth= 1] . ( 2 sec) [ -13728.1893] [ 3120] [depth= 9] . ( 2 sec) [ -13524.4498] [ 3137] [depth= 1] . ( 2 sec) [ -13050.6554] [ 3070] [depth= 9] . ( 2 sec) [ -12799.7263] [ 3040] [depth= 2] . ( 2 sec) [ -12723.2801] [ 3024] [depth= 7] . ( 2 sec) [ -12697.6245] [ 3027] [depth= 9] . ( 2 sec) [ -12616.1281] [ 3018] [depth= 4] . ( 2 sec) [ -12424.5034] [ 2994] [depth= 11] . ( 2 sec) [ -12255.4944] [ 2927] [depth= 5] . ( 3 sec) [ -12072.5714] [ 2903] [depth= 3] . ( 3 sec) [ -12038.9460] [ 2858] [depth= 16] . ( 3 sec) [ -11906.1767] [ 2773] [depth= 10] . ( 3 sec) [ -11669.7873] [ 2679] [depth= 4] . ( 3 sec) [ -11643.5767] [ 2672] [depth= 2] . ( 3 sec) [ -11550.3605] [ 2601] [depth= 1] . ( 3 sec) [ -11546.8529] [ 2600] [depth= 1] . ( 3 sec) [ -11514.4981] [ 2578] [depth= 3] . ( 3 sec) [ -11450.9434] [ 2569] [depth= 10] . ( 3 sec) [ -11167.1623] [ 2504] [depth= 6] . ( 3 sec) [ -11154.0528] [ 2515] [depth= 1] . ( 3 sec) [ -11105.9920] [ 2517] [depth= 1] . ( 3 sec) [ -11095.1299] [ 2514] [depth= 1] . ( 3 sec) [ -10990.2822] [ 2477] [depth= 9] . ( 3 sec) [ -10680.0531] [ 2405] [depth= 5] . ( 3 sec) [ -10659.2541] [ 2412] [depth= 1] . ( 4 sec) [ -10641.1810] [ 2402] [depth= 1] . ( 4 sec) [ -10615.4338] [ 2398] [depth= 1] . ( 4 sec) [ -10595.9465] [ 2388] [depth= 1] . ( 4 sec) [ -10478.1946] [ 2370] [depth= 1] . ( 4 sec) [ -10437.6284] [ 2378] [depth= 1] . ( 4 sec) [ -10422.2708] [ 2379] [depth= 1] . ( 4 sec) [ -10129.9016] [ 2303] [depth= 5] . ( 4 sec) [ -10127.2649] [ 2302] [depth= 1] . ( 4 sec) [ -10034.9106] [ 2265] [depth= 1] . ( 4 sec) [ -10000.3742] [ 2240] [depth= 1] . ( 4 sec) [ -9992.3616] [ 2260] [depth= 1] . ( 4 sec) [ -9982.2628] [ 2247] [depth= 1] . ( 4 sec) [ -9979.5519] [ 2246] [depth= 1] . ( 4 sec) [ -9979.1380] [ 2246] [depth= 1] . ( 4 sec) [ -9977.1273] [ 2246] [depth= 1] . ( 4 sec) [ -9974.1924] [ 2247] [depth= 1] . ( 4 sec) [ -9970.9344] [ 2246] [depth= 1] . ( 4 sec) [ -9968.8965] [ 2246] [depth= 1] . ( 5 sec) [ -9968.4785] [ 2246] [depth= 1] . ( 5 sec) [ -9968.4671] [ 2246] [depth= 1] . ( 5 sec) [ -9567.5460] [Branch lengths ] . ( 5 sec) [ -9561.7753] [GTR parameters ] . ( 6 sec) [ -9535.7126] [Alpha ][ 0.786952] . ( 6 sec) [ -9433.7150] [ 2156] [depth= 7] . ( 6 sec) [ -9429.0598] [ 2154] [depth= 1] . ( 6 sec) [ -9428.0188] [ 2154] [depth= 1] . ( 6 sec) [ -9420.9921] [ 2150] [depth= 3] . ( 6 sec) [ -9418.8245] [ 2149] [depth= 1] . ( 6 sec) [ -9418.2297] [ 2148] [depth= 1] . ( 6 sec) [ -9413.8324] [ 2142] [depth= 1] . ( 6 sec) [ -9413.5130] [ 2143] [depth= 1] . ( 6 sec) [ -9404.7019] [ 2134] [depth= 1] . ( 7 sec) [ -9401.5895] [ 2132] [depth= 1] . ( 7 sec) [ -9338.9080] [ 2104] [depth= 1] . ( 7 sec) [ -9338.5753] [ 2109] [depth= 1] . ( 7 sec) [ -9338.3601] [ 2104] [depth= 1] . ( 7 sec) [ -9337.5295] [ 2105] [depth= 1] . ( 7 sec) [ -9328.9542] [ 2104] [depth= 2] . ( 7 sec) [ -9328.4528] [ 2107] [depth= 1] . ( 7 sec) [ -9328.4060] [ 2107] [depth= 1] . ( 8 sec) [ -9327.0674] [ 2108] [depth= 1] . ( 8 sec) [ -9323.1917] [ 2114] [depth= 2] . ( 9 sec) [ -9323.1816] [ 2114] [depth= 1] . ( 9 sec) [ -9323.1575] [ 2114] [depth= 1] . ( 9 sec) [ -9287.4470] [Branch lengths ] . ( 10 sec) [ -9286.9239] [GTR parameters ] . ( 10 sec) [ -9283.2864] [Alpha ][ 0.946018] . ( 10 sec) [ -9281.9635] [ 2119] [depth= 1] . ( 11 sec) [ -9281.8898] [ 2118] [depth= 2] . ( 11 sec) [ -9281.6644] [ 2121] [depth= 1] . ( 11 sec) [ -9281.1818] [ 2112] [depth= 1] . ( 12 sec) [ -9280.9885] [ 2112] [depth= 1] . ( 12 sec) [ -9280.4727] [ 2111] [depth= 1] . ( 13 sec) [ -9280.3803] [ 2108] [depth= 2] . ( 14 sec) [ -9272.6156] [Branch lengths ] . ( 14 sec) [ -9272.5692] [GTR parameters ] . ( 14 sec) [ -9272.4270] [Alpha ][ 0.982273] . ( 14 sec) [ -9272.3862] [ 2108] [depth= 1] . ( 14 sec) [ -9272.3320] [ 2104] [depth= 1] . ( 15 sec) [ -9272.2225] [ 2104] [depth= 1] . ( 16 sec) [ -9272.2061] [ 2109] [depth= 1] . ( 16 sec) [ -9272.1894] [ 2109] [depth= 1] . ( 18 sec) [ -9272.1783] [ 2109] [depth= 1] . ( 18 sec) [ -9270.5447] [Branch lengths ] . ( 18 sec) [ -9270.5396] [GTR parameters ] . ( 18 sec) [ -9270.5323] [Alpha ][ 0.990944] . ( 22 sec) [ -9270.1111] [Branch lengths ] . ( 43 sec) [ -9270.0331] [Branch lengths ] . ( 43 sec) [ -9270.0331] [Topology ] . ( 44 sec) [ -9270.0226] [Topology ] . ( 45 sec) [ -9270.0185] [Topology ] . ( 45 sec) [ -9270.0164] [Topology ] . ( 46 sec) [ -9270.0153] [Topology ] . ( 47 sec) [ -9270.0147] [Topology ] . ( 47 sec) [ -9270.0127] [GTR parameters ] . ( 47 sec) [ -9270.0120] [Alpha ][ 0.993600] . ( 47 sec) [ -9270.0120] [Topology ] . ( 48 sec) [ -9270.0115] [Topology ] . ( 48 sec) [ -9270.0115] [GTR parameters ] . ( 48 sec) [ -9270.0115] [Alpha ][ 0.993600] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9270.011493. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21657.5388] [GTR parameters ] . ( 1 sec) [ -21213.8334] [Alpha ][ 0.500960] . ( 1 sec) [ -20699.6697] [ 4614] [depth= 6] . ( 1 sec) [ -20349.2122] [ 4513] [depth= 11] . ( 1 sec) [ -20208.8514] [ 4478] [depth= 5] . ( 1 sec) [ -20159.6525] [ 4473] [depth= 1] . ( 1 sec) [ -20019.3234] [ 4410] [depth= 3] . ( 1 sec) [ -19978.7125] [ 4396] [depth= 3] . ( 1 sec) [ -19761.9992] [ 4371] [depth= 6] . ( 1 sec) [ -19604.8426] [ 4296] [depth= 1] . ( 1 sec) [ -19516.3406] [ 4229] [depth= 8] . ( 1 sec) [ -19469.1269] [ 4285] [depth= 10] . ( 1 sec) [ -18992.3688] [ 4078] [depth= 11] . ( 1 sec) [ -18760.4241] [ 4078] [depth= 11] . ( 1 sec) [ -18594.5989] [ 4055] [depth= 15] . ( 1 sec) [ -18536.8780] [ 4025] [depth= 13] . ( 1 sec) [ -18349.7514] [ 4009] [depth= 8] . ( 1 sec) [ -18277.6193] [ 3998] [depth= 2] . ( 1 sec) [ -18038.3940] [ 3929] [depth= 5] . ( 1 sec) [ -18024.4953] [ 3933] [depth= 1] . ( 1 sec) [ -17928.3396] [ 3893] [depth= 6] . ( 1 sec) [ -17842.8311] [ 3900] [depth= 1] . ( 2 sec) [ -17783.9284] [ 3877] [depth= 2] . ( 2 sec) [ -17733.0374] [ 3877] [depth= 9] . ( 2 sec) [ -17656.3761] [ 3878] [depth= 8] . ( 2 sec) [ -17412.4484] [ 3873] [depth= 1] . ( 2 sec) [ -17044.8075] [ 3837] [depth= 11] . ( 2 sec) [ -16783.3863] [ 3752] [depth= 10] . ( 2 sec) [ -16671.6515] [ 3675] [depth= 7] . ( 2 sec) [ -16513.3344] [ 3602] [depth= 11] . ( 2 sec) [ -16203.3136] [ 3547] [depth= 4] . ( 2 sec) [ -16004.2849] [ 3490] [depth= 5] . ( 2 sec) [ -15750.5816] [ 3394] [depth= 9] . ( 2 sec) [ -15444.7220] [ 3345] [depth= 5] . ( 2 sec) [ -14361.0418] [ 3289] [depth= 1] . ( 2 sec) [ -14079.0962] [ 3147] [depth= 8] . ( 2 sec) [ -13998.6026] [ 3079] [depth= 2] . ( 2 sec) [ -13963.4044] [ 3061] [depth= 8] . ( 2 sec) [ -13958.4777] [ 3080] [depth= 3] . ( 2 sec) [ -13419.6968] [ 3032] [depth= 9] . ( 2 sec) [ -13319.7543] [ 2962] [depth= 8] . ( 3 sec) [ -13275.9607] [ 2961] [depth= 7] . ( 3 sec) [ -13252.0104] [ 2954] [depth= 1] . ( 3 sec) [ -12852.9175] [ 2810] [depth= 12] . ( 3 sec) [ -12401.1311] [ 2706] [depth= 9] . ( 3 sec) [ -12400.9792] [ 2725] [depth= 1] . ( 3 sec) [ -12157.5946] [ 2630] [depth= 8] . ( 3 sec) [ -12124.1386] [ 2626] [depth= 2] . ( 3 sec) [ -12083.1922] [ 2595] [depth= 4] . ( 3 sec) [ -11829.8645] [ 2521] [depth= 8] . ( 3 sec) [ -11694.8183] [ 2491] [depth= 2] . ( 3 sec) [ -11691.5830] [ 2491] [depth= 2] . ( 3 sec) [ -11659.7404] [ 2449] [depth= 3] . ( 3 sec) [ -11496.5511] [ 2415] [depth= 2] . ( 3 sec) [ -10762.3744] [ 2406] [depth= 2] . ( 3 sec) [ -10680.3798] [ 2379] [depth= 1] . ( 3 sec) [ -10635.5477] [ 2381] [depth= 1] . ( 3 sec) [ -10507.9527] [ 2344] [depth= 6] . ( 3 sec) [ -10467.1076] [ 2300] [depth= 1] . ( 3 sec) [ -10455.0668] [ 2266] [depth= 2] . ( 3 sec) [ -10451.5382] [ 2268] [depth= 1] . ( 4 sec) [ -10421.8071] [ 2292] [depth= 1] . ( 4 sec) [ -10239.8700] [ 2307] [depth= 1] . ( 4 sec) [ -10239.5019] [ 2307] [depth= 1] . ( 4 sec) [ -10235.2192] [ 2292] [depth= 1] . ( 4 sec) [ -10229.8332] [ 2293] [depth= 1] . ( 4 sec) [ -10175.1866] [ 2257] [depth= 2] . ( 4 sec) [ -10019.1689] [ 2256] [depth= 3] . ( 4 sec) [ -10012.8083] [ 2258] [depth= 1] . ( 4 sec) [ -9894.5468] [ 2232] [depth= 2] . ( 4 sec) [ -9863.9002] [ 2233] [depth= 3] . ( 4 sec) [ -9849.3084] [ 2223] [depth= 2] . ( 4 sec) [ -9844.1464] [ 2214] [depth= 1] . ( 4 sec) [ -9841.0937] [ 2214] [depth= 1] . ( 4 sec) [ -9798.9034] [ 2204] [depth= 2] . ( 4 sec) [ -9783.7900] [ 2202] [depth= 1] . ( 4 sec) [ -9775.1428] [ 2203] [depth= 1] . ( 4 sec) [ -9719.8869] [ 2181] [depth= 1] . ( 5 sec) [ -9691.6885] [ 2177] [depth= 1] . ( 5 sec) [ -9602.7859] [ 2158] [depth= 3] . ( 5 sec) [ -9464.2426] [Branch lengths ] . ( 6 sec) [ -9461.6465] [GTR parameters ] . ( 6 sec) [ -9423.6289] [Alpha ][ 0.924839] . ( 6 sec) [ -9423.3761] [ 2156] [depth= 1] . ( 6 sec) [ -9391.7568] [ 2151] [depth= 1] . ( 6 sec) [ -9385.9994] [ 2154] [depth= 1] . ( 6 sec) [ -9385.9881] [ 2154] [depth= 1] . ( 6 sec) [ -9385.9778] [ 2154] [depth= 1] . ( 6 sec) [ -9382.1633] [ 2151] [depth= 2] . ( 6 sec) [ -9380.3224] [ 2149] [depth= 1] . ( 6 sec) [ -9378.7870] [ 2149] [depth= 1] . ( 7 sec) [ -9336.1189] [ 2132] [depth= 1] . ( 7 sec) [ -9310.1458] [ 2125] [depth= 2] . ( 7 sec) [ -9309.9341] [ 2123] [depth= 1] . ( 7 sec) [ -9305.7119] [ 2123] [depth= 1] . ( 7 sec) [ -9305.4732] [ 2118] [depth= 1] . ( 7 sec) [ -9298.1292] [ 2101] [depth= 2] . ( 8 sec) [ -9298.0652] [ 2101] [depth= 1] . ( 8 sec) [ -9284.2245] [ 2103] [depth= 2] . ( 8 sec) [ -9282.4370] [ 2106] [depth= 1] . ( 8 sec) [ -9282.2902] [ 2106] [depth= 1] . ( 9 sec) [ -9282.2428] [ 2103] [depth= 1] . ( 9 sec) [ -9281.3676] [ 2103] [depth= 1] . ( 9 sec) [ -9272.1550] [Branch lengths ] . ( 10 sec) [ -9271.7567] [GTR parameters ] . ( 10 sec) [ -9271.2497] [Alpha ][ 0.995214] . ( 10 sec) [ -9271.2339] [ 2103] [depth= 1] . ( 11 sec) [ -9271.2053] [ 2105] [depth= 1] . ( 11 sec) [ -9271.1192] [ 2105] [depth= 1] . ( 12 sec) [ -9270.7952] [ 2105] [depth= 1] . ( 12 sec) [ -9270.7807] [ 2104] [depth= 1] . ( 13 sec) [ -9270.1044] [Branch lengths ] . ( 13 sec) [ -9270.1009] [GTR parameters ] . ( 13 sec) [ -9270.1009] [Alpha ][ 0.994218] . ( 16 sec) [ -9270.0296] [Branch lengths ] . ( 37 sec) [ -9270.0150] [Branch lengths ] . ( 37 sec) [ -9270.0150] [Topology ] . ( 37 sec) [ -9270.0132] [Topology ] . ( 38 sec) [ -9270.0124] [Topology ] . ( 38 sec) [ -9270.0120] [GTR parameters ] . ( 38 sec) [ -9270.0120] [Alpha ][ 0.994218] . ( 38 sec) [ -9270.0120] [Topology ] . ( 39 sec) [ -9270.0116] [Topology ] . ( 39 sec) [ -9270.0116] [GTR parameters ] . ( 39 sec) [ -9270.0116] [Alpha ][ 0.994218] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -9269.9306] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9269.930639. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9344.513092 . ( 1 sec) [ -9340.2121] [GTR parameters ] . ( 1 sec) [ -9340.0840] [Alpha ][ 0.961734] . ( 1 sec) [ -9340.0840] [Topology ] . ( 2 sec) [ -9287.2686] [Topology ] . ( 3 sec) [ -9278.1083] [Topology ] . ( 3 sec) [ -9274.7836] [Topology ] . ( 4 sec) [ -9273.3477] [Topology ] . ( 5 sec) [ -9272.6564] [Topology ] . ( 6 sec) [ -9272.3013] [Topology ] . ( 6 sec) [ -9272.1066] [Topology ] . ( 7 sec) [ -9271.9490] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9271.949043 . ( 15 sec) [ -9271.7805] [GTR parameters ] . ( 15 sec) [ -9271.6934] [Alpha ][ 0.991117] . ( 15 sec) [ -9271.6934] [Topology ] . ( 16 sec) [ -9271.2852] [Topology ] . ( 17 sec) [ -9270.4779] [Topology ] . ( 17 sec) [ -9270.1417] [Topology ] . ( 18 sec) [ -9270.0517] [Topology ] . ( 19 sec) [ -9270.0278] [Topology ] . ( 19 sec) [ -9270.0205] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.020474 . ( 27 sec) [ -9270.0170] [GTR parameters ] . ( 27 sec) [ -9270.0164] [Alpha ][ 0.993723] . ( 27 sec) [ -9270.0164] [Topology ] . ( 28 sec) [ -9270.0135] [Topology ] . ( 29 sec) [ -9270.0123] [Topology ] . ( 30 sec) [ -9270.0117] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.011651 . ( 37 sec) [ -9270.0117] [GTR parameters ] . ( 37 sec) [ -9270.0117] [Alpha ][ 0.993723] . ( 37 sec) [ -9270.0117] [Topology ] . ( 38 sec) [ -9270.0113] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -9340.2121] [GTR parameters ] . ( 53 sec) [ -9340.0840] [Alpha ][ 0.961734] . ( 53 sec) [ -9338.6513] [ 2106] [depth= 1] . ( 53 sec) [ -9338.3221] [ 2106] [depth= 1] . ( 54 sec) [ -9335.2727] [ 2110] [depth= 1] . ( 54 sec) [ -9335.2017] [ 2106] [depth= 1] . ( 54 sec) [ -9332.7874] [ 2110] [depth= 1] . ( 54 sec) [ -9329.7893] [ 2105] [depth= 2] . ( 54 sec) [ -9329.4975] [ 2105] [depth= 1] . ( 54 sec) [ -9328.4316] [ 2102] [depth= 2] . ( 54 sec) [ -9327.9485] [ 2114] [depth= 1] . ( 54 sec) [ -9326.2099] [ 2102] [depth= 1] . ( 55 sec) [ -9324.5767] [ 2107] [depth= 1] . ( 55 sec) [ -9324.1124] [ 2106] [depth= 1] . ( 55 sec) [ -9323.9033] [ 2107] [depth= 1] . ( 55 sec) [ -9322.4336] [ 2102] [depth= 1] . ( 55 sec) [ -9322.3497] [ 2101] [depth= 1] . ( 56 sec) [ -9320.8473] [ 2102] [depth= 1] . ( 56 sec) [ -9320.2342] [ 2105] [depth= 1] . ( 56 sec) [ -9319.3029] [ 2102] [depth= 1] . ( 56 sec) [ -9318.3908] [ 2104] [depth= 1] . ( 56 sec) [ -9318.1942] [ 2108] [depth= 1] . ( 56 sec) [ -9275.2031] [Branch lengths ] . ( 57 sec) [ -9275.0740] [GTR parameters ] . ( 57 sec) [ -9274.9916] [Alpha ][ 0.990784] . ( 57 sec) [ -9274.9632] [ 2108] [depth= 1] . ( 57 sec) [ -9274.9292] [ 2113] [depth= 1] . ( 58 sec) [ -9274.2702] [ 2112] [depth= 1] . ( 59 sec) [ -9274.1537] [ 2108] [depth= 1] . ( 60 sec) [ -9271.2878] [Branch lengths ] . ( 61 sec) [ -9271.2832] [GTR parameters ] . ( 61 sec) [ -9271.2822] [Alpha ][ 0.994088] . ( 61 sec) [ -9270.9026] [ 2108] [depth= 1] . ( 61 sec) [ -9270.8766] [ 2107] [depth= 1] . ( 64 sec) [ -9270.4357] [Branch lengths ] . ( 64 sec) [ -9270.4339] [GTR parameters ] . ( 64 sec) [ -9270.4338] [Alpha ][ 0.993094] . ( 69 sec) [ -9270.4200] [ 2108] [depth= 1] . ( 69 sec) [ -9270.4041] [ 2107] [depth= 1] . ( 84 sec) [ -9270.3085] [Branch lengths ] . ( 84 sec) [ -9270.3081] [GTR parameters ] . ( 84 sec) [ -9270.3081] [Alpha ][ 0.993094] . ( 84 sec) [ -9270.3081] [Topology ] . ( 85 sec) [ -9270.2939] [Topology ] . ( 86 sec) [ -9270.2882] [Topology ] . ( 87 sec) [ -9270.2852] [Topology ] . ( 87 sec) [ -9270.2836] [Topology ] . ( 88 sec) [ -9270.2827] [Topology ] . ( 88 sec) [ -9270.2825] [GTR parameters ] . ( 88 sec) [ -9270.2825] [Alpha ][ 0.993094] . ( 88 sec) [ -9270.2825] [Topology ] . ( 89 sec) [ -9270.2820] [Topology ] . ( 89 sec) [ -9270.2820] [GTR parameters ] . ( 89 sec) [ -9270.2820] [Alpha ][ 0.993094] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -9270.2818] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9270.011349 . Log likelihood obtained after SPR moves : -9270.281846 . Log likelihood of the current tree: -9270.011349. . Printing the most likely tree in file 'data99.phy_phyml_tree.txt'... . Best log likelihood : -9269.930639 . Time used 0h1m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo