.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data13.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... . 440 patterns found. (out of a total of 500 sites) . 60 sites without polymorphism (12.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24324.8949] [GTR parameters ] . ( 1 sec) [ -23751.4643] [Alpha ][ 0.500960] . ( 1 sec) [ -22867.0178] [ 5340] [depth= 8] . ( 1 sec) [ -22341.7952] [ 5322] [depth= 6] . ( 1 sec) [ -22173.0940] [ 5313] [depth= 1] . ( 1 sec) [ -21931.7425] [ 5287] [depth= 7] . ( 1 sec) [ -21054.0364] [ 5182] [depth= 7] . ( 1 sec) [ -20795.5508] [ 5188] [depth= 7] . ( 1 sec) [ -20645.7357] [ 5130] [depth= 5] . ( 1 sec) [ -20428.3935] [ 5114] [depth= 1] . ( 1 sec) [ -20417.6784] [ 5132] [depth= 11] . ( 1 sec) [ -19423.9836] [ 4992] [depth= 11] . ( 1 sec) [ -19253.2662] [ 4911] [depth= 1] . ( 1 sec) [ -18989.8172] [ 4899] [depth= 5] . ( 1 sec) [ -18934.5140] [ 4880] [depth= 1] . ( 1 sec) [ -18680.1109] [ 4855] [depth= 4] . ( 1 sec) [ -18627.7802] [ 4789] [depth= 7] . ( 1 sec) [ -18545.8422] [ 4786] [depth= 12] . ( 1 sec) [ -18405.9074] [ 4745] [depth= 3] . ( 2 sec) [ -18194.7965] [ 4652] [depth= 2] . ( 2 sec) [ -18096.8313] [ 4646] [depth= 2] . ( 2 sec) [ -18090.5146] [ 4682] [depth= 1] . ( 2 sec) [ -18061.0069] [ 4642] [depth= 1] . ( 2 sec) [ -18018.1658] [ 4623] [depth= 7] . ( 2 sec) [ -17695.1907] [ 4513] [depth= 5] . ( 2 sec) [ -17508.1552] [ 4326] [depth= 5] . ( 2 sec) [ -17412.4239] [ 4321] [depth= 3] . ( 2 sec) [ -17010.1633] [ 4318] [depth= 1] . ( 2 sec) [ -16839.6168] [ 4204] [depth= 3] . ( 2 sec) [ -16605.8264] [ 4115] [depth= 13] . ( 2 sec) [ -16469.7232] [ 4052] [depth= 1] . ( 2 sec) [ -16428.9943] [ 4060] [depth= 1] . ( 2 sec) [ -16427.1179] [ 4072] [depth= 1] . ( 2 sec) [ -16129.1964] [ 3873] [depth= 8] . ( 2 sec) [ -16106.2667] [ 3862] [depth= 1] . ( 2 sec) [ -15697.8924] [ 3758] [depth= 1] . ( 2 sec) [ -15629.6913] [ 3744] [depth= 1] . ( 2 sec) [ -15617.8782] [ 3735] [depth= 1] . ( 2 sec) [ -15563.1927] [ 3737] [depth= 7] . ( 3 sec) [ -15381.9739] [ 3669] [depth= 9] . ( 3 sec) [ -14869.6037] [ 3509] [depth= 5] . ( 3 sec) [ -14747.5617] [ 3493] [depth= 1] . ( 3 sec) [ -14731.4836] [ 3484] [depth= 1] . ( 3 sec) [ -14724.7540] [ 3489] [depth= 7] . ( 3 sec) [ -14714.8190] [ 3499] [depth= 1] . ( 3 sec) [ -14490.8247] [ 3458] [depth= 7] . ( 3 sec) [ -14481.9488] [ 3449] [depth= 1] . ( 3 sec) [ -14409.6877] [ 3454] [depth= 1] . ( 3 sec) [ -14363.9143] [ 3437] [depth= 1] . ( 3 sec) [ -14242.9992] [ 3448] [depth= 10] . ( 3 sec) [ -13547.0288] [ 3338] [depth= 1] . ( 3 sec) [ -13156.0833] [ 3174] [depth= 10] . ( 3 sec) [ -13022.0007] [ 3099] [depth= 9] . ( 3 sec) [ -12649.1014] [ 3085] [depth= 2] . ( 3 sec) [ -12582.5808] [ 3055] [depth= 1] . ( 3 sec) [ -12162.8268] [ 2954] [depth= 8] . ( 3 sec) [ -12150.0619] [ 2955] [depth= 1] . ( 3 sec) [ -12118.4339] [ 2964] [depth= 3] . ( 3 sec) [ -12064.1587] [ 2989] [depth= 1] . ( 3 sec) [ -11995.6689] [ 2961] [depth= 1] . ( 4 sec) [ -11982.5081] [ 2973] [depth= 1] . ( 4 sec) [ -11868.2476] [ 2966] [depth= 2] . ( 4 sec) [ -11835.2288] [ 2971] [depth= 2] . ( 4 sec) [ -11535.8589] [ 2780] [depth= 12] . ( 4 sec) [ -11520.1799] [ 2779] [depth= 4] . ( 4 sec) [ -11506.0652] [ 2767] [depth= 2] . ( 4 sec) [ -11418.4457] [ 2697] [depth= 2] . ( 4 sec) [ -11415.0845] [ 2687] [depth= 6] . ( 4 sec) [ -11348.6542] [ 2668] [depth= 3] . ( 4 sec) [ -11228.7468] [ 2622] [depth= 2] . ( 4 sec) [ -11121.9866] [ 2605] [depth= 1] . ( 4 sec) [ -10984.9687] [ 2548] [depth= 1] . ( 4 sec) [ -10930.3634] [ 2543] [depth= 2] . ( 4 sec) [ -10928.5188] [ 2539] [depth= 1] . ( 4 sec) [ -10853.2422] [ 2537] [depth= 1] . ( 4 sec) [ -10833.9217] [ 2536] [depth= 3] . ( 4 sec) [ -10830.7596] [ 2571] [depth= 1] . ( 5 sec) [ -10827.9572] [ 2536] [depth= 1] . ( 5 sec) [ -10822.1712] [ 2535] [depth= 1] . ( 5 sec) [ -10548.8771] [Branch lengths ] . ( 5 sec) [ -10547.2172] [GTR parameters ] . ( 6 sec) [ -10518.2206] [Alpha ][ 0.825163] . ( 6 sec) [ -10514.0820] [ 2525] [depth= 1] . ( 6 sec) [ -10511.2769] [ 2515] [depth= 1] . ( 6 sec) [ -10510.3381] [ 2513] [depth= 1] . ( 6 sec) [ -10505.8549] [ 2505] [depth= 1] . ( 6 sec) [ -10505.5315] [ 2512] [depth= 1] . ( 6 sec) [ -10499.5896] [ 2511] [depth= 1] . ( 6 sec) [ -10498.1969] [ 2505] [depth= 1] . ( 6 sec) [ -10493.2933] [ 2500] [depth= 2] . ( 6 sec) [ -10478.2619] [ 2502] [depth= 1] . ( 6 sec) [ -10471.8904] [ 2502] [depth= 1] . ( 7 sec) [ -10471.6393] [ 2502] [depth= 1] . ( 7 sec) [ -10469.2935] [ 2502] [depth= 1] . ( 7 sec) [ -10458.0396] [ 2493] [depth= 2] . ( 7 sec) [ -10457.5452] [ 2508] [depth= 1] . ( 7 sec) [ -10457.0413] [ 2512] [depth= 1] . ( 7 sec) [ -10457.0277] [ 2511] [depth= 1] . ( 8 sec) [ -10456.4569] [ 2513] [depth= 1] . ( 8 sec) [ -10455.2870] [ 2514] [depth= 1] . ( 8 sec) [ -10455.2533] [ 2513] [depth= 1] . ( 8 sec) [ -10455.2269] [ 2513] [depth= 1] . ( 9 sec) [ -10426.0313] [Branch lengths ] . ( 10 sec) [ -10425.8466] [GTR parameters ] . ( 10 sec) [ -10425.4337] [Alpha ][ 0.876743] . ( 10 sec) [ -10424.9928] [ 2517] [depth= 1] . ( 11 sec) [ -10424.5660] [ 2515] [depth= 1] . ( 11 sec) [ -10421.7685] [ 2503] [depth= 3] . ( 12 sec) [ -10420.7471] [ 2510] [depth= 1] . ( 12 sec) [ -10420.5902] [ 2508] [depth= 1] . ( 12 sec) [ -10419.9923] [ 2512] [depth= 1] . ( 12 sec) [ -10419.4767] [ 2505] [depth= 1] . ( 14 sec) [ -10416.6699] [Branch lengths ] . ( 14 sec) [ -10416.6605] [GTR parameters ] . ( 14 sec) [ -10416.6465] [Alpha ][ 0.886788] . ( 18 sec) [ -10415.9946] [Branch lengths ] . ( 33 sec) [ -10415.8199] [ 2514] [depth= 1] . ( 33 sec) [ -10415.2023] [ 2518] [depth= 1] . ( 39 sec) [ -10414.4202] [Branch lengths ] . ( 39 sec) [ -10414.4160] [GTR parameters ] . ( 39 sec) [ -10414.4139] [Alpha ][ 0.890630] . ( 54 sec) [ -10414.0831] [ 2516] [depth= 1] . ( 61 sec) [ -10413.5682] [Branch lengths ] . ( 61 sec) [ -10413.5634] [GTR parameters ] . ( 61 sec) [ -10413.5634] [Alpha ][ 0.890630] . ( 61 sec) [ -10413.5634] [Topology ] . ( 62 sec) [ -10413.4417] [Topology ] . ( 63 sec) [ -10413.3629] [Topology ] . ( 64 sec) [ -10413.3055] [Topology ] . ( 65 sec) [ -10413.2787] [Topology ] . ( 65 sec) [ -10413.2710] [Topology ] . ( 66 sec) [ -10413.2692] [Topology ] . ( 66 sec) [ -10413.2688] [GTR parameters ] . ( 66 sec) [ -10413.2688] [Alpha ][ 0.889740] . ( 66 sec) [ -10413.2688] [Topology ] . ( 67 sec) [ -10413.2683] [Topology ] . ( 67 sec) [ -10413.2682] [GTR parameters ] . ( 67 sec) [ -10413.2682] [Alpha ][ 0.889740] . Checking for NNIs, optimizing five branches... . ( 74 sec) [ -10413.2310] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10413.230979. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -25213.2980] [GTR parameters ] . ( 1 sec) [ -24685.7214] [Alpha ][ 0.500960] . ( 1 sec) [ -23579.5581] [ 5485] [depth= 3] . ( 2 sec) [ -23089.4039] [ 5396] [depth= 3] . ( 2 sec) [ -23005.6981] [ 5377] [depth= 1] . ( 2 sec) [ -22679.7539] [ 5352] [depth= 6] . ( 2 sec) [ -22355.4063] [ 5238] [depth= 3] . ( 2 sec) [ -22220.7842] [ 5227] [depth= 1] . ( 2 sec) [ -21632.6671] [ 5209] [depth= 1] . ( 2 sec) [ -21557.3043] [ 5170] [depth= 4] . ( 2 sec) [ -21188.5547] [ 5095] [depth= 1] . ( 2 sec) [ -21174.5060] [ 5075] [depth= 6] . ( 2 sec) [ -20995.0470] [ 5042] [depth= 7] . ( 2 sec) [ -20842.7176] [ 5021] [depth= 1] . ( 2 sec) [ -20517.1748] [ 4880] [depth= 12] . ( 2 sec) [ -19560.8868] [ 4885] [depth= 3] . ( 2 sec) [ -19241.1329] [ 4757] [depth= 4] . ( 2 sec) [ -19044.3658] [ 4756] [depth= 1] . ( 2 sec) [ -18594.0135] [ 4678] [depth= 2] . ( 2 sec) [ -18265.8061] [ 4547] [depth= 4] . ( 2 sec) [ -17578.7873] [ 4435] [depth= 3] . ( 2 sec) [ -17386.9296] [ 4379] [depth= 13] . ( 2 sec) [ -17359.4540] [ 4350] [depth= 1] . ( 2 sec) [ -17265.9050] [ 4345] [depth= 1] . ( 2 sec) [ -17220.6412] [ 4350] [depth= 1] . ( 2 sec) [ -17211.5912] [ 4345] [depth= 1] . ( 3 sec) [ -16982.3447] [ 4292] [depth= 11] . ( 3 sec) [ -16806.1468] [ 4252] [depth= 7] . ( 3 sec) [ -16683.5136] [ 4204] [depth= 3] . ( 3 sec) [ -15683.8085] [ 3970] [depth= 7] . ( 3 sec) [ -15595.9239] [ 3959] [depth= 13] . ( 3 sec) [ -15385.3166] [ 3908] [depth= 1] . ( 3 sec) [ -15361.3746] [ 3887] [depth= 6] . ( 3 sec) [ -15066.2884] [ 3852] [depth= 1] . ( 3 sec) [ -14466.6606] [ 3851] [depth= 1] . ( 3 sec) [ -14243.9311] [ 3812] [depth= 3] . ( 3 sec) [ -14224.8960] [ 3821] [depth= 1] . ( 3 sec) [ -13844.5828] [ 3710] [depth= 2] . ( 3 sec) [ -13689.3662] [ 3649] [depth= 3] . ( 3 sec) [ -13635.8441] [ 3600] [depth= 1] . ( 3 sec) [ -13311.7024] [ 3529] [depth= 5] . ( 3 sec) [ -13258.7626] [ 3528] [depth= 2] . ( 3 sec) [ -13243.5513] [ 3516] [depth= 1] . ( 3 sec) [ -13227.8745] [ 3506] [depth= 1] . ( 3 sec) [ -13188.6826] [ 3483] [depth= 1] . ( 4 sec) [ -13149.5902] [ 3534] [depth= 1] . ( 4 sec) [ -13132.7876] [ 3536] [depth= 1] . ( 4 sec) [ -12917.2638] [ 3485] [depth= 1] . ( 4 sec) [ -12690.7256] [ 3527] [depth= 4] . ( 4 sec) [ -12576.7600] [ 3457] [depth= 6] . ( 4 sec) [ -12557.3056] [ 3469] [depth= 1] . ( 4 sec) [ -12521.7342] [ 3457] [depth= 1] . ( 4 sec) [ -12507.4712] [ 3443] [depth= 3] . ( 4 sec) [ -12464.6399] [ 3427] [depth= 3] . ( 4 sec) [ -12459.8860] [ 3418] [depth= 1] . ( 4 sec) [ -12419.0272] [ 3406] [depth= 4] . ( 4 sec) [ -12399.6188] [ 3403] [depth= 1] . ( 4 sec) [ -12065.3779] [ 3284] [depth= 4] . ( 4 sec) [ -11953.0428] [ 3268] [depth= 1] . ( 4 sec) [ -11950.8050] [ 3268] [depth= 1] . ( 4 sec) [ -11847.7801] [ 3172] [depth= 4] . ( 4 sec) [ -11846.6455] [ 3172] [depth= 1] . ( 5 sec) [ -11689.6547] [ 3072] [depth= 9] . ( 5 sec) [ -11673.6729] [ 3075] [depth= 1] . ( 5 sec) [ -11620.6128] [ 3042] [depth= 8] . ( 5 sec) [ -11592.1496] [ 3016] [depth= 3] . ( 5 sec) [ -11420.9674] [ 2946] [depth= 2] . ( 5 sec) [ -11309.3264] [ 2768] [depth= 5] . ( 5 sec) [ -11299.2794] [ 2774] [depth= 1] . ( 5 sec) [ -11298.8536] [ 2768] [depth= 1] . ( 5 sec) [ -11213.4989] [ 2703] [depth= 2] . ( 5 sec) [ -11204.1104] [ 2689] [depth= 1] . ( 5 sec) [ -11191.1819] [ 2687] [depth= 1] . ( 5 sec) [ -11178.9906] [ 2689] [depth= 1] . ( 5 sec) [ -11172.8331] [ 2674] [depth= 2] . ( 6 sec) [ -10876.4258] [ 2653] [depth= 1] . ( 6 sec) [ -10642.9468] [Branch lengths ] . ( 7 sec) [ -10640.2266] [GTR parameters ] . ( 7 sec) [ -10621.1732] [Alpha ][ 0.747374] . ( 7 sec) [ -10551.2853] [ 2586] [depth= 2] . ( 7 sec) [ -10546.1999] [ 2588] [depth= 2] . ( 7 sec) [ -10545.8874] [ 2590] [depth= 1] . ( 7 sec) [ -10545.8450] [ 2588] [depth= 2] . ( 7 sec) [ -10545.4184] [ 2590] [depth= 1] . ( 7 sec) [ -10518.4198] [ 2545] [depth= 7] . ( 7 sec) [ -10516.5009] [ 2543] [depth= 2] . ( 8 sec) [ -10509.6461] [ 2542] [depth= 2] . ( 8 sec) [ -10508.0658] [ 2540] [depth= 1] . ( 8 sec) [ -10507.3680] [ 2541] [depth= 1] . ( 8 sec) [ -10506.0474] [ 2544] [depth= 1] . ( 8 sec) [ -10505.0866] [ 2539] [depth= 3] . ( 8 sec) [ -10492.2337] [ 2535] [depth= 1] . ( 8 sec) [ -10461.6223] [ 2508] [depth= 1] . ( 9 sec) [ -10454.8701] [ 2503] [depth= 2] . ( 9 sec) [ -10454.4741] [ 2507] [depth= 1] . ( 9 sec) [ -10454.4113] [ 2496] [depth= 1] . ( 9 sec) [ -10454.3958] [ 2498] [depth= 1] . ( 9 sec) [ -10452.9472] [ 2503] [depth= 1] . ( 10 sec) [ -10451.0569] [ 2505] [depth= 2] . ( 10 sec) [ -10445.6739] [ 2507] [depth= 1] . ( 10 sec) [ -10424.4123] [Branch lengths ] . ( 11 sec) [ -10424.0485] [GTR parameters ] . ( 11 sec) [ -10421.6733] [Alpha ][ 0.865868] . ( 11 sec) [ -10421.3614] [ 2512] [depth= 2] . ( 12 sec) [ -10421.3350] [ 2512] [depth= 1] . ( 13 sec) [ -10421.0631] [ 2513] [depth= 1] . ( 13 sec) [ -10420.7406] [ 2512] [depth= 1] . ( 15 sec) [ -10417.7832] [Branch lengths ] . ( 15 sec) [ -10417.7749] [GTR parameters ] . ( 15 sec) [ -10417.7478] [Alpha ][ 0.879726] . ( 19 sec) [ -10417.1157] [Branch lengths ] . ( 19 sec) [ -10417.0929] [ 2519] [depth= 1] . ( 41 sec) [ -10416.1692] [Branch lengths ] . ( 41 sec) [ -10416.1687] [GTR parameters ] . ( 41 sec) [ -10416.1653] [Alpha ][ 0.884615] . ( 41 sec) [ -10416.1653] [Topology ] . ( 42 sec) [ -10414.9284] [Topology ] . ( 42 sec) [ -10414.2319] [Topology ] . ( 43 sec) [ -10413.8373] [Topology ] . ( 44 sec) [ -10413.5927] [Topology ] . ( 45 sec) [ -10413.4476] [Topology ] . ( 46 sec) [ -10413.3597] [Topology ] . ( 46 sec) [ -10413.3567] [GTR parameters ] . ( 46 sec) [ -10413.3535] [Alpha ][ 0.889386] . ( 46 sec) [ -10413.3535] [Topology ] . ( 47 sec) [ -10413.3016] [Topology ] . ( 47 sec) [ -10413.2716] [Topology ] . ( 48 sec) [ -10413.2542] [Topology ] . ( 49 sec) [ -10413.2441] [Topology ] . ( 50 sec) [ -10413.2384] [Topology ] . ( 51 sec) [ -10413.2351] [Topology ] . ( 51 sec) [ -10413.2349] [GTR parameters ] . ( 51 sec) [ -10413.2349] [Alpha ][ 0.889386] . ( 51 sec) [ -10413.2349] [Topology ] . ( 52 sec) [ -10413.2330] [Topology ] . ( 52 sec) [ -10413.2319] [Topology ] . ( 53 sec) [ -10413.2313] [Topology ] . ( 53 sec) [ -10413.2313] [GTR parameters ] . ( 53 sec) [ -10413.2313] [Alpha ][ 0.889386] . ( 53 sec) [ -10413.2313] [Topology ] . ( 54 sec) [ -10413.2309] [Topology ] . ( 54 sec) [ -10413.2309] [GTR parameters ] . ( 54 sec) [ -10413.2309] [Alpha ][ 0.889386] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10413.230893. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24414.0732] [GTR parameters ] . ( 1 sec) [ -23875.0385] [Alpha ][ 0.500960] . ( 1 sec) [ -23188.0245] [ 5544] [depth= 8] . ( 1 sec) [ -23031.4679] [ 5468] [depth= 8] . ( 1 sec) [ -22890.0374] [ 5436] [depth= 4] . ( 1 sec) [ -22659.6620] [ 5422] [depth= 6] . ( 1 sec) [ -22291.1553] [ 5334] [depth= 2] . ( 1 sec) [ -21995.6921] [ 5322] [depth= 2] . ( 2 sec) [ -21747.9199] [ 5249] [depth= 7] . ( 2 sec) [ -21612.6128] [ 5199] [depth= 12] . ( 2 sec) [ -20620.4849] [ 5161] [depth= 1] . ( 2 sec) [ -20150.0791] [ 4982] [depth= 15] . ( 2 sec) [ -20132.8449] [ 4976] [depth= 12] . ( 2 sec) [ -20105.6724] [ 4955] [depth= 1] . ( 2 sec) [ -19763.2841] [ 4938] [depth= 1] . ( 2 sec) [ -19320.7094] [ 4773] [depth= 4] . ( 2 sec) [ -19124.8053] [ 4764] [depth= 11] . ( 2 sec) [ -18977.2004] [ 4750] [depth= 2] . ( 2 sec) [ -18814.7434] [ 4745] [depth= 1] . ( 2 sec) [ -18428.6942] [ 4602] [depth= 9] . ( 2 sec) [ -18415.2735] [ 4597] [depth= 1] . ( 2 sec) [ -18236.9930] [ 4572] [depth= 7] . ( 2 sec) [ -17897.1722] [ 4491] [depth= 4] . ( 2 sec) [ -17806.7960] [ 4445] [depth= 7] . ( 2 sec) [ -17635.4108] [ 4415] [depth= 7] . ( 2 sec) [ -16517.0612] [ 4232] [depth= 13] . ( 2 sec) [ -16359.0539] [ 4117] [depth= 10] . ( 2 sec) [ -16341.7542] [ 4122] [depth= 2] . ( 2 sec) [ -16132.5286] [ 4017] [depth= 2] . ( 3 sec) [ -16132.3912] [ 4001] [depth= 7] . ( 3 sec) [ -16001.3954] [ 4004] [depth= 1] . ( 3 sec) [ -15549.8686] [ 3763] [depth= 12] . ( 3 sec) [ -15460.3493] [ 3760] [depth= 1] . ( 3 sec) [ -15137.1797] [ 3551] [depth= 6] . ( 3 sec) [ -14740.0292] [ 3523] [depth= 10] . ( 3 sec) [ -14576.1117] [ 3469] [depth= 2] . ( 3 sec) [ -14506.7402] [ 3444] [depth= 1] . ( 3 sec) [ -14499.2558] [ 3444] [depth= 9] . ( 3 sec) [ -14477.9801] [ 3460] [depth= 1] . ( 3 sec) [ -13694.3186] [ 3356] [depth= 3] . ( 3 sec) [ -13310.0097] [ 3205] [depth= 3] . ( 3 sec) [ -13307.3047] [ 3215] [depth= 2] . ( 3 sec) [ -13083.9365] [ 3218] [depth= 1] . ( 3 sec) [ -12839.1721] [ 3163] [depth= 6] . ( 3 sec) [ -12719.4405] [ 3113] [depth= 3] . ( 3 sec) [ -12715.1704] [ 3112] [depth= 1] . ( 3 sec) [ -12705.6375] [ 3107] [depth= 1] . ( 3 sec) [ -12694.2439] [ 3103] [depth= 2] . ( 3 sec) [ -12585.3625] [ 3073] [depth= 5] . ( 4 sec) [ -12555.9075] [ 3014] [depth= 3] . ( 4 sec) [ -12182.8639] [ 2953] [depth= 1] . ( 4 sec) [ -12067.3942] [ 2890] [depth= 4] . ( 4 sec) [ -12033.4147] [ 2883] [depth= 1] . ( 4 sec) [ -11902.4328] [ 2870] [depth= 9] . ( 4 sec) [ -11896.9952] [ 2871] [depth= 1] . ( 4 sec) [ -11583.2408] [ 2866] [depth= 1] . ( 4 sec) [ -11509.9258] [ 2871] [depth= 1] . ( 4 sec) [ -11412.4664] [ 2857] [depth= 2] . ( 4 sec) [ -11396.4831] [ 2878] [depth= 2] . ( 4 sec) [ -11281.9001] [ 2830] [depth= 1] . ( 4 sec) [ -11263.6992] [ 2826] [depth= 2] . ( 4 sec) [ -11263.2780] [ 2828] [depth= 1] . ( 4 sec) [ -11230.5716] [ 2821] [depth= 3] . ( 4 sec) [ -11227.3170] [ 2822] [depth= 1] . ( 4 sec) [ -11162.4604] [ 2808] [depth= 4] . ( 4 sec) [ -11150.5176] [ 2826] [depth= 1] . ( 4 sec) [ -11141.8600] [ 2823] [depth= 2] . ( 5 sec) [ -11129.2459] [ 2824] [depth= 1] . ( 5 sec) [ -11125.5629] [ 2804] [depth= 1] . ( 5 sec) [ -11124.5654] [ 2806] [depth= 2] . ( 5 sec) [ -11035.3960] [ 2768] [depth= 2] . ( 5 sec) [ -11026.3317] [ 2773] [depth= 1] . ( 5 sec) [ -10871.5069] [ 2672] [depth= 2] . ( 5 sec) [ -10870.9285] [ 2668] [depth= 1] . ( 5 sec) [ -10866.0184] [ 2665] [depth= 1] . ( 5 sec) [ -10865.4000] [ 2670] [depth= 1] . ( 5 sec) [ -10863.3758] [ 2671] [depth= 1] . ( 5 sec) [ -10857.1276] [ 2668] [depth= 4] . ( 5 sec) [ -10823.4367] [ 2634] [depth= 1] . ( 5 sec) [ -10806.3372] [ 2617] [depth= 1] . ( 6 sec) [ -10683.5547] [Branch lengths ] . ( 6 sec) [ -10682.2688] [GTR parameters ] . ( 6 sec) [ -10663.5739] [Alpha ][ 0.758133] . ( 6 sec) [ -10662.1786] [ 2617] [depth= 1] . ( 6 sec) [ -10649.2083] [ 2602] [depth= 2] . ( 6 sec) [ -10647.5409] [ 2594] [depth= 1] . ( 6 sec) [ -10571.6163] [ 2547] [depth= 7] . ( 6 sec) [ -10558.4237] [ 2540] [depth= 1] . ( 6 sec) [ -10557.5318] [ 2540] [depth= 1] . ( 7 sec) [ -10557.0948] [ 2542] [depth= 2] . ( 7 sec) [ -10557.0653] [ 2544] [depth= 1] . ( 7 sec) [ -10556.5065] [ 2544] [depth= 1] . ( 7 sec) [ -10553.9725] [ 2540] [depth= 1] . ( 7 sec) [ -10551.5206] [ 2537] [depth= 1] . ( 7 sec) [ -10545.8081] [ 2549] [depth= 2] . ( 7 sec) [ -10535.1050] [ 2545] [depth= 1] . ( 7 sec) [ -10521.7718] [ 2556] [depth= 3] . ( 8 sec) [ -10492.2947] [ 2538] [depth= 1] . ( 8 sec) [ -10491.9495] [ 2538] [depth= 1] . ( 8 sec) [ -10491.8761] [ 2538] [depth= 1] . ( 8 sec) [ -10483.0183] [ 2530] [depth= 2] . ( 8 sec) [ -10475.6651] [ 2517] [depth= 2] . ( 8 sec) [ -10465.1608] [ 2517] [depth= 1] . ( 9 sec) [ -10464.8802] [ 2520] [depth= 2] . ( 9 sec) [ -10457.1163] [ 2516] [depth= 5] . ( 9 sec) [ -10448.0867] [ 2502] [depth= 2] . ( 9 sec) [ -10445.3605] [ 2503] [depth= 1] . ( 10 sec) [ -10422.6239] [Branch lengths ] . ( 10 sec) [ -10422.5220] [GTR parameters ] . ( 10 sec) [ -10420.5308] [Alpha ][ 0.868390] . ( 11 sec) [ -10420.1747] [ 2506] [depth= 1] . ( 12 sec) [ -10419.6239] [ 2505] [depth= 1] . ( 13 sec) [ -10419.5548] [ 2512] [depth= 1] . ( 13 sec) [ -10419.5422] [ 2512] [depth= 1] . ( 14 sec) [ -10415.3944] [Branch lengths ] . ( 14 sec) [ -10415.3870] [GTR parameters ] . ( 14 sec) [ -10415.3557] [Alpha ][ 0.883435] . ( 15 sec) [ -10414.5635] [ 2512] [depth= 2] . ( 18 sec) [ -10413.5649] [Branch lengths ] . ( 18 sec) [ -10413.5590] [GTR parameters ] . ( 18 sec) [ -10413.5563] [Alpha ][ 0.887855] . ( 22 sec) [ -10413.2845] [Branch lengths ] . ( 44 sec) [ -10413.2711] [Branch lengths ] . ( 44 sec) [ -10413.2711] [Topology ] . ( 45 sec) [ -10413.2697] [Topology ] . ( 45 sec) [ -10413.2691] [Topology ] . ( 45 sec) [ -10413.2690] [GTR parameters ] . ( 46 sec) [ -10413.2686] [Alpha ][ 0.889541] . ( 46 sec) [ -10413.2686] [Topology ] . ( 46 sec) [ -10413.2682] [Topology ] . ( 46 sec) [ -10413.2682] [GTR parameters ] . ( 47 sec) [ -10413.2682] [Alpha ][ 0.889541] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -10413.2309] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10413.230864. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -23420.5343] [GTR parameters ] . ( 0 sec) [ -22894.1417] [Alpha ][ 0.500960] . ( 0 sec) [ -21476.1694] [ 5392] [depth= 8] . ( 0 sec) [ -21269.8956] [ 5266] [depth= 9] . ( 0 sec) [ -21177.4478] [ 5143] [depth= 8] . ( 0 sec) [ -21120.2584] [ 5018] [depth= 1] . ( 1 sec) [ -20997.3458] [ 4959] [depth= 3] . ( 1 sec) [ -20551.6498] [ 4949] [depth= 3] . ( 1 sec) [ -20043.7239] [ 4944] [depth= 4] . ( 1 sec) [ -19911.9636] [ 4882] [depth= 6] . ( 1 sec) [ -19906.1172] [ 4870] [depth= 7] . ( 1 sec) [ -19516.1800] [ 4871] [depth= 10] . ( 1 sec) [ -19454.2452] [ 4870] [depth= 3] . ( 1 sec) [ -18941.2044] [ 4770] [depth= 9] . ( 1 sec) [ -18664.4038] [ 4660] [depth= 12] . ( 1 sec) [ -18545.6691] [ 4659] [depth= 2] . ( 1 sec) [ -18057.2004] [ 4625] [depth= 8] . ( 1 sec) [ -17692.0011] [ 4523] [depth= 1] . ( 1 sec) [ -17630.1323] [ 4509] [depth= 1] . ( 1 sec) [ -17320.0711] [ 4506] [depth= 1] . ( 1 sec) [ -16906.6614] [ 4478] [depth= 8] . ( 1 sec) [ -16805.1165] [ 4458] [depth= 1] . ( 1 sec) [ -16527.7336] [ 4388] [depth= 10] . ( 1 sec) [ -16198.8880] [ 4269] [depth= 5] . ( 1 sec) [ -15916.5953] [ 4279] [depth= 1] . ( 1 sec) [ -15713.7143] [ 4259] [depth= 5] . ( 2 sec) [ -15606.1407] [ 4242] [depth= 1] . ( 2 sec) [ -15436.2086] [ 4069] [depth= 10] . ( 2 sec) [ -15363.9998] [ 4048] [depth= 1] . ( 2 sec) [ -15111.5112] [ 3991] [depth= 11] . ( 2 sec) [ -14779.7192] [ 3929] [depth= 1] . ( 2 sec) [ -14698.2838] [ 3844] [depth= 11] . ( 2 sec) [ -14670.9465] [ 3865] [depth= 1] . ( 2 sec) [ -14611.3369] [ 3810] [depth= 2] . ( 2 sec) [ -14573.6918] [ 3814] [depth= 10] . ( 2 sec) [ -14382.5518] [ 3764] [depth= 1] . ( 2 sec) [ -14376.5301] [ 3768] [depth= 1] . ( 2 sec) [ -14085.6161] [ 3731] [depth= 1] . ( 2 sec) [ -14009.1064] [ 3675] [depth= 6] . ( 2 sec) [ -13756.1983] [ 3660] [depth= 5] . ( 2 sec) [ -13723.4901] [ 3615] [depth= 6] . ( 2 sec) [ -13687.4865] [ 3608] [depth= 1] . ( 2 sec) [ -13601.4888] [ 3554] [depth= 2] . ( 2 sec) [ -13520.9080] [ 3453] [depth= 7] . ( 2 sec) [ -13482.6125] [ 3456] [depth= 1] . ( 3 sec) [ -13348.8796] [ 3441] [depth= 3] . ( 3 sec) [ -13283.6519] [ 3441] [depth= 1] . ( 3 sec) [ -13191.0625] [ 3436] [depth= 1] . ( 3 sec) [ -12608.7193] [ 3299] [depth= 1] . ( 3 sec) [ -12243.2917] [ 3225] [depth= 1] . ( 3 sec) [ -12073.6508] [ 3163] [depth= 2] . ( 3 sec) [ -11900.7066] [ 3110] [depth= 2] . ( 3 sec) [ -11873.5200] [ 3121] [depth= 1] . ( 3 sec) [ -11827.7864] [ 3106] [depth= 2] . ( 3 sec) [ -11797.8011] [ 3109] [depth= 2] . ( 3 sec) [ -11790.1450] [ 3106] [depth= 3] . ( 3 sec) [ -11777.1211] [ 3090] [depth= 1] . ( 3 sec) [ -11769.5029] [ 3081] [depth= 1] . ( 3 sec) [ -11767.9219] [ 3071] [depth= 4] . ( 3 sec) [ -11740.5019] [ 3069] [depth= 4] . ( 3 sec) [ -11740.2058] [ 3056] [depth= 3] . ( 3 sec) [ -11698.7909] [ 3110] [depth= 1] . ( 3 sec) [ -11686.3308] [ 3056] [depth= 1] . ( 4 sec) [ -11654.6167] [ 3073] [depth= 1] . ( 4 sec) [ -11634.7328] [ 3065] [depth= 2] . ( 4 sec) [ -11628.2558] [ 3075] [depth= 1] . ( 4 sec) [ -11625.1465] [ 3056] [depth= 5] . ( 4 sec) [ -11276.3089] [ 2891] [depth= 9] . ( 4 sec) [ -11150.0364] [ 2725] [depth= 7] . ( 4 sec) [ -11131.5521] [ 2716] [depth= 1] . ( 4 sec) [ -11075.6557] [ 2708] [depth= 4] . ( 4 sec) [ -11050.8489] [ 2706] [depth= 1] . ( 4 sec) [ -11040.6631] [ 2706] [depth= 2] . ( 4 sec) [ -10952.1326] [ 2706] [depth= 1] . ( 4 sec) [ -10952.0966] [ 2705] [depth= 2] . ( 5 sec) [ -10948.8099] [ 2707] [depth= 1] . ( 5 sec) [ -10941.7842] [ 2704] [depth= 1] . ( 5 sec) [ -10847.4418] [ 2667] [depth= 1] . ( 5 sec) [ -10845.5905] [ 2665] [depth= 1] . ( 5 sec) [ -10735.2631] [Branch lengths ] . ( 5 sec) [ -10734.2896] [GTR parameters ] . ( 6 sec) [ -10718.2750] [Alpha ][ 0.728957] . ( 6 sec) [ -10717.6054] [ 2669] [depth= 1] . ( 6 sec) [ -10639.1995] [ 2604] [depth= 1] . ( 6 sec) [ -10633.0675] [ 2602] [depth= 1] . ( 6 sec) [ -10631.4688] [ 2602] [depth= 1] . ( 6 sec) [ -10631.3190] [ 2610] [depth= 1] . ( 6 sec) [ -10630.8969] [ 2602] [depth= 1] . ( 6 sec) [ -10630.6265] [ 2607] [depth= 1] . ( 7 sec) [ -10629.8485] [ 2606] [depth= 1] . ( 7 sec) [ -10620.7037] [ 2597] [depth= 1] . ( 7 sec) [ -10620.2785] [ 2592] [depth= 1] . ( 7 sec) [ -10619.7105] [ 2595] [depth= 1] . ( 7 sec) [ -10619.2470] [ 2596] [depth= 1] . ( 7 sec) [ -10547.4052] [ 2520] [depth= 6] . ( 7 sec) [ -10540.5079] [ 2510] [depth= 1] . ( 7 sec) [ -10517.6833] [ 2510] [depth= 1] . ( 8 sec) [ -10515.9115] [ 2510] [depth= 2] . ( 8 sec) [ -10509.3664] [ 2514] [depth= 1] . ( 8 sec) [ -10487.4749] [ 2498] [depth= 2] . ( 8 sec) [ -10485.0067] [ 2505] [depth= 1] . ( 8 sec) [ -10484.5851] [ 2509] [depth= 1] . ( 9 sec) [ -10480.0980] [ 2514] [depth= 6] . ( 9 sec) [ -10479.7844] [ 2519] [depth= 1] . ( 9 sec) [ -10476.1353] [ 2518] [depth= 2] . ( 9 sec) [ -10434.6807] [Branch lengths ] . ( 10 sec) [ -10434.3427] [GTR parameters ] . ( 10 sec) [ -10431.2126] [Alpha ][ 0.861738] . ( 10 sec) [ -10429.8904] [ 2515] [depth= 1] . ( 11 sec) [ -10422.6716] [ 2513] [depth= 3] . ( 11 sec) [ -10422.2338] [ 2511] [depth= 1] . ( 11 sec) [ -10422.1040] [ 2516] [depth= 2] . ( 13 sec) [ -10422.0342] [ 2518] [depth= 1] . ( 13 sec) [ -10415.2705] [Branch lengths ] . ( 14 sec) [ -10415.2252] [GTR parameters ] . ( 14 sec) [ -10415.1376] [Alpha ][ 0.885792] . ( 17 sec) [ -10414.3071] [Branch lengths ] . ( 19 sec) [ -10413.9988] [ 2527] [depth= 1] . ( 39 sec) [ -10413.9016] [Branch lengths ] . ( 39 sec) [ -10413.8999] [GTR parameters ] . ( 39 sec) [ -10413.8985] [Alpha ][ 0.889027] . ( 39 sec) [ -10413.8985] [Topology ] . ( 40 sec) [ -10413.8646] [Topology ] . ( 41 sec) [ -10413.8370] [Topology ] . ( 41 sec) [ -10413.8134] [Topology ] . ( 42 sec) [ -10413.6807] [Topology ] . ( 43 sec) [ -10413.3294] [Topology ] . ( 44 sec) [ -10413.2882] [Topology ] . ( 45 sec) [ -10413.2761] [Topology ] . ( 45 sec) [ -10413.2720] [Topology ] . ( 46 sec) [ -10413.2705] [Topology ] . ( 47 sec) [ -10413.2684] [GTR parameters ] . ( 47 sec) [ -10413.2683] [Alpha ][ 0.889916] . ( 47 sec) [ -10413.2683] [Topology ] . ( 48 sec) [ -10413.2680] [Topology ] . ( 48 sec) [ -10413.2680] [GTR parameters ] . ( 48 sec) [ -10413.2680] [Alpha ][ 0.889916] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -10413.2307] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10413.230731. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24229.6533] [GTR parameters ] . ( 1 sec) [ -23698.0077] [Alpha ][ 0.500960] . ( 1 sec) [ -22372.8534] [ 5568] [depth= 6] . ( 1 sec) [ -21822.4488] [ 5458] [depth= 11] . ( 1 sec) [ -21507.4818] [ 5415] [depth= 6] . ( 1 sec) [ -21360.4536] [ 5408] [depth= 1] . ( 1 sec) [ -21291.8536] [ 5260] [depth= 10] . ( 1 sec) [ -21122.4512] [ 5227] [depth= 6] . ( 1 sec) [ -20718.6168] [ 5154] [depth= 1] . ( 1 sec) [ -20668.5613] [ 5052] [depth= 17] . ( 1 sec) [ -20349.3275] [ 4970] [depth= 16] . ( 1 sec) [ -19974.2624] [ 4969] [depth= 1] . ( 1 sec) [ -19427.6901] [ 4928] [depth= 9] . ( 1 sec) [ -19320.7295] [ 4887] [depth= 6] . ( 1 sec) [ -19250.2234] [ 4860] [depth= 3] . ( 1 sec) [ -19161.8593] [ 4836] [depth= 14] . ( 1 sec) [ -18917.9601] [ 4706] [depth= 11] . ( 2 sec) [ -18726.3581] [ 4702] [depth= 1] . ( 2 sec) [ -18545.5531] [ 4640] [depth= 9] . ( 2 sec) [ -18112.6907] [ 4454] [depth= 4] . ( 2 sec) [ -18064.2166] [ 4536] [depth= 6] . ( 2 sec) [ -17892.5746] [ 4421] [depth= 5] . ( 2 sec) [ -17814.3991] [ 4411] [depth= 10] . ( 2 sec) [ -17345.1163] [ 4272] [depth= 1] . ( 2 sec) [ -17312.1490] [ 4219] [depth= 14] . ( 2 sec) [ -16910.0659] [ 4145] [depth= 1] . ( 2 sec) [ -16811.9209] [ 4098] [depth= 14] . ( 2 sec) [ -16576.2787] [ 4086] [depth= 8] . ( 2 sec) [ -16055.9790] [ 4097] [depth= 1] . ( 2 sec) [ -15446.2478] [ 3990] [depth= 2] . ( 2 sec) [ -15298.2658] [ 3904] [depth= 8] . ( 2 sec) [ -15153.3352] [ 3859] [depth= 8] . ( 2 sec) [ -14940.2879] [ 3649] [depth= 7] . ( 2 sec) [ -14732.5492] [ 3558] [depth= 14] . ( 2 sec) [ -14613.2548] [ 3479] [depth= 3] . ( 2 sec) [ -14519.1473] [ 3464] [depth= 8] . ( 3 sec) [ -14299.5681] [ 3377] [depth= 8] . ( 3 sec) [ -14154.4187] [ 3395] [depth= 1] . ( 3 sec) [ -13996.3717] [ 3337] [depth= 5] . ( 3 sec) [ -13824.1297] [ 3246] [depth= 5] . ( 3 sec) [ -13780.0911] [ 3248] [depth= 1] . ( 3 sec) [ -13460.6375] [ 3140] [depth= 4] . ( 3 sec) [ -13255.1090] [ 3145] [depth= 1] . ( 3 sec) [ -12968.2832] [ 2912] [depth= 5] . ( 3 sec) [ -12892.2746] [ 2920] [depth= 8] . ( 3 sec) [ -12868.4708] [ 2910] [depth= 8] . ( 3 sec) [ -12859.7266] [ 2935] [depth= 1] . ( 3 sec) [ -12540.3616] [ 2888] [depth= 3] . ( 3 sec) [ -12457.7205] [ 2858] [depth= 5] . ( 3 sec) [ -12148.1890] [ 2854] [depth= 1] . ( 3 sec) [ -12071.4254] [ 2858] [depth= 1] . ( 3 sec) [ -11525.4028] [ 2672] [depth= 8] . ( 3 sec) [ -11502.0111] [ 2670] [depth= 1] . ( 3 sec) [ -11472.4074] [ 2660] [depth= 2] . ( 3 sec) [ -11449.9598] [ 2665] [depth= 1] . ( 3 sec) [ -11444.1379] [ 2667] [depth= 2] . ( 4 sec) [ -11415.0598] [ 2660] [depth= 2] . ( 4 sec) [ -11323.7210] [ 2649] [depth= 2] . ( 4 sec) [ -11315.6299] [ 2646] [depth= 1] . ( 4 sec) [ -11269.6513] [ 2644] [depth= 2] . ( 4 sec) [ -11261.9516] [ 2647] [depth= 1] . ( 4 sec) [ -11244.5718] [ 2641] [depth= 1] . ( 4 sec) [ -11242.1626] [ 2639] [depth= 1] . ( 4 sec) [ -11217.4139] [ 2633] [depth= 3] . ( 4 sec) [ -11217.0969] [ 2617] [depth= 3] . ( 4 sec) [ -11216.2547] [ 2631] [depth= 1] . ( 4 sec) [ -11179.9847] [ 2635] [depth= 1] . ( 4 sec) [ -11160.8225] [ 2631] [depth= 1] . ( 4 sec) [ -11159.0104] [ 2631] [depth= 1] . ( 4 sec) [ -10976.7164] [ 2622] [depth= 1] . ( 5 sec) [ -10835.9037] [ 2624] [depth= 1] . ( 5 sec) [ -10805.2501] [ 2632] [depth= 1] . ( 5 sec) [ -10575.2006] [Branch lengths ] . ( 6 sec) [ -10573.7721] [GTR parameters ] . ( 6 sec) [ -10545.8578] [Alpha ][ 0.797201] . ( 6 sec) [ -10531.2205] [ 2554] [depth= 7] . ( 6 sec) [ -10507.3883] [ 2537] [depth= 3] . ( 6 sec) [ -10504.5306] [ 2537] [depth= 2] . ( 6 sec) [ -10499.1773] [ 2524] [depth= 2] . ( 6 sec) [ -10493.9263] [ 2524] [depth= 1] . ( 7 sec) [ -10491.2224] [ 2523] [depth= 1] . ( 7 sec) [ -10490.2074] [ 2519] [depth= 1] . ( 7 sec) [ -10482.0697] [ 2524] [depth= 1] . ( 7 sec) [ -10481.7663] [ 2526] [depth= 1] . ( 7 sec) [ -10473.3611] [ 2522] [depth= 1] . ( 7 sec) [ -10472.7869] [ 2512] [depth= 1] . ( 7 sec) [ -10462.8912] [ 2502] [depth= 2] . ( 7 sec) [ -10456.8173] [ 2501] [depth= 3] . ( 7 sec) [ -10451.4322] [ 2502] [depth= 1] . ( 8 sec) [ -10450.5091] [ 2500] [depth= 1] . ( 8 sec) [ -10450.0317] [ 2504] [depth= 1] . ( 8 sec) [ -10448.0230] [ 2505] [depth= 1] . ( 8 sec) [ -10447.8972] [ 2505] [depth= 1] . ( 9 sec) [ -10424.3737] [Branch lengths ] . ( 10 sec) [ -10424.1239] [GTR parameters ] . ( 10 sec) [ -10422.8598] [Alpha ][ 0.883978] . ( 10 sec) [ -10422.3221] [ 2509] [depth= 2] . ( 12 sec) [ -10422.3001] [ 2509] [depth= 1] . ( 13 sec) [ -10416.6591] [Branch lengths ] . ( 13 sec) [ -10416.6554] [GTR parameters ] . ( 14 sec) [ -10416.6447] [Alpha ][ 0.892672] . ( 14 sec) [ -10416.6276] [ 2509] [depth= 1] . ( 17 sec) [ -10415.0997] [Branch lengths ] . ( 18 sec) [ -10415.0987] [GTR parameters ] . ( 18 sec) [ -10415.0985] [Alpha ][ 0.891183] . ( 21 sec) [ -10414.2584] [Branch lengths ] . ( 31 sec) [ -10414.0306] [ 2518] [depth= 1] . ( 42 sec) [ -10413.8986] [Branch lengths ] . ( 43 sec) [ -10413.8970] [GTR parameters ] . ( 43 sec) [ -10413.8968] [Alpha ][ 0.890145] . ( 43 sec) [ -10413.8968] [Topology ] . ( 43 sec) [ -10413.8608] [Topology ] . ( 44 sec) [ -10413.8341] [Topology ] . ( 45 sec) [ -10413.8102] [Topology ] . ( 46 sec) [ -10413.6526] [Topology ] . ( 47 sec) [ -10413.3276] [Topology ] . ( 47 sec) [ -10413.2877] [Topology ] . ( 48 sec) [ -10413.2759] [Topology ] . ( 49 sec) [ -10413.2718] [Topology ] . ( 50 sec) [ -10413.2703] [Topology ] . ( 51 sec) [ -10413.2682] [GTR parameters ] . ( 51 sec) [ -10413.2682] [Alpha ][ 0.890145] . ( 51 sec) [ -10413.2682] [Topology ] . ( 52 sec) [ -10413.2679] [Topology ] . ( 52 sec) [ -10413.2679] [GTR parameters ] . ( 52 sec) [ -10413.2679] [Alpha ][ 0.890145] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -10413.2306] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10413.230649. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10546.845838 . ( 1 sec) [ -10543.7747] [GTR parameters ] . ( 1 sec) [ -10542.3913] [Alpha ][ 0.887695] . ( 1 sec) [ -10542.3913] [Topology ] . ( 2 sec) [ -10460.0048] [Topology ] . ( 3 sec) [ -10440.8259] [Topology ] . ( 3 sec) [ -10432.6380] [Topology ] . ( 4 sec) [ -10421.9951] [Topology ] . ( 5 sec) [ -10416.4032] [Topology ] . ( 6 sec) [ -10414.6769] [Topology ] . ( 7 sec) [ -10413.9441] [Topology ] . ( 8 sec) [ -10413.6686] [Topology ] . ( 8 sec) [ -10413.5911] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -10413.3990] [Topology ] . Before opt ts/t=1.000000 LK=-10413.399007 . ( 17 sec) [ -10413.2633] [GTR parameters ] . ( 17 sec) [ -10413.2633] [Alpha ][ 0.887695] . ( 17 sec) [ -10413.2633] [Topology ] . ( 18 sec) [ -10413.2479] [Topology ] . ( 18 sec) [ -10413.2403] [Topology ] . ( 19 sec) [ -10413.2362] [Topology ] . ( 20 sec) [ -10413.2340] [Topology ] . ( 21 sec) [ -10413.2326] [Topology ] . ( 22 sec) [ -10413.2319] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10413.231925 . ( 29 sec) [ -10413.2319] [GTR parameters ] . ( 29 sec) [ -10413.2316] [Alpha ][ 0.889193] . ( 29 sec) [ -10413.2316] [Topology ] . ( 30 sec) [ -10413.2311] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -10543.7747] [GTR parameters ] . ( 44 sec) [ -10542.3913] [Alpha ][ 0.887695] . ( 45 sec) [ -10536.5809] [ 2504] [depth= 1] . ( 45 sec) [ -10526.7558] [ 2500] [depth= 1] . ( 45 sec) [ -10515.3687] [ 2509] [depth= 1] . ( 45 sec) [ -10511.6005] [ 2510] [depth= 1] . ( 45 sec) [ -10507.5594] [ 2509] [depth= 1] . ( 45 sec) [ -10502.9401] [ 2510] [depth= 1] . ( 45 sec) [ -10501.8837] [ 2503] [depth= 1] . ( 46 sec) [ -10500.3942] [ 2504] [depth= 2] . ( 46 sec) [ -10494.6069] [ 2504] [depth= 1] . ( 46 sec) [ -10483.0385] [ 2503] [depth= 2] . ( 46 sec) [ -10474.6558] [ 2512] [depth= 3] . ( 46 sec) [ -10472.9685] [ 2513] [depth= 1] . ( 46 sec) [ -10472.7260] [ 2519] [depth= 1] . ( 46 sec) [ -10471.6765] [ 2521] [depth= 1] . ( 47 sec) [ -10457.5637] [ 2507] [depth= 2] . ( 47 sec) [ -10455.6164] [ 2511] [depth= 1] . ( 47 sec) [ -10455.4959] [ 2507] [depth= 2] . ( 47 sec) [ -10452.3761] [ 2507] [depth= 1] . ( 47 sec) [ -10452.3631] [ 2509] [depth= 1] . ( 48 sec) [ -10417.5918] [Branch lengths ] . ( 48 sec) [ -10417.4853] [GTR parameters ] . ( 48 sec) [ -10417.4849] [Alpha ][ 0.885927] . ( 49 sec) [ -10417.3977] [ 2514] [depth= 2] . ( 49 sec) [ -10417.1800] [ 2515] [depth= 1] . ( 50 sec) [ -10416.6037] [ 2513] [depth= 1] . ( 52 sec) [ -10414.5094] [Branch lengths ] . ( 52 sec) [ -10414.5051] [GTR parameters ] . ( 52 sec) [ -10414.5048] [Alpha ][ 0.887345] . ( 52 sec) [ -10414.4790] [ 2513] [depth= 1] . ( 56 sec) [ -10414.1965] [Branch lengths ] . ( 56 sec) [ -10414.1963] [GTR parameters ] . ( 56 sec) [ -10414.1962] [Alpha ][ 0.888232] . ( 71 sec) [ -10413.9349] [ 2522] [depth= 1] . ( 77 sec) [ -10413.8585] [Branch lengths ] . ( 78 sec) [ -10413.8570] [GTR parameters ] . ( 78 sec) [ -10413.8570] [Alpha ][ 0.888232] . ( 78 sec) [ -10413.8570] [Topology ] . ( 78 sec) [ -10413.8240] [Topology ] . ( 79 sec) [ -10413.7969] [Topology ] . ( 80 sec) [ -10413.7736] [Topology ] . ( 81 sec) [ -10413.6336] [Topology ] . ( 82 sec) [ -10413.2913] [Topology ] . ( 82 sec) [ -10413.2507] [Topology ] . ( 83 sec) [ -10413.2387] [Topology ] . ( 84 sec) [ -10413.2346] [Topology ] . ( 85 sec) [ -10413.2331] [Topology ] . ( 86 sec) [ -10413.2310] [GTR parameters ] . ( 86 sec) [ -10413.2308] [Alpha ][ 0.889464] . ( 86 sec) [ -10413.2308] [Topology ] . ( 86 sec) [ -10413.2305] [Topology ] . ( 87 sec) [ -10413.2305] [GTR parameters ] . ( 87 sec) [ -10413.2305] [Alpha ][ 0.889464] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10413.231081 . Log likelihood obtained after SPR moves : -10413.230492 . Log likelihood of the current tree: -10413.230492. . Printing the most likely tree in file 'data13.phy_phyml_tree.txt'... . Best log likelihood : -10413.230492 . Time used 0h1m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo