.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data15.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... . 424 patterns found. (out of a total of 500 sites) . 69 sites without polymorphism (13.80%). . [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) [ -20435.6949] [GTR parameters ] . ( 2 sec) [ -20000.9224] [Alpha ][ 0.500960] . ( 2 sec) [ -19560.4330] [ 4442] [depth= 4] . ( 2 sec) [ -19029.9024] [ 4302] [depth= 6] . ( 2 sec) [ -18894.5509] [ 4273] [depth= 1] . ( 2 sec) [ -18712.5645] [ 4264] [depth= 7] . ( 2 sec) [ -18196.9869] [ 4153] [depth= 5] . ( 2 sec) [ -18138.1314] [ 4146] [depth= 1] . ( 2 sec) [ -17823.5585] [ 4131] [depth= 8] . ( 2 sec) [ -17715.1427] [ 4090] [depth= 11] . ( 2 sec) [ -17273.5458] [ 3967] [depth= 9] . ( 2 sec) [ -17064.5530] [ 3979] [depth= 13] . ( 2 sec) [ -16727.4275] [ 3865] [depth= 12] . ( 2 sec) [ -16700.2240] [ 3863] [depth= 3] . ( 2 sec) [ -16653.8955] [ 3856] [depth= 2] . ( 2 sec) [ -16634.1368] [ 3836] [depth= 1] . ( 2 sec) [ -16615.0390] [ 3825] [depth= 4] . ( 2 sec) [ -16250.5030] [ 3797] [depth= 2] . ( 3 sec) [ -16133.3284] [ 3788] [depth= 2] . ( 3 sec) [ -15947.9727] [ 3732] [depth= 4] . ( 3 sec) [ -15711.6872] [ 3655] [depth= 5] . ( 3 sec) [ -15667.2989] [ 3650] [depth= 1] . ( 3 sec) [ -15569.3261] [ 3646] [depth= 4] . ( 3 sec) [ -15444.6730] [ 3616] [depth= 12] . ( 3 sec) [ -15317.6466] [ 3636] [depth= 6] . ( 3 sec) [ -15274.6363] [ 3604] [depth= 1] . ( 3 sec) [ -15196.5679] [ 3590] [depth= 1] . ( 3 sec) [ -15019.8033] [ 3604] [depth= 4] . ( 3 sec) [ -14924.5701] [ 3617] [depth= 10] . ( 3 sec) [ -14512.4834] [ 3476] [depth= 13] . ( 3 sec) [ -14263.8571] [ 3466] [depth= 2] . ( 3 sec) [ -14032.9069] [ 3388] [depth= 4] . ( 3 sec) [ -13962.8813] [ 3310] [depth= 4] . ( 3 sec) [ -13941.6571] [ 3305] [depth= 11] . ( 3 sec) [ -13915.1777] [ 3299] [depth= 1] . ( 3 sec) [ -13845.0528] [ 3278] [depth= 7] . ( 3 sec) [ -13685.2159] [ 3246] [depth= 2] . ( 3 sec) [ -13619.4365] [ 3241] [depth= 1] . ( 3 sec) [ -13538.0076] [ 3181] [depth= 1] . ( 3 sec) [ -13524.5907] [ 3175] [depth= 2] . ( 4 sec) [ -13387.9599] [ 3141] [depth= 14] . ( 4 sec) [ -13324.6826] [ 3133] [depth= 10] . ( 4 sec) [ -13292.5538] [ 3124] [depth= 1] . ( 4 sec) [ -13045.0084] [ 3072] [depth= 5] . ( 4 sec) [ -13039.7738] [ 3070] [depth= 1] . ( 4 sec) [ -12916.3071] [ 3011] [depth= 11] . ( 4 sec) [ -12654.9469] [ 2923] [depth= 3] . ( 4 sec) [ -12510.7786] [ 2891] [depth= 12] . ( 4 sec) [ -12415.9475] [ 2880] [depth= 9] . ( 4 sec) [ -12203.0188] [ 2841] [depth= 2] . ( 4 sec) [ -11654.2992] [ 2768] [depth= 1] . ( 4 sec) [ -11620.2354] [ 2750] [depth= 3] . ( 4 sec) [ -11285.4972] [ 2648] [depth= 7] . ( 4 sec) [ -11126.0604] [ 2617] [depth= 2] . ( 4 sec) [ -11083.1515] [ 2572] [depth= 1] . ( 4 sec) [ -10990.7646] [ 2547] [depth= 2] . ( 4 sec) [ -10803.5155] [ 2454] [depth= 10] . ( 4 sec) [ -10721.7273] [ 2433] [depth= 8] . ( 5 sec) [ -10721.5456] [ 2431] [depth= 1] . ( 5 sec) [ -10580.5909] [ 2353] [depth= 7] . ( 5 sec) [ -10577.4365] [ 2374] [depth= 5] . ( 5 sec) [ -10573.5155] [ 2379] [depth= 1] . ( 5 sec) [ -10549.2567] [ 2372] [depth= 1] . ( 5 sec) [ -10541.5907] [ 2372] [depth= 1] . ( 5 sec) [ -10267.9701] [ 2290] [depth= 4] . ( 5 sec) [ -10110.5005] [ 2275] [depth= 1] . ( 5 sec) [ -10056.1035] [ 2226] [depth= 1] . ( 5 sec) [ -9969.7641] [ 2217] [depth= 1] . ( 5 sec) [ -9855.5485] [ 2227] [depth= 1] . ( 5 sec) [ -9833.7124] [ 2202] [depth= 2] . ( 5 sec) [ -9828.3001] [ 2205] [depth= 1] . ( 5 sec) [ -9820.0825] [ 2188] [depth= 2] . ( 5 sec) [ -9813.0290] [ 2188] [depth= 1] . ( 5 sec) [ -9799.0437] [ 2189] [depth= 2] . ( 5 sec) [ -9798.0135] [ 2188] [depth= 1] . ( 6 sec) [ -9797.8462] [ 2189] [depth= 2] . ( 6 sec) [ -9491.3826] [Branch lengths ] . ( 6 sec) [ -9490.1969] [GTR parameters ] . ( 6 sec) [ -9463.0759] [Alpha ][ 0.843319] . ( 7 sec) [ -9462.7479] [ 2186] [depth= 1] . ( 7 sec) [ -9460.5129] [ 2186] [depth= 1] . ( 7 sec) [ -9442.4937] [ 2187] [depth= 1] . ( 7 sec) [ -9442.3967] [ 2187] [depth= 1] . ( 7 sec) [ -9415.0676] [ 2162] [depth= 1] . ( 7 sec) [ -9402.5990] [ 2156] [depth= 1] . ( 7 sec) [ -9394.0559] [ 2147] [depth= 1] . ( 7 sec) [ -9394.0381] [ 2149] [depth= 1] . ( 7 sec) [ -9393.9497] [ 2146] [depth= 1] . ( 7 sec) [ -9390.1520] [ 2138] [depth= 1] . ( 7 sec) [ -9390.1133] [ 2138] [depth= 1] . ( 7 sec) [ -9338.0245] [ 2117] [depth= 2] . ( 7 sec) [ -9336.3218] [ 2125] [depth= 1] . ( 8 sec) [ -9335.4432] [ 2118] [depth= 1] . ( 8 sec) [ -9335.1382] [ 2118] [depth= 1] . ( 8 sec) [ -9335.0852] [ 2118] [depth= 1] . ( 8 sec) [ -9333.6400] [ 2114] [depth= 1] . ( 8 sec) [ -9231.3389] [ 2052] [depth= 2] . ( 8 sec) [ -9225.4330] [ 2056] [depth= 1] . ( 8 sec) [ -9200.6382] [ 2061] [depth= 1] . ( 8 sec) [ -9200.4098] [ 2062] [depth= 1] . ( 8 sec) [ -9194.2629] [ 2061] [depth= 1] . ( 8 sec) [ -9186.4873] [ 2055] [depth= 2] . ( 8 sec) [ -9186.0296] [ 2049] [depth= 1] . ( 8 sec) [ -9185.4333] [ 2043] [depth= 1] . ( 9 sec) [ -9184.0540] [ 2039] [depth= 1] . ( 9 sec) [ -9183.0643] [ 2038] [depth= 2] . ( 9 sec) [ -9180.3352] [ 2041] [depth= 1] . ( 9 sec) [ -9178.8882] [ 2040] [depth= 2] . ( 9 sec) [ -9178.3735] [ 2038] [depth= 1] . ( 9 sec) [ -9178.1394] [ 2038] [depth= 1] . ( 9 sec) [ -9177.0432] [ 2040] [depth= 1] . ( 10 sec) [ -9141.5705] [Branch lengths ] . ( 10 sec) [ -9141.1559] [GTR parameters ] . ( 10 sec) [ -9140.7730] [Alpha ][ 0.898169] . ( 10 sec) [ -9138.5672] [ 2043] [depth= 1] . ( 10 sec) [ -9138.5535] [ 2043] [depth= 1] . ( 11 sec) [ -9138.0602] [ 2040] [depth= 1] . ( 12 sec) [ -9137.9446] [ 2040] [depth= 1] . ( 13 sec) [ -9135.5637] [Branch lengths ] . ( 13 sec) [ -9135.5588] [GTR parameters ] . ( 13 sec) [ -9135.5554] [Alpha ][ 0.892763] . ( 16 sec) [ -9135.2840] [Branch lengths ] . ( 38 sec) [ -9135.2351] [Branch lengths ] . ( 38 sec) [ -9135.2351] [Topology ] . ( 38 sec) [ -9135.2293] [Topology ] . ( 39 sec) [ -9135.2272] [Topology ] . ( 40 sec) [ -9135.2261] [Topology ] . ( 41 sec) [ -9135.2255] [Topology ] . ( 41 sec) [ -9135.2251] [GTR parameters ] . ( 41 sec) [ -9135.2251] [Alpha ][ 0.892763] . ( 41 sec) [ -9135.2251] [Topology ] . ( 42 sec) [ -9135.2248] [Topology ] . ( 42 sec) [ -9135.2248] [GTR parameters ] . ( 42 sec) [ -9135.2248] [Alpha ][ 0.892763] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.224798. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20918.9806] [GTR parameters ] . ( 1 sec) [ -20482.6582] [Alpha ][ 0.500960] . ( 1 sec) [ -19891.9313] [ 4409] [depth= 4] . ( 1 sec) [ -19181.2823] [ 4295] [depth= 3] . ( 1 sec) [ -19106.9488] [ 4278] [depth= 4] . ( 1 sec) [ -18752.1278] [ 4255] [depth= 7] . ( 1 sec) [ -18535.8092] [ 4146] [depth= 6] . ( 1 sec) [ -17746.8052] [ 4148] [depth= 10] . ( 1 sec) [ -17683.3319] [ 4139] [depth= 4] . ( 2 sec) [ -17620.7997] [ 4113] [depth= 1] . ( 2 sec) [ -17462.9436] [ 4099] [depth= 4] . ( 2 sec) [ -17412.9145] [ 4061] [depth= 5] . ( 2 sec) [ -17316.0745] [ 4028] [depth= 12] . ( 2 sec) [ -17189.2791] [ 4007] [depth= 3] . ( 2 sec) [ -16947.7921] [ 3999] [depth= 8] . ( 2 sec) [ -16397.6337] [ 3859] [depth= 9] . ( 2 sec) [ -16194.6185] [ 3809] [depth= 4] . ( 2 sec) [ -16131.1166] [ 3798] [depth= 1] . ( 2 sec) [ -16056.9579] [ 3795] [depth= 1] . ( 2 sec) [ -15709.3085] [ 3803] [depth= 1] . ( 2 sec) [ -15625.2042] [ 3757] [depth= 3] . ( 2 sec) [ -15500.6870] [ 3727] [depth= 1] . ( 2 sec) [ -15023.9938] [ 3582] [depth= 9] . ( 2 sec) [ -14894.2875] [ 3558] [depth= 2] . ( 2 sec) [ -14682.9626] [ 3475] [depth= 10] . ( 2 sec) [ -14503.2864] [ 3492] [depth= 1] . ( 2 sec) [ -14359.0052] [ 3493] [depth= 4] . ( 2 sec) [ -14321.6849] [ 3429] [depth= 2] . ( 2 sec) [ -14274.9231] [ 3370] [depth= 3] . ( 2 sec) [ -14172.7373] [ 3311] [depth= 7] . ( 2 sec) [ -13973.6810] [ 3301] [depth= 1] . ( 3 sec) [ -13515.3411] [ 3210] [depth= 12] . ( 3 sec) [ -13423.2988] [ 3149] [depth= 3] . ( 3 sec) [ -13260.8854] [ 3137] [depth= 9] . ( 3 sec) [ -13084.4611] [ 3073] [depth= 9] . ( 3 sec) [ -13076.2895] [ 3061] [depth= 1] . ( 3 sec) [ -12963.6754] [ 3041] [depth= 2] . ( 3 sec) [ -12953.1690] [ 3038] [depth= 1] . ( 3 sec) [ -12541.8813] [ 3013] [depth= 5] . ( 3 sec) [ -12380.6974] [ 2949] [depth= 8] . ( 3 sec) [ -12363.9906] [ 2958] [depth= 1] . ( 3 sec) [ -12163.9962] [ 2881] [depth= 2] . ( 3 sec) [ -12025.1625] [ 2804] [depth= 2] . ( 3 sec) [ -12002.4625] [ 2800] [depth= 1] . ( 3 sec) [ -11868.3549] [ 2787] [depth= 1] . ( 3 sec) [ -11856.5466] [ 2796] [depth= 1] . ( 3 sec) [ -11755.0318] [ 2786] [depth= 5] . ( 3 sec) [ -11578.1532] [ 2753] [depth= 4] . ( 3 sec) [ -11495.5170] [ 2719] [depth= 4] . ( 3 sec) [ -11393.1086] [ 2720] [depth= 4] . ( 3 sec) [ -11388.5167] [ 2726] [depth= 1] . ( 3 sec) [ -11359.2068] [ 2728] [depth= 6] . ( 3 sec) [ -11059.8261] [ 2615] [depth= 9] . ( 4 sec) [ -11004.0991] [ 2549] [depth= 1] . ( 4 sec) [ -10965.9287] [ 2542] [depth= 1] . ( 4 sec) [ -10854.6723] [ 2488] [depth= 5] . ( 4 sec) [ -10852.2093] [ 2483] [depth= 1] . ( 4 sec) [ -10818.4568] [ 2485] [depth= 2] . ( 4 sec) [ -10683.0905] [ 2472] [depth= 1] . ( 4 sec) [ -10669.0309] [ 2445] [depth= 4] . ( 4 sec) [ -10666.2355] [ 2444] [depth= 2] . ( 4 sec) [ -10650.8865] [ 2444] [depth= 1] . ( 4 sec) [ -10549.5453] [ 2370] [depth= 5] . ( 4 sec) [ -10477.5739] [ 2363] [depth= 1] . ( 4 sec) [ -10299.6605] [ 2348] [depth= 1] . ( 4 sec) [ -10285.9813] [ 2345] [depth= 1] . ( 4 sec) [ -10151.7887] [ 2356] [depth= 3] . ( 4 sec) [ -10068.7988] [ 2371] [depth= 3] . ( 4 sec) [ -9998.6314] [ 2319] [depth= 3] . ( 4 sec) [ -9997.9408] [ 2323] [depth= 1] . ( 4 sec) [ -9992.3717] [ 2323] [depth= 1] . ( 4 sec) [ -9972.9968] [ 2330] [depth= 6] . ( 4 sec) [ -9967.7711] [ 2326] [depth= 1] . ( 5 sec) [ -9937.2221] [ 2300] [depth= 1] . ( 5 sec) [ -9838.0150] [ 2239] [depth= 5] . ( 5 sec) [ -9808.2573] [ 2252] [depth= 3] . ( 5 sec) [ -9800.7416] [ 2250] [depth= 1] . ( 5 sec) [ -9616.3260] [ 2182] [depth= 7] . ( 5 sec) [ -9580.3136] [ 2174] [depth= 1] . ( 5 sec) [ -9571.4834] [ 2174] [depth= 1] . ( 5 sec) [ -9568.9508] [ 2177] [depth= 1] . ( 5 sec) [ -9567.7118] [ 2178] [depth= 1] . ( 5 sec) [ -9384.3167] [Branch lengths ] . ( 6 sec) [ -9384.0694] [GTR parameters ] . ( 6 sec) [ -9360.4159] [Alpha ][ 0.812053] . ( 6 sec) [ -9345.2081] [ 2163] [depth= 4] . ( 6 sec) [ -9334.6032] [ 2162] [depth= 1] . ( 6 sec) [ -9334.1958] [ 2163] [depth= 1] . ( 6 sec) [ -9310.3214] [ 2153] [depth= 2] . ( 6 sec) [ -9299.0458] [ 2141] [depth= 1] . ( 7 sec) [ -9295.0158] [ 2143] [depth= 1] . ( 7 sec) [ -9294.9805] [ 2143] [depth= 1] . ( 7 sec) [ -9282.3667] [ 2140] [depth= 1] . ( 7 sec) [ -9188.2899] [ 2056] [depth= 7] . ( 8 sec) [ -9187.4962] [ 2056] [depth= 2] . ( 8 sec) [ -9187.2341] [ 2059] [depth= 3] . ( 8 sec) [ -9178.5099] [ 2063] [depth= 1] . ( 8 sec) [ -9178.4548] [ 2063] [depth= 1] . ( 8 sec) [ -9173.3421] [ 2049] [depth= 3] . ( 8 sec) [ -9168.9449] [ 2044] [depth= 1] . ( 8 sec) [ -9167.8864] [ 2054] [depth= 1] . ( 8 sec) [ -9166.7707] [ 2047] [depth= 1] . ( 8 sec) [ -9164.0652] [ 2045] [depth= 2] . ( 8 sec) [ -9163.1110] [ 2050] [depth= 1] . ( 8 sec) [ -9162.8934] [ 2051] [depth= 1] . ( 9 sec) [ -9162.0183] [ 2057] [depth= 1] . ( 9 sec) [ -9160.3949] [ 2060] [depth= 1] . ( 9 sec) [ -9139.2100] [Branch lengths ] . ( 10 sec) [ -9138.7871] [GTR parameters ] . ( 10 sec) [ -9137.9055] [Alpha ][ 0.892100] . ( 11 sec) [ -9137.1948] [ 2059] [depth= 1] . ( 13 sec) [ -9136.9646] [ 2057] [depth= 1] . ( 14 sec) [ -9136.0018] [Branch lengths ] . ( 14 sec) [ -9135.9994] [GTR parameters ] . ( 14 sec) [ -9135.9993] [Alpha ][ 0.892997] . ( 18 sec) [ -9135.9431] [Branch lengths ] . ( 20 sec) [ -9135.7541] [ 2056] [depth= 1] . ( 39 sec) [ -9135.3282] [Branch lengths ] . ( 39 sec) [ -9135.3271] [GTR parameters ] . ( 39 sec) [ -9135.3270] [Alpha ][ 0.892104] . ( 39 sec) [ -9135.3270] [Topology ] . ( 40 sec) [ -9135.2559] [Topology ] . ( 41 sec) [ -9135.2332] [Topology ] . ( 42 sec) [ -9135.2280] [Topology ] . ( 43 sec) [ -9135.2260] [Topology ] . ( 43 sec) [ -9135.2252] [Topology ] . ( 44 sec) [ -9135.2251] [GTR parameters ] . ( 44 sec) [ -9135.2250] [Alpha ][ 0.892997] . ( 44 sec) [ -9135.2250] [Topology ] . ( 44 sec) [ -9135.2247] [Topology ] . ( 45 sec) [ -9135.2246] [GTR parameters ] . ( 45 sec) [ -9135.2246] [Alpha ][ 0.892997] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.224632. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21474.2593] [GTR parameters ] . ( 1 sec) [ -21026.1092] [Alpha ][ 0.500960] . ( 1 sec) [ -20789.3293] [ 4552] [depth= 1] . ( 1 sec) [ -20399.7936] [ 4439] [depth= 8] . ( 1 sec) [ -20280.4926] [ 4428] [depth= 3] . ( 1 sec) [ -20057.0115] [ 4416] [depth= 2] . ( 1 sec) [ -19810.6119] [ 4311] [depth= 7] . ( 1 sec) [ -19806.0600] [ 4313] [depth= 3] . ( 1 sec) [ -19408.2396] [ 4215] [depth= 6] . ( 1 sec) [ -19395.1794] [ 4213] [depth= 6] . ( 1 sec) [ -19330.6355] [ 4239] [depth= 8] . ( 2 sec) [ -19252.9447] [ 4172] [depth= 16] . ( 2 sec) [ -18894.3718] [ 4066] [depth= 8] . ( 2 sec) [ -17757.8174] [ 3984] [depth= 11] . ( 2 sec) [ -17662.2535] [ 3977] [depth= 4] . ( 2 sec) [ -17436.1417] [ 3953] [depth= 1] . ( 2 sec) [ -17180.2174] [ 3851] [depth= 4] . ( 2 sec) [ -17100.0974] [ 3840] [depth= 9] . ( 2 sec) [ -16628.6258] [ 3782] [depth= 8] . ( 2 sec) [ -16419.6238] [ 3756] [depth= 1] . ( 2 sec) [ -16217.5064] [ 3720] [depth= 10] . ( 2 sec) [ -16141.1175] [ 3709] [depth= 1] . ( 2 sec) [ -15793.3567] [ 3626] [depth= 8] . ( 2 sec) [ -15574.8231] [ 3559] [depth= 6] . ( 2 sec) [ -15543.9787] [ 3563] [depth= 2] . ( 2 sec) [ -15445.8799] [ 3504] [depth= 2] . ( 2 sec) [ -15274.8172] [ 3459] [depth= 1] . ( 2 sec) [ -15222.0915] [ 3422] [depth= 1] . ( 2 sec) [ -15063.8795] [ 3366] [depth= 3] . ( 2 sec) [ -14816.4230] [ 3257] [depth= 9] . ( 2 sec) [ -14589.3994] [ 3178] [depth= 5] . ( 2 sec) [ -14581.4463] [ 3187] [depth= 1] . ( 2 sec) [ -14525.6788] [ 3175] [depth= 1] . ( 2 sec) [ -14397.2091] [ 3155] [depth= 7] . ( 3 sec) [ -14118.8353] [ 3074] [depth= 9] . ( 3 sec) [ -14089.5334] [ 3066] [depth= 1] . ( 3 sec) [ -14063.1541] [ 3073] [depth= 1] . ( 3 sec) [ -14019.3492] [ 3066] [depth= 1] . ( 3 sec) [ -13653.6918] [ 2919] [depth= 9] . ( 3 sec) [ -13640.1257] [ 2918] [depth= 1] . ( 3 sec) [ -13241.5325] [ 2830] [depth= 6] . ( 3 sec) [ -12744.2159] [ 2817] [depth= 7] . ( 3 sec) [ -11970.9891] [ 2745] [depth= 2] . ( 3 sec) [ -11807.8209] [ 2732] [depth= 11] . ( 3 sec) [ -11595.4294] [ 2645] [depth= 7] . ( 3 sec) [ -11569.6477] [ 2625] [depth= 2] . ( 3 sec) [ -11559.5960] [ 2622] [depth= 2] . ( 3 sec) [ -11462.8297] [ 2568] [depth= 7] . ( 3 sec) [ -11417.9250] [ 2539] [depth= 3] . ( 3 sec) [ -11292.1142] [ 2537] [depth= 3] . ( 3 sec) [ -11209.2497] [ 2522] [depth= 3] . ( 3 sec) [ -11174.0205] [ 2518] [depth= 1] . ( 3 sec) [ -11165.7558] [ 2518] [depth= 1] . ( 3 sec) [ -11146.9140] [ 2498] [depth= 7] . ( 3 sec) [ -11145.7649] [ 2498] [depth= 1] . ( 4 sec) [ -11023.4931] [ 2462] [depth= 7] . ( 4 sec) [ -10620.5761] [ 2404] [depth= 5] . ( 4 sec) [ -10596.0479] [ 2402] [depth= 2] . ( 4 sec) [ -10443.7076] [ 2339] [depth= 1] . ( 4 sec) [ -10276.1931] [ 2333] [depth= 6] . ( 4 sec) [ -10270.0546] [ 2332] [depth= 1] . ( 4 sec) [ -10251.9339] [ 2349] [depth= 7] . ( 4 sec) [ -10236.3351] [ 2340] [depth= 1] . ( 4 sec) [ -10207.4264] [ 2325] [depth= 1] . ( 4 sec) [ -10204.4052] [ 2327] [depth= 1] . ( 4 sec) [ -9945.6936] [ 2266] [depth= 3] . ( 4 sec) [ -9925.5030] [ 2262] [depth= 1] . ( 4 sec) [ -9897.7366] [ 2250] [depth= 3] . ( 4 sec) [ -9733.8211] [ 2207] [depth= 1] . ( 4 sec) [ -9643.6952] [ 2161] [depth= 2] . ( 4 sec) [ -9642.5067] [ 2159] [depth= 3] . ( 4 sec) [ -9640.5244] [ 2159] [depth= 1] . ( 4 sec) [ -9577.2122] [ 2097] [depth= 1] . ( 5 sec) [ -9574.6643] [ 2096] [depth= 1] . ( 5 sec) [ -9565.4745] [ 2088] [depth= 1] . ( 5 sec) [ -9563.1116] [ 2085] [depth= 1] . ( 5 sec) [ -9559.4408] [ 2086] [depth= 1] . ( 5 sec) [ -9523.0428] [ 2071] [depth= 4] . ( 5 sec) [ -9520.3377] [ 2082] [depth= 1] . ( 5 sec) [ -9474.6770] [ 2076] [depth= 1] . ( 5 sec) [ -9467.1454] [ 2088] [depth= 1] . ( 5 sec) [ -9269.0021] [Branch lengths ] . ( 6 sec) [ -9268.6352] [GTR parameters ] . ( 6 sec) [ -9243.8256] [Alpha ][ 0.815579] . ( 6 sec) [ -9243.0481] [ 2096] [depth= 1] . ( 6 sec) [ -9240.1657] [ 2094] [depth= 1] . ( 6 sec) [ -9225.6289] [ 2087] [depth= 3] . ( 6 sec) [ -9225.6152] [ 2088] [depth= 1] . ( 7 sec) [ -9224.0684] [ 2067] [depth= 1] . ( 7 sec) [ -9190.3075] [ 2072] [depth= 1] . ( 7 sec) [ -9190.2361] [ 2072] [depth= 1] . ( 7 sec) [ -9172.9969] [ 2060] [depth= 2] . ( 7 sec) [ -9158.2428] [ 2050] [depth= 1] . ( 8 sec) [ -9157.9525] [ 2040] [depth= 1] . ( 8 sec) [ -9155.1312] [ 2044] [depth= 2] . ( 8 sec) [ -9154.9706] [ 2043] [depth= 1] . ( 8 sec) [ -9154.8455] [ 2047] [depth= 2] . ( 9 sec) [ -9141.2546] [Branch lengths ] . ( 9 sec) [ -9141.0918] [GTR parameters ] . ( 9 sec) [ -9140.3963] [Alpha ][ 0.886102] . ( 10 sec) [ -9139.3663] [ 2045] [depth= 1] . ( 10 sec) [ -9138.5638] [ 2040] [depth= 1] . ( 12 sec) [ -9135.3263] [Branch lengths ] . ( 13 sec) [ -9135.3184] [GTR parameters ] . ( 13 sec) [ -9135.3133] [Alpha ][ 0.892514] . ( 15 sec) [ -9135.2294] [Branch lengths ] . ( 37 sec) [ -9135.2248] [Branch lengths ] . ( 37 sec) [ -9135.2248] [Topology ] . ( 38 sec) [ -9135.2246] [Topology ] . ( 38 sec) [ -9135.2244] [GTR parameters ] . ( 38 sec) [ -9135.2244] [Alpha ][ 0.893407] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.224384. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20888.3203] [GTR parameters ] . ( 1 sec) [ -20477.0463] [Alpha ][ 0.500960] . ( 1 sec) [ -20196.0344] [ 4488] [depth= 8] . ( 1 sec) [ -19785.0996] [ 4359] [depth= 9] . ( 1 sec) [ -19415.9277] [ 4276] [depth= 8] . ( 1 sec) [ -19278.8078] [ 4241] [depth= 1] . ( 1 sec) [ -18851.6819] [ 4155] [depth= 6] . ( 1 sec) [ -18696.7083] [ 4151] [depth= 2] . ( 1 sec) [ -18041.1297] [ 4141] [depth= 5] . ( 1 sec) [ -17961.3171] [ 4034] [depth= 2] . ( 1 sec) [ -17797.3404] [ 4030] [depth= 1] . ( 2 sec) [ -17521.4200] [ 4007] [depth= 6] . ( 2 sec) [ -17434.0301] [ 3997] [depth= 6] . ( 2 sec) [ -17099.9315] [ 3906] [depth= 5] . ( 2 sec) [ -17033.3461] [ 3882] [depth= 1] . ( 2 sec) [ -16952.0708] [ 3878] [depth= 2] . ( 2 sec) [ -16728.1744] [ 3830] [depth= 8] . ( 2 sec) [ -16555.3352] [ 3806] [depth= 4] . ( 2 sec) [ -16289.3365] [ 3825] [depth= 4] . ( 2 sec) [ -16109.1956] [ 3755] [depth= 3] . ( 2 sec) [ -16072.5903] [ 3747] [depth= 1] . ( 2 sec) [ -15920.6781] [ 3688] [depth= 1] . ( 2 sec) [ -15757.1987] [ 3684] [depth= 3] . ( 2 sec) [ -15639.1421] [ 3652] [depth= 9] . ( 2 sec) [ -15545.8799] [ 3593] [depth= 1] . ( 2 sec) [ -15434.1847] [ 3558] [depth= 1] . ( 2 sec) [ -15015.3364] [ 3551] [depth= 12] . ( 2 sec) [ -14988.8448] [ 3567] [depth= 1] . ( 2 sec) [ -14765.5247] [ 3534] [depth= 15] . ( 2 sec) [ -14678.8369] [ 3491] [depth= 4] . ( 2 sec) [ -14440.3474] [ 3465] [depth= 6] . ( 2 sec) [ -13987.7743] [ 3381] [depth= 14] . ( 2 sec) [ -13647.9088] [ 3356] [depth= 6] . ( 3 sec) [ -13553.8332] [ 3265] [depth= 1] . ( 3 sec) [ -13392.0211] [ 3199] [depth= 12] . ( 3 sec) [ -13363.6093] [ 3205] [depth= 1] . ( 3 sec) [ -13326.7854] [ 3199] [depth= 1] . ( 3 sec) [ -13099.8704] [ 3175] [depth= 1] . ( 3 sec) [ -12729.3080] [ 3103] [depth= 10] . ( 3 sec) [ -12453.8648] [ 2941] [depth= 7] . ( 3 sec) [ -12232.9255] [ 2884] [depth= 2] . ( 3 sec) [ -11957.0128] [ 2798] [depth= 3] . ( 3 sec) [ -11891.6066] [ 2790] [depth= 3] . ( 3 sec) [ -11783.9279] [ 2766] [depth= 8] . ( 3 sec) [ -11761.3945] [ 2742] [depth= 3] . ( 3 sec) [ -11369.6410] [ 2616] [depth= 11] . ( 3 sec) [ -11295.8119] [ 2592] [depth= 1] . ( 3 sec) [ -11163.4816] [ 2580] [depth= 5] . ( 3 sec) [ -11028.0424] [ 2558] [depth= 4] . ( 3 sec) [ -10999.2157] [ 2528] [depth= 2] . ( 3 sec) [ -10829.9847] [ 2510] [depth= 2] . ( 3 sec) [ -10736.9528] [ 2507] [depth= 1] . ( 3 sec) [ -10735.4401] [ 2503] [depth= 1] . ( 3 sec) [ -10646.4433] [ 2481] [depth= 3] . ( 3 sec) [ -10388.5524] [ 2376] [depth= 5] . ( 4 sec) [ -10332.2772] [ 2350] [depth= 1] . ( 4 sec) [ -10312.3908] [ 2337] [depth= 2] . ( 4 sec) [ -10219.0430] [ 2285] [depth= 7] . ( 4 sec) [ -10216.8373] [ 2285] [depth= 1] . ( 4 sec) [ -10203.8182] [ 2285] [depth= 1] . ( 4 sec) [ -10112.7051] [ 2268] [depth= 6] . ( 4 sec) [ -9949.5839] [ 2212] [depth= 1] . ( 4 sec) [ -9949.2015] [ 2208] [depth= 3] . ( 4 sec) [ -9835.3820] [ 2199] [depth= 1] . ( 4 sec) [ -9775.7183] [ 2197] [depth= 4] . ( 4 sec) [ -9756.9482] [ 2252] [depth= 1] . ( 4 sec) [ -9686.9387] [ 2191] [depth= 2] . ( 4 sec) [ -9640.9609] [ 2200] [depth= 6] . ( 4 sec) [ -9414.8634] [ 2129] [depth= 3] . ( 4 sec) [ -9410.6806] [ 2129] [depth= 1] . ( 4 sec) [ -9396.8829] [ 2122] [depth= 1] . ( 5 sec) [ -9395.1749] [ 2118] [depth= 1] . ( 5 sec) [ -9389.1827] [ 2122] [depth= 1] . ( 5 sec) [ -9304.9040] [Branch lengths ] . ( 6 sec) [ -9304.5523] [GTR parameters ] . ( 6 sec) [ -9279.7457] [Alpha ][ 0.823000] . ( 6 sec) [ -9279.6633] [ 2122] [depth= 1] . ( 6 sec) [ -9277.0495] [ 2116] [depth= 1] . ( 6 sec) [ -9213.0168] [ 2073] [depth= 2] . ( 6 sec) [ -9207.8599] [ 2079] [depth= 1] . ( 7 sec) [ -9207.6227] [ 2066] [depth= 1] . ( 7 sec) [ -9206.6798] [ 2065] [depth= 1] . ( 7 sec) [ -9206.3886] [ 2069] [depth= 1] . ( 7 sec) [ -9195.6896] [ 2061] [depth= 2] . ( 7 sec) [ -9191.4696] [ 2056] [depth= 1] . ( 7 sec) [ -9169.7478] [ 2052] [depth= 1] . ( 7 sec) [ -9167.1958] [ 2049] [depth= 1] . ( 7 sec) [ -9166.9254] [ 2049] [depth= 1] . ( 7 sec) [ -9166.7528] [ 2052] [depth= 1] . ( 8 sec) [ -9165.7448] [ 2060] [depth= 1] . ( 9 sec) [ -9165.0340] [ 2057] [depth= 1] . ( 9 sec) [ -9152.0042] [Branch lengths ] . ( 9 sec) [ -9151.9091] [GTR parameters ] . ( 9 sec) [ -9151.4162] [Alpha ][ 0.883540] . ( 10 sec) [ -9147.2753] [ 2055] [depth= 1] . ( 10 sec) [ -9145.3789] [ 2048] [depth= 1] . ( 11 sec) [ -9145.2839] [ 2050] [depth= 1] . ( 11 sec) [ -9142.7596] [ 2053] [depth= 1] . ( 12 sec) [ -9142.7441] [ 2053] [depth= 1] . ( 13 sec) [ -9136.6034] [Branch lengths ] . ( 13 sec) [ -9136.5580] [GTR parameters ] . ( 13 sec) [ -9136.5417] [Alpha ][ 0.895214] . ( 14 sec) [ -9136.3892] [ 2051] [depth= 1] . ( 17 sec) [ -9135.9160] [Branch lengths ] . ( 17 sec) [ -9135.9157] [GTR parameters ] . ( 17 sec) [ -9135.9156] [Alpha ][ 0.894319] . ( 23 sec) [ -9135.3777] [ 2050] [depth= 1] . ( 38 sec) [ -9135.2360] [Branch lengths ] . ( 39 sec) [ -9135.2351] [GTR parameters ] . ( 39 sec) [ -9135.2349] [Alpha ][ 0.893081] . ( 39 sec) [ -9135.2349] [Topology ] . ( 39 sec) [ -9135.2277] [Topology ] . ( 40 sec) [ -9135.2260] [Topology ] . ( 41 sec) [ -9135.2252] [Topology ] . ( 41 sec) [ -9135.2252] [GTR parameters ] . ( 41 sec) [ -9135.2252] [Alpha ][ 0.893081] . ( 41 sec) [ -9135.2252] [Topology ] . ( 42 sec) [ -9135.2248] [Topology ] . ( 42 sec) [ -9135.2248] [GTR parameters ] . ( 42 sec) [ -9135.2248] [Alpha ][ 0.893081] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.224768. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20677.1709] [GTR parameters ] . ( 0 sec) [ -20249.2109] [Alpha ][ 0.500960] . ( 0 sec) [ -19710.8606] [ 4566] [depth= 6] . ( 1 sec) [ -19193.1337] [ 4425] [depth= 11] . ( 1 sec) [ -19101.2181] [ 4405] [depth= 5] . ( 1 sec) [ -18929.3183] [ 4391] [depth= 7] . ( 1 sec) [ -18405.0304] [ 4299] [depth= 8] . ( 1 sec) [ -18187.7137] [ 4288] [depth= 6] . ( 1 sec) [ -18081.1987] [ 4211] [depth= 1] . ( 1 sec) [ -17463.9607] [ 4124] [depth= 6] . ( 1 sec) [ -17252.6386] [ 4081] [depth= 1] . ( 1 sec) [ -16985.0724] [ 4043] [depth= 13] . ( 1 sec) [ -16624.0238] [ 3938] [depth= 9] . ( 1 sec) [ -16563.2622] [ 3934] [depth= 1] . ( 1 sec) [ -16426.8718] [ 3908] [depth= 10] . ( 1 sec) [ -16375.3506] [ 3913] [depth= 1] . ( 1 sec) [ -16328.4753] [ 3899] [depth= 4] . ( 1 sec) [ -16070.4024] [ 3789] [depth= 3] . ( 1 sec) [ -16057.2433] [ 3775] [depth= 1] . ( 1 sec) [ -15828.9298] [ 3723] [depth= 12] . ( 1 sec) [ -15661.7696] [ 3694] [depth= 1] . ( 1 sec) [ -15463.5719] [ 3625] [depth= 6] . ( 1 sec) [ -15255.3888] [ 3560] [depth= 8] . ( 1 sec) [ -15237.5035] [ 3539] [depth= 1] . ( 1 sec) [ -15124.9262] [ 3550] [depth= 11] . ( 2 sec) [ -15106.9381] [ 3551] [depth= 2] . ( 2 sec) [ -14843.5148] [ 3474] [depth= 8] . ( 2 sec) [ -14482.7003] [ 3363] [depth= 8] . ( 2 sec) [ -14480.0174] [ 3363] [depth= 1] . ( 2 sec) [ -13971.9508] [ 3317] [depth= 9] . ( 2 sec) [ -13703.8108] [ 3306] [depth= 1] . ( 2 sec) [ -13437.5680] [ 3273] [depth= 3] . ( 2 sec) [ -13171.2101] [ 3110] [depth= 11] . ( 2 sec) [ -13167.6782] [ 3174] [depth= 1] . ( 2 sec) [ -13022.9415] [ 3075] [depth= 3] . ( 2 sec) [ -12940.4810] [ 3060] [depth= 1] . ( 2 sec) [ -12628.4709] [ 2964] [depth= 9] . ( 2 sec) [ -12588.3629] [ 2957] [depth= 1] . ( 2 sec) [ -12391.4643] [ 2950] [depth= 4] . ( 2 sec) [ -12318.6404] [ 2970] [depth= 1] . ( 2 sec) [ -12031.1433] [ 2898] [depth= 12] . ( 2 sec) [ -11751.8175] [ 2794] [depth= 5] . ( 2 sec) [ -11739.5070] [ 2804] [depth= 5] . ( 2 sec) [ -11480.6589] [ 2736] [depth= 5] . ( 2 sec) [ -11475.8864] [ 2736] [depth= 1] . ( 2 sec) [ -11410.1359] [ 2726] [depth= 2] . ( 2 sec) [ -10970.0947] [ 2591] [depth= 5] . ( 3 sec) [ -10968.3621] [ 2592] [depth= 2] . ( 3 sec) [ -10928.3007] [ 2581] [depth= 3] . ( 3 sec) [ -10877.1812] [ 2565] [depth= 3] . ( 3 sec) [ -10830.8476] [ 2556] [depth= 5] . ( 3 sec) [ -10790.8189] [ 2552] [depth= 6] . ( 3 sec) [ -10723.1457] [ 2497] [depth= 1] . ( 3 sec) [ -10681.9132] [ 2514] [depth= 8] . ( 3 sec) [ -10512.8933] [ 2447] [depth= 5] . ( 3 sec) [ -10502.5236] [ 2437] [depth= 7] . ( 3 sec) [ -10472.7390] [ 2432] [depth= 1] . ( 3 sec) [ -10385.6126] [ 2400] [depth= 1] . ( 3 sec) [ -10256.9953] [ 2340] [depth= 2] . ( 3 sec) [ -10229.7860] [ 2330] [depth= 1] . ( 3 sec) [ -10223.7014] [ 2329] [depth= 1] . ( 3 sec) [ -10071.3659] [ 2288] [depth= 2] . ( 3 sec) [ -9996.6128] [ 2282] [depth= 3] . ( 3 sec) [ -9848.1626] [ 2224] [depth= 2] . ( 4 sec) [ -9846.6563] [ 2216] [depth= 3] . ( 4 sec) [ -9833.5894] [ 2204] [depth= 1] . ( 4 sec) [ -9752.5187] [ 2151] [depth= 3] . ( 4 sec) [ -9742.5202] [ 2142] [depth= 1] . ( 4 sec) [ -9742.3561] [ 2143] [depth= 1] . ( 4 sec) [ -9736.9369] [ 2142] [depth= 2] . ( 4 sec) [ -9736.8197] [ 2144] [depth= 2] . ( 4 sec) [ -9722.2018] [ 2138] [depth= 1] . ( 4 sec) [ -9702.6241] [ 2135] [depth= 2] . ( 4 sec) [ -9644.8762] [ 2131] [depth= 1] . ( 4 sec) [ -9638.6999] [ 2128] [depth= 1] . ( 5 sec) [ -9373.9725] [Branch lengths ] . ( 5 sec) [ -9373.4892] [GTR parameters ] . ( 5 sec) [ -9349.5040] [Alpha ][ 0.811380] . ( 5 sec) [ -9341.5243] [ 2120] [depth= 1] . ( 5 sec) [ -9282.1488] [ 2109] [depth= 5] . ( 5 sec) [ -9259.1657] [ 2100] [depth= 3] . ( 5 sec) [ -9259.0708] [ 2100] [depth= 1] . ( 5 sec) [ -9254.7129] [ 2107] [depth= 1] . ( 5 sec) [ -9254.6646] [ 2107] [depth= 1] . ( 5 sec) [ -9252.0045] [ 2100] [depth= 1] . ( 5 sec) [ -9226.2641] [ 2109] [depth= 3] . ( 5 sec) [ -9225.4947] [ 2111] [depth= 3] . ( 6 sec) [ -9189.5654] [ 2057] [depth= 2] . ( 6 sec) [ -9185.6343] [ 2055] [depth= 1] . ( 6 sec) [ -9184.0650] [ 2052] [depth= 2] . ( 6 sec) [ -9183.9651] [ 2052] [depth= 1] . ( 6 sec) [ -9175.5850] [ 2051] [depth= 1] . ( 6 sec) [ -9175.0193] [ 2050] [depth= 1] . ( 6 sec) [ -9174.9167] [ 2050] [depth= 1] . ( 7 sec) [ -9174.5042] [ 2049] [depth= 1] . ( 7 sec) [ -9174.0819] [ 2046] [depth= 3] . ( 7 sec) [ -9173.3506] [ 2053] [depth= 1] . ( 7 sec) [ -9173.2219] [ 2053] [depth= 1] . ( 7 sec) [ -9169.2365] [ 2053] [depth= 1] . ( 8 sec) [ -9169.2221] [ 2053] [depth= 1] . ( 8 sec) [ -9167.7902] [ 2046] [depth= 1] . ( 8 sec) [ -9156.1972] [ 2049] [depth= 1] . ( 8 sec) [ -9148.3002] [Branch lengths ] . ( 8 sec) [ -9148.1278] [GTR parameters ] . ( 8 sec) [ -9147.2983] [Alpha ][ 0.889527] . ( 9 sec) [ -9147.1282] [ 2046] [depth= 1] . ( 12 sec) [ -9146.0467] [Branch lengths ] . ( 12 sec) [ -9146.0466] [GTR parameters ] . ( 12 sec) [ -9146.0456] [Alpha ][ 0.892257] . ( 15 sec) [ -9144.0377] [Branch lengths ] . ( 20 sec) [ -9143.8050] [ 2046] [depth= 1] . ( 36 sec) [ -9136.2722] [Branch lengths ] . ( 36 sec) [ -9136.2685] [GTR parameters ] . ( 36 sec) [ -9136.2676] [Alpha ][ 0.889394] . ( 58 sec) [ -9135.3714] [Branch lengths ] . ( 58 sec) [ -9135.3714] [Topology ] . ( 59 sec) [ -9135.2739] [Topology ] . ( 60 sec) [ -9135.2412] [Topology ] . ( 60 sec) [ -9135.2321] [Topology ] . ( 61 sec) [ -9135.2285] [Topology ] . ( 62 sec) [ -9135.2271] [Topology ] . ( 63 sec) [ -9135.2265] [Topology ] . ( 63 sec) [ -9135.2263] [GTR parameters ] . ( 63 sec) [ -9135.2247] [Alpha ][ 0.892981] . ( 63 sec) [ -9135.2247] [Topology ] . ( 64 sec) [ -9135.2244] [Topology ] . ( 64 sec) [ -9135.2244] [GTR parameters ] . ( 64 sec) [ -9135.2244] [Alpha ][ 0.892981] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.224413. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9232.261190 . ( 1 sec) [ -9223.1516] [GTR parameters ] . ( 1 sec) [ -9221.6649] [Alpha ][ 0.876656] . ( 1 sec) [ -9221.6649] [Topology ] . ( 2 sec) [ -9163.9155] [Topology ] . ( 3 sec) [ -9152.7065] [Topology ] . ( 4 sec) [ -9149.0056] [Topology ] . ( 4 sec) [ -9147.2834] [Topology ] . ( 5 sec) [ -9146.3846] [Topology ] . ( 6 sec) [ -9145.8961] [Topology ] . ( 7 sec) [ -9145.6216] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.621608 . ( 13 sec) [ -9145.5746] [GTR parameters ] . ( 13 sec) [ -9145.5006] [Alpha ][ 0.900803] . ( 13 sec) [ -9145.5006] [Topology ] . ( 14 sec) [ -9145.3417] [Topology ] . ( 15 sec) [ -9145.2518] [Topology ] . ( 16 sec) [ -9145.2001] [Topology ] . ( 17 sec) [ -9145.1700] [Topology ] . ( 17 sec) [ -9145.1523] [Topology ] . ( 18 sec) [ -9145.1419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.141931 . ( 25 sec) [ -9145.1415] [GTR parameters ] . ( 25 sec) [ -9145.1414] [Alpha ][ 0.899898] . ( 25 sec) [ -9145.1414] [Topology ] . ( 25 sec) [ -9145.1352] [Topology ] . ( 26 sec) [ -9145.1314] [Topology ] . ( 27 sec) [ -9145.1292] [Topology ] . ( 28 sec) [ -9145.1279] [Topology ] . ( 29 sec) [ -9145.1272] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.127155 . ( 35 sec) [ -9145.1272] [GTR parameters ] . ( 35 sec) [ -9145.1271] [Alpha ][ 0.898998] . ( 35 sec) [ -9145.1271] [Topology ] . ( 36 sec) [ -9145.1266] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -9223.1516] [GTR parameters ] . ( 49 sec) [ -9221.6649] [Alpha ][ 0.876656] . ( 49 sec) [ -9214.3897] [ 2046] [depth= 1] . ( 49 sec) [ -9212.3115] [ 2046] [depth= 1] . ( 49 sec) [ -9212.0305] [ 2046] [depth= 1] . ( 49 sec) [ -9211.9235] [ 2046] [depth= 1] . ( 50 sec) [ -9211.8882] [ 2046] [depth= 1] . ( 50 sec) [ -9211.1258] [ 2045] [depth= 1] . ( 50 sec) [ -9210.5856] [ 2050] [depth= 1] . ( 50 sec) [ -9210.4695] [ 2045] [depth= 1] . ( 50 sec) [ -9208.4230] [ 2048] [depth= 1] . ( 50 sec) [ -9200.4094] [ 2054] [depth= 1] . ( 50 sec) [ -9194.9303] [ 2057] [depth= 1] . ( 50 sec) [ -9194.8775] [ 2057] [depth= 4] . ( 51 sec) [ -9191.4959] [ 2059] [depth= 1] . ( 51 sec) [ -9190.8781] [ 2058] [depth= 1] . ( 51 sec) [ -9190.0593] [ 2061] [depth= 1] . ( 51 sec) [ -9189.6955] [ 2060] [depth= 1] . ( 51 sec) [ -9187.7893] [ 2065] [depth= 1] . ( 51 sec) [ -9187.5841] [ 2066] [depth= 1] . ( 52 sec) [ -9186.7844] [ 2071] [depth= 1] . ( 52 sec) [ -9159.8013] [Branch lengths ] . ( 52 sec) [ -9159.7196] [GTR parameters ] . ( 52 sec) [ -9159.7175] [Alpha ][ 0.880815] . ( 53 sec) [ -9159.7012] [ 2071] [depth= 1] . ( 53 sec) [ -9154.4040] [ 2068] [depth= 4] . ( 54 sec) [ -9153.6993] [ 2066] [depth= 1] . ( 54 sec) [ -9150.7759] [ 2070] [depth= 2] . ( 54 sec) [ -9150.0219] [ 2068] [depth= 2] . ( 54 sec) [ -9149.8851] [ 2064] [depth= 1] . ( 54 sec) [ -9149.7144] [ 2067] [depth= 1] . ( 55 sec) [ -9148.7675] [ 2070] [depth= 1] . ( 55 sec) [ -9147.4543] [ 2062] [depth= 1] . ( 55 sec) [ -9146.1291] [ 2056] [depth= 1] . ( 56 sec) [ -9139.5273] [Branch lengths ] . ( 56 sec) [ -9139.5110] [GTR parameters ] . ( 56 sec) [ -9139.4912] [Alpha ][ 0.893707] . ( 56 sec) [ -9138.7577] [ 2053] [depth= 1] . ( 57 sec) [ -9138.7451] [ 2048] [depth= 1] . ( 59 sec) [ -9135.5791] [Branch lengths ] . ( 59 sec) [ -9135.5657] [GTR parameters ] . ( 59 sec) [ -9135.5657] [Alpha ][ 0.893707] . ( 62 sec) [ -9135.2588] [Branch lengths ] . ( 84 sec) [ -9135.2299] [Branch lengths ] . ( 84 sec) [ -9135.2299] [Topology ] . ( 85 sec) [ -9135.2267] [Topology ] . ( 86 sec) [ -9135.2255] [Topology ] . ( 87 sec) [ -9135.2249] [Topology ] . ( 87 sec) [ -9135.2248] [GTR parameters ] . ( 87 sec) [ -9135.2248] [Alpha ][ 0.892814] . ( 87 sec) [ -9135.2248] [Topology ] . ( 88 sec) [ -9135.2244] [Topology ] . ( 88 sec) [ -9135.2244] [GTR parameters ] . ( 88 sec) [ -9135.2244] [Alpha ][ 0.892814] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9145.126630 . Log likelihood obtained after SPR moves : -9135.224424 . Log likelihood of the current tree: -9135.224424. . Printing the most likely tree in file 'data15.phy_phyml_tree.txt'... . Best log likelihood : -9135.224384 . Time used 0h1m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo