.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data35.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... . 446 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . [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)... . ( 1 sec) [ -21718.2316] [GTR parameters ] . ( 1 sec) [ -21308.8129] [Alpha ][ 0.500960] . ( 2 sec) [ -20923.7224] [ 5067] [depth= 8] . ( 2 sec) [ -20381.3675] [ 5054] [depth= 9] . ( 2 sec) [ -20316.4048] [ 5021] [depth= 4] . ( 2 sec) [ -19969.0537] [ 5006] [depth= 6] . ( 2 sec) [ -19866.8683] [ 4979] [depth= 1] . ( 2 sec) [ -19669.2445] [ 4972] [depth= 8] . ( 2 sec) [ -19483.2667] [ 4949] [depth= 11] . ( 2 sec) [ -19251.7403] [ 4935] [depth= 1] . ( 2 sec) [ -19029.2837] [ 4823] [depth= 19] . ( 2 sec) [ -18569.8199] [ 4754] [depth= 8] . ( 2 sec) [ -18248.1982] [ 4610] [depth= 17] . ( 3 sec) [ -18013.9265] [ 4610] [depth= 15] . ( 3 sec) [ -17640.9546] [ 4499] [depth= 14] . ( 3 sec) [ -17524.3653] [ 4467] [depth= 5] . ( 3 sec) [ -17480.1086] [ 4463] [depth= 2] . ( 3 sec) [ -17364.6152] [ 4421] [depth= 1] . ( 3 sec) [ -17329.0437] [ 4401] [depth= 4] . ( 3 sec) [ -17194.4217] [ 4278] [depth= 8] . ( 3 sec) [ -17153.3252] [ 4293] [depth= 1] . ( 3 sec) [ -17103.8295] [ 4289] [depth= 1] . ( 3 sec) [ -17058.7402] [ 4261] [depth= 13] . ( 4 sec) [ -16895.1652] [ 4244] [depth= 1] . ( 4 sec) [ -16623.7209] [ 4198] [depth= 10] . ( 4 sec) [ -16007.7126] [ 4081] [depth= 17] . ( 4 sec) [ -15786.3676] [ 4006] [depth= 7] . ( 4 sec) [ -15605.7093] [ 3963] [depth= 12] . ( 4 sec) [ -15567.3831] [ 3932] [depth= 1] . ( 4 sec) [ -15495.5340] [ 3919] [depth= 2] . ( 4 sec) [ -15426.2067] [ 3903] [depth= 3] . ( 4 sec) [ -15203.7996] [ 3814] [depth= 8] . ( 4 sec) [ -15014.1105] [ 3771] [depth= 3] . ( 4 sec) [ -14896.7855] [ 3742] [depth= 8] . ( 4 sec) [ -14623.3435] [ 3674] [depth= 1] . ( 5 sec) [ -14622.3590] [ 3675] [depth= 1] . ( 5 sec) [ -14535.3896] [ 3675] [depth= 14] . ( 5 sec) [ -14354.4947] [ 3637] [depth= 4] . ( 5 sec) [ -14275.2374] [ 3629] [depth= 1] . ( 5 sec) [ -14115.0525] [ 3560] [depth= 12] . ( 5 sec) [ -13963.8790] [ 3537] [depth= 1] . ( 5 sec) [ -13405.6271] [ 3424] [depth= 5] . ( 5 sec) [ -13377.0771] [ 3425] [depth= 4] . ( 5 sec) [ -13350.1774] [ 3419] [depth= 1] . ( 5 sec) [ -13098.8096] [ 3353] [depth= 3] . ( 6 sec) [ -12948.5437] [ 3313] [depth= 3] . ( 6 sec) [ -12916.9817] [ 3324] [depth= 7] . ( 6 sec) [ -12911.4417] [ 3300] [depth= 1] . ( 6 sec) [ -12721.0742] [ 3282] [depth= 1] . ( 6 sec) [ -12528.8929] [ 3175] [depth= 4] . ( 6 sec) [ -12506.2888] [ 3175] [depth= 1] . ( 6 sec) [ -12401.1278] [ 3139] [depth= 10] . ( 6 sec) [ -12349.8108] [ 3131] [depth= 1] . ( 6 sec) [ -12222.3950] [ 3051] [depth= 7] . ( 6 sec) [ -12218.1747] [ 3056] [depth= 1] . ( 6 sec) [ -12095.8213] [ 3000] [depth= 2] . ( 6 sec) [ -12066.4605] [ 2991] [depth= 2] . ( 7 sec) [ -12044.4481] [ 3006] [depth= 1] . ( 7 sec) [ -11952.6537] [ 2903] [depth= 2] . ( 7 sec) [ -11894.5270] [ 2908] [depth= 1] . ( 7 sec) [ -11680.8993] [ 2809] [depth= 7] . ( 7 sec) [ -11561.6758] [ 2756] [depth= 3] . ( 7 sec) [ -11441.0446] [ 2657] [depth= 1] . ( 7 sec) [ -11416.0750] [ 2624] [depth= 4] . ( 7 sec) [ -11282.8788] [ 2620] [depth= 1] . ( 7 sec) [ -11280.4712] [ 2620] [depth= 1] . ( 7 sec) [ -11247.5727] [ 2615] [depth= 1] . ( 7 sec) [ -11240.2365] [ 2617] [depth= 1] . ( 7 sec) [ -11209.6358] [ 2603] [depth= 1] . ( 7 sec) [ -11035.1272] [ 2542] [depth= 1] . ( 8 sec) [ -11011.9196] [ 2547] [depth= 2] . ( 8 sec) [ -10988.9133] [ 2547] [depth= 1] . ( 8 sec) [ -10973.4780] [ 2518] [depth= 2] . ( 8 sec) [ -10972.5398] [ 2515] [depth= 1] . ( 8 sec) [ -10952.4796] [ 2509] [depth= 1] . ( 8 sec) [ -10942.8946] [ 2513] [depth= 1] . ( 8 sec) [ -10926.3191] [ 2503] [depth= 2] . ( 8 sec) [ -10923.3879] [ 2489] [depth= 1] . ( 8 sec) [ -10922.2602] [ 2488] [depth= 1] . ( 8 sec) [ -10917.5834] [ 2487] [depth= 1] . ( 8 sec) [ -10915.7971] [ 2492] [depth= 1] . ( 8 sec) [ -10913.8692] [ 2490] [depth= 1] . ( 9 sec) [ -10546.1965] [Branch lengths ] . ( 9 sec) [ -10543.3424] [GTR parameters ] . ( 9 sec) [ -10511.5673] [Alpha ][ 0.860367] . ( 9 sec) [ -10508.1588] [ 2485] [depth= 1] . ( 10 sec) [ -10506.5998] [ 2481] [depth= 1] . ( 10 sec) [ -10506.5257] [ 2481] [depth= 1] . ( 10 sec) [ -10506.4160] [ 2483] [depth= 1] . ( 10 sec) [ -10505.7994] [ 2486] [depth= 1] . ( 11 sec) [ -10505.5293] [ 2486] [depth= 1] . ( 11 sec) [ -10505.3531] [ 2486] [depth= 1] . ( 11 sec) [ -10484.9651] [ 2466] [depth= 3] . ( 11 sec) [ -10483.4695] [ 2459] [depth= 2] . ( 12 sec) [ -10481.9921] [ 2463] [depth= 1] . ( 12 sec) [ -10481.0834] [ 2458] [depth= 2] . ( 13 sec) [ -10481.0633] [ 2459] [depth= 1] . ( 14 sec) [ -10471.6948] [Branch lengths ] . ( 14 sec) [ -10471.6796] [GTR parameters ] . ( 14 sec) [ -10471.3009] [Alpha ][ 0.913097] . ( 15 sec) [ -10469.8461] [ 2456] [depth= 1] . ( 17 sec) [ -10469.2112] [ 2457] [depth= 1] . ( 19 sec) [ -10467.2241] [Branch lengths ] . ( 19 sec) [ -10467.2176] [GTR parameters ] . ( 19 sec) [ -10467.2132] [Alpha ][ 0.919069] . ( 24 sec) [ -10466.5064] [Branch lengths ] . ( 59 sec) [ -10466.3356] [Branch lengths ] . ( 59 sec) [ -10466.3356] [Topology ] . ( 60 sec) [ -10466.3059] [Topology ] . ( 62 sec) [ -10466.2926] [Topology ] . ( 63 sec) [ -10466.2851] [Topology ] . ( 64 sec) [ -10466.2805] [Topology ] . ( 65 sec) [ -10466.2775] [Topology ] . ( 66 sec) [ -10466.2757] [Topology ] . ( 66 sec) [ -10466.2754] [GTR parameters ] . ( 67 sec) [ -10466.2754] [Alpha ][ 0.919069] . ( 67 sec) [ -10466.2754] [Topology ] . ( 68 sec) [ -10466.2742] [Topology ] . ( 69 sec) [ -10466.2734] [Topology ] . ( 69 sec) [ -10466.2734] [GTR parameters ] . ( 70 sec) [ -10466.2734] [Alpha ][ 0.919069] . ( 70 sec) [ -10466.2734] [Topology ] . ( 71 sec) [ -10466.2729] [Topology ] . ( 71 sec) [ -10466.2729] [GTR parameters ] . ( 71 sec) [ -10466.2729] [Alpha ][ 0.919069] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.272857. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21434.5904] [GTR parameters ] . ( 1 sec) [ -21069.9147] [Alpha ][ 0.500960] . ( 1 sec) [ -20616.8966] [ 4865] [depth= 3] . ( 1 sec) [ -19825.2284] [ 4805] [depth= 11] . ( 1 sec) [ -19648.5482] [ 4779] [depth= 4] . ( 1 sec) [ -19526.4045] [ 4766] [depth= 4] . ( 1 sec) [ -19383.5334] [ 4714] [depth= 1] . ( 1 sec) [ -19182.1696] [ 4677] [depth= 5] . ( 1 sec) [ -19147.7123] [ 4681] [depth= 1] . ( 1 sec) [ -19111.3111] [ 4676] [depth= 1] . ( 2 sec) [ -19010.0165] [ 4645] [depth= 2] . ( 2 sec) [ -18923.6075] [ 4630] [depth= 3] . ( 2 sec) [ -18867.8855] [ 4597] [depth= 3] . ( 2 sec) [ -18820.7124] [ 4582] [depth= 1] . ( 2 sec) [ -18552.1173] [ 4556] [depth= 7] . ( 2 sec) [ -18441.8867] [ 4529] [depth= 5] . ( 2 sec) [ -18157.1348] [ 4444] [depth= 3] . ( 2 sec) [ -18083.9235] [ 4424] [depth= 10] . ( 2 sec) [ -18030.3681] [ 4395] [depth= 1] . ( 2 sec) [ -17897.5288] [ 4336] [depth= 11] . ( 2 sec) [ -17648.4413] [ 4311] [depth= 2] . ( 2 sec) [ -17190.0355] [ 4310] [depth= 1] . ( 2 sec) [ -17121.4673] [ 4188] [depth= 6] . ( 3 sec) [ -17050.2266] [ 4181] [depth= 1] . ( 3 sec) [ -16678.0865] [ 4112] [depth= 10] . ( 3 sec) [ -16462.4414] [ 4014] [depth= 5] . ( 3 sec) [ -16072.1999] [ 3974] [depth= 3] . ( 3 sec) [ -15844.5734] [ 3947] [depth= 9] . ( 3 sec) [ -15809.9511] [ 3927] [depth= 1] . ( 3 sec) [ -15691.8746] [ 3886] [depth= 1] . ( 3 sec) [ -15507.9141] [ 3813] [depth= 9] . ( 3 sec) [ -15448.1497] [ 3806] [depth= 8] . ( 3 sec) [ -15046.8237] [ 3649] [depth= 4] . ( 3 sec) [ -15045.8742] [ 3654] [depth= 1] . ( 3 sec) [ -14684.1913] [ 3546] [depth= 9] . ( 4 sec) [ -14681.9866] [ 3550] [depth= 1] . ( 4 sec) [ -14604.1139] [ 3541] [depth= 1] . ( 4 sec) [ -14586.3063] [ 3518] [depth= 1] . ( 4 sec) [ -14504.0375] [ 3525] [depth= 1] . ( 4 sec) [ -14387.2063] [ 3479] [depth= 2] . ( 4 sec) [ -14138.7662] [ 3408] [depth= 5] . ( 4 sec) [ -14055.2231] [ 3404] [depth= 3] . ( 4 sec) [ -13893.8171] [ 3381] [depth= 1] . ( 4 sec) [ -13772.8507] [ 3319] [depth= 9] . ( 4 sec) [ -13509.4219] [ 3273] [depth= 11] . ( 4 sec) [ -13443.0196] [ 3274] [depth= 15] . ( 4 sec) [ -13403.5289] [ 3263] [depth= 4] . ( 5 sec) [ -13249.0788] [ 3200] [depth= 4] . ( 5 sec) [ -13138.2589] [ 3197] [depth= 1] . ( 5 sec) [ -13124.1819] [ 3193] [depth= 1] . ( 5 sec) [ -12940.4695] [ 3166] [depth= 4] . ( 5 sec) [ -12740.2745] [ 3078] [depth= 1] . ( 5 sec) [ -12680.9607] [ 3068] [depth= 2] . ( 5 sec) [ -12612.3411] [ 3019] [depth= 10] . ( 5 sec) [ -12520.5688] [ 2969] [depth= 2] . ( 5 sec) [ -12193.7949] [ 2912] [depth= 9] . ( 5 sec) [ -12161.8137] [ 2903] [depth= 1] . ( 5 sec) [ -12135.4624] [ 2876] [depth= 1] . ( 6 sec) [ -12134.3340] [ 2879] [depth= 1] . ( 6 sec) [ -12091.3122] [ 2860] [depth= 1] . ( 6 sec) [ -11881.7016] [ 2801] [depth= 7] . ( 6 sec) [ -11881.2767] [ 2806] [depth= 1] . ( 6 sec) [ -11722.9805] [ 2758] [depth= 7] . ( 6 sec) [ -11706.1124] [ 2760] [depth= 1] . ( 6 sec) [ -11594.9489] [ 2735] [depth= 5] . ( 6 sec) [ -11497.7019] [ 2722] [depth= 4] . ( 6 sec) [ -11459.1087] [ 2706] [depth= 1] . ( 7 sec) [ -11455.4359] [ 2710] [depth= 1] . ( 7 sec) [ -11442.6662] [ 2698] [depth= 2] . ( 7 sec) [ -11395.0665] [ 2704] [depth= 1] . ( 7 sec) [ -11371.0082] [ 2701] [depth= 1] . ( 7 sec) [ -11234.7675] [ 2680] [depth= 1] . ( 7 sec) [ -11037.4584] [ 2586] [depth= 2] . ( 7 sec) [ -10975.8998] [ 2589] [depth= 2] . ( 7 sec) [ -10973.4434] [ 2587] [depth= 1] . ( 7 sec) [ -10924.9932] [ 2567] [depth= 2] . ( 8 sec) [ -10870.7710] [ 2564] [depth= 1] . ( 8 sec) [ -10864.6161] [ 2557] [depth= 5] . ( 8 sec) [ -10863.5286] [ 2554] [depth= 5] . ( 8 sec) [ -10858.3669] [ 2557] [depth= 1] . ( 8 sec) [ -10857.8913] [ 2554] [depth= 1] . ( 8 sec) [ -10809.7169] [ 2538] [depth= 5] . ( 8 sec) [ -10802.1379] [ 2545] [depth= 1] . ( 9 sec) [ -10618.7344] [Branch lengths ] . ( 10 sec) [ -10615.0249] [GTR parameters ] . ( 10 sec) [ -10591.9394] [Alpha ][ 0.808501] . ( 10 sec) [ -10582.0205] [ 2518] [depth= 2] . ( 10 sec) [ -10576.7355] [ 2513] [depth= 1] . ( 10 sec) [ -10575.0499] [ 2510] [depth= 1] . ( 10 sec) [ -10574.0844] [ 2514] [depth= 1] . ( 11 sec) [ -10561.5308] [ 2494] [depth= 3] . ( 11 sec) [ -10545.4066] [ 2484] [depth= 1] . ( 12 sec) [ -10545.2043] [ 2484] [depth= 1] . ( 12 sec) [ -10536.9357] [ 2474] [depth= 1] . ( 12 sec) [ -10512.2750] [ 2453] [depth= 2] . ( 12 sec) [ -10509.8678] [ 2453] [depth= 1] . ( 12 sec) [ -10509.0386] [ 2453] [depth= 1] . ( 13 sec) [ -10508.4844] [ 2453] [depth= 1] . ( 13 sec) [ -10508.1096] [ 2457] [depth= 1] . ( 13 sec) [ -10504.7345] [ 2461] [depth= 1] . ( 14 sec) [ -10503.4509] [ 2458] [depth= 1] . ( 14 sec) [ -10502.1254] [ 2459] [depth= 1] . ( 15 sec) [ -10473.1898] [Branch lengths ] . ( 15 sec) [ -10473.0332] [GTR parameters ] . ( 16 sec) [ -10471.8679] [Alpha ][ 0.900596] . ( 17 sec) [ -10471.7478] [ 2459] [depth= 1] . ( 17 sec) [ -10471.7319] [ 2459] [depth= 1] . ( 19 sec) [ -10471.7164] [ 2459] [depth= 1] . ( 21 sec) [ -10467.2710] [Branch lengths ] . ( 21 sec) [ -10467.2679] [GTR parameters ] . ( 21 sec) [ -10467.2374] [Alpha ][ 0.916466] . ( 22 sec) [ -10467.2222] [ 2459] [depth= 1] . ( 25 sec) [ -10466.4609] [Branch lengths ] . ( 26 sec) [ -10466.4605] [GTR parameters ] . ( 26 sec) [ -10466.4598] [Alpha ][ 0.918748] . ( 52 sec) [ -10466.3062] [Branch lengths ] . ( 52 sec) [ -10466.3062] [Topology ] . ( 53 sec) [ -10466.2871] [Topology ] . ( 54 sec) [ -10466.2798] [Topology ] . ( 55 sec) [ -10466.2763] [Topology ] . ( 56 sec) [ -10466.2745] [Topology ] . ( 57 sec) [ -10466.2735] [Topology ] . ( 57 sec) [ -10466.2733] [GTR parameters ] . ( 58 sec) [ -10466.2733] [Alpha ][ 0.918748] . ( 58 sec) [ -10466.2733] [Topology ] . ( 59 sec) [ -10466.2727] [Topology ] . ( 59 sec) [ -10466.2727] [GTR parameters ] . ( 59 sec) [ -10466.2727] [Alpha ][ 0.918748] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.272711. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22673.1035] [GTR parameters ] . ( 1 sec) [ -22239.5066] [Alpha ][ 0.500960] . ( 1 sec) [ -21713.9094] [ 5131] [depth= 8] . ( 1 sec) [ -21358.5978] [ 5073] [depth= 8] . ( 1 sec) [ -21348.7656] [ 5068] [depth= 4] . ( 1 sec) [ -21086.1929] [ 5059] [depth= 2] . ( 1 sec) [ -20883.9307] [ 4993] [depth= 9] . ( 2 sec) [ -20763.4856] [ 4990] [depth= 8] . ( 2 sec) [ -20406.1547] [ 4933] [depth= 15] . ( 2 sec) [ -20039.8858] [ 4872] [depth= 4] . ( 2 sec) [ -19823.0490] [ 4877] [depth= 7] . ( 2 sec) [ -19699.8851] [ 4876] [depth= 7] . ( 2 sec) [ -19440.9495] [ 4808] [depth= 7] . ( 2 sec) [ -19034.3167] [ 4705] [depth= 13] . ( 2 sec) [ -19027.3646] [ 4682] [depth= 3] . ( 2 sec) [ -18910.2662] [ 4669] [depth= 3] . ( 2 sec) [ -18416.4784] [ 4534] [depth= 8] . ( 2 sec) [ -18106.1776] [ 4530] [depth= 1] . ( 2 sec) [ -17969.6345] [ 4478] [depth= 12] . ( 2 sec) [ -17609.0554] [ 4316] [depth= 9] . ( 2 sec) [ -17498.8690] [ 4316] [depth= 1] . ( 3 sec) [ -17082.1127] [ 4117] [depth= 10] . ( 3 sec) [ -16972.1121] [ 4113] [depth= 1] . ( 3 sec) [ -16658.2849] [ 3947] [depth= 7] . ( 3 sec) [ -16558.1154] [ 3959] [depth= 7] . ( 3 sec) [ -16463.8799] [ 3951] [depth= 2] . ( 3 sec) [ -16382.6987] [ 3947] [depth= 1] . ( 3 sec) [ -16214.1271] [ 3899] [depth= 7] . ( 3 sec) [ -15945.7245] [ 3856] [depth= 6] . ( 3 sec) [ -15609.3583] [ 3746] [depth= 3] . ( 3 sec) [ -15356.1226] [ 3660] [depth= 8] . ( 3 sec) [ -15354.7991] [ 3661] [depth= 1] . ( 4 sec) [ -15004.7464] [ 3684] [depth= 7] . ( 4 sec) [ -14661.8379] [ 3619] [depth= 8] . ( 4 sec) [ -14441.8448] [ 3582] [depth= 10] . ( 4 sec) [ -14414.6698] [ 3579] [depth= 1] . ( 4 sec) [ -14364.0161] [ 3543] [depth= 1] . ( 4 sec) [ -14362.3241] [ 3548] [depth= 1] . ( 4 sec) [ -14140.2526] [ 3451] [depth= 3] . ( 4 sec) [ -13972.5071] [ 3400] [depth= 9] . ( 4 sec) [ -13971.0430] [ 3397] [depth= 1] . ( 4 sec) [ -13970.0152] [ 3400] [depth= 1] . ( 4 sec) [ -13744.9061] [ 3332] [depth= 9] . ( 4 sec) [ -13691.4562] [ 3287] [depth= 1] . ( 5 sec) [ -13446.9635] [ 3250] [depth= 6] . ( 5 sec) [ -13416.0468] [ 3232] [depth= 1] . ( 5 sec) [ -13396.0695] [ 3224] [depth= 1] . ( 5 sec) [ -13305.3026] [ 3187] [depth= 1] . ( 5 sec) [ -13304.1551] [ 3189] [depth= 2] . ( 5 sec) [ -13194.8003] [ 3138] [depth= 1] . ( 5 sec) [ -12847.6913] [ 3119] [depth= 5] . ( 5 sec) [ -12830.5997] [ 3135] [depth= 1] . ( 5 sec) [ -12777.8105] [ 3126] [depth= 2] . ( 5 sec) [ -12774.1755] [ 3122] [depth= 2] . ( 6 sec) [ -12670.1684] [ 3029] [depth= 5] . ( 6 sec) [ -12495.3890] [ 3029] [depth= 1] . ( 6 sec) [ -12119.2398] [ 2820] [depth= 7] . ( 6 sec) [ -12090.3331] [ 2815] [depth= 1] . ( 6 sec) [ -12088.9643] [ 2812] [depth= 1] . ( 6 sec) [ -12076.6685] [ 2789] [depth= 4] . ( 6 sec) [ -11958.8479] [ 2810] [depth= 1] . ( 6 sec) [ -11854.7609] [ 2775] [depth= 5] . ( 6 sec) [ -11694.4341] [ 2713] [depth= 3] . ( 6 sec) [ -11672.0929] [ 2698] [depth= 1] . ( 7 sec) [ -11490.9326] [ 2641] [depth= 1] . ( 7 sec) [ -11476.5387] [ 2648] [depth= 1] . ( 7 sec) [ -11285.1770] [ 2635] [depth= 1] . ( 7 sec) [ -11282.0324] [ 2636] [depth= 1] . ( 7 sec) [ -11273.0344] [ 2627] [depth= 1] . ( 7 sec) [ -11271.1945] [ 2627] [depth= 1] . ( 7 sec) [ -11135.3600] [ 2598] [depth= 2] . ( 7 sec) [ -11064.9606] [ 2581] [depth= 2] . ( 7 sec) [ -11000.6016] [ 2585] [depth= 1] . ( 7 sec) [ -10911.9079] [ 2569] [depth= 1] . ( 7 sec) [ -10788.2871] [ 2553] [depth= 1] . ( 8 sec) [ -10778.4454] [ 2550] [depth= 1] . ( 8 sec) [ -10769.0842] [ 2561] [depth= 1] . ( 8 sec) [ -10711.4152] [ 2549] [depth= 1] . ( 8 sec) [ -10687.7656] [ 2532] [depth= 1] . ( 8 sec) [ -10681.7095] [ 2504] [depth= 2] . ( 8 sec) [ -10655.7076] [ 2498] [depth= 2] . ( 8 sec) [ -10655.1635] [ 2500] [depth= 1] . ( 8 sec) [ -10645.6847] [ 2498] [depth= 1] . ( 9 sec) [ -10541.2193] [Branch lengths ] . ( 9 sec) [ -10538.4168] [GTR parameters ] . ( 10 sec) [ -10511.0055] [Alpha ][ 0.842430] . ( 10 sec) [ -10501.9071] [ 2487] [depth= 1] . ( 10 sec) [ -10501.7183] [ 2491] [depth= 1] . ( 10 sec) [ -10497.6262] [ 2484] [depth= 1] . ( 11 sec) [ -10494.3071] [ 2479] [depth= 1] . ( 11 sec) [ -10492.3300] [ 2476] [depth= 1] . ( 11 sec) [ -10492.0891] [ 2477] [depth= 1] . ( 12 sec) [ -10486.5899] [ 2463] [depth= 1] . ( 12 sec) [ -10485.9079] [ 2463] [depth= 1] . ( 12 sec) [ -10485.2906] [ 2462] [depth= 1] . ( 13 sec) [ -10482.2933] [ 2458] [depth= 2] . ( 14 sec) [ -10482.2168] [ 2458] [depth= 1] . ( 14 sec) [ -10480.8644] [ 2459] [depth= 1] . ( 15 sec) [ -10468.9209] [Branch lengths ] . ( 15 sec) [ -10468.9030] [GTR parameters ] . ( 15 sec) [ -10468.2045] [Alpha ][ 0.914289] . ( 17 sec) [ -10468.1764] [ 2459] [depth= 1] . ( 20 sec) [ -10466.5925] [Branch lengths ] . ( 21 sec) [ -10466.5901] [GTR parameters ] . ( 21 sec) [ -10466.5876] [Alpha ][ 0.918715] . ( 24 sec) [ -10466.3433] [Branch lengths ] . ( 49 sec) [ -10466.2915] [Branch lengths ] . ( 50 sec) [ -10466.2915] [Topology ] . ( 50 sec) [ -10466.2833] [Topology ] . ( 51 sec) [ -10466.2794] [Topology ] . ( 52 sec) [ -10466.2770] [Topology ] . ( 53 sec) [ -10466.2755] [Topology ] . ( 54 sec) [ -10466.2745] [Topology ] . ( 54 sec) [ -10466.2739] [GTR parameters ] . ( 54 sec) [ -10466.2739] [Alpha ][ 0.918715] . ( 54 sec) [ -10466.2739] [Topology ] . ( 55 sec) [ -10466.2732] [Topology ] . ( 55 sec) [ -10466.2732] [GTR parameters ] . ( 55 sec) [ -10466.2732] [Alpha ][ 0.918715] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.273172. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21841.7427] [GTR parameters ] . ( 1 sec) [ -21401.3257] [Alpha ][ 0.500960] . ( 1 sec) [ -21120.9417] [ 5175] [depth= 8] . ( 1 sec) [ -20849.3124] [ 5108] [depth= 8] . ( 1 sec) [ -20507.4090] [ 5073] [depth= 7] . ( 1 sec) [ -20238.4718] [ 4959] [depth= 1] . ( 1 sec) [ -20062.5640] [ 4912] [depth= 3] . ( 1 sec) [ -19993.0496] [ 4899] [depth= 2] . ( 1 sec) [ -19880.9501] [ 4901] [depth= 6] . ( 1 sec) [ -19739.5663] [ 4876] [depth= 5] . ( 2 sec) [ -19610.9225] [ 4841] [depth= 5] . ( 2 sec) [ -19450.1674] [ 4807] [depth= 4] . ( 2 sec) [ -19326.4848] [ 4805] [depth= 11] . ( 2 sec) [ -19123.4890] [ 4742] [depth= 11] . ( 2 sec) [ -18725.7012] [ 4669] [depth= 8] . ( 2 sec) [ -18722.4350] [ 4676] [depth= 10] . ( 2 sec) [ -18613.7666] [ 4719] [depth= 1] . ( 2 sec) [ -18414.0514] [ 4611] [depth= 1] . ( 2 sec) [ -18279.2238] [ 4558] [depth= 11] . ( 2 sec) [ -17959.4072] [ 4564] [depth= 1] . ( 2 sec) [ -17559.5695] [ 4509] [depth= 5] . ( 2 sec) [ -17404.3770] [ 4511] [depth= 4] . ( 2 sec) [ -16938.9334] [ 4307] [depth= 5] . ( 2 sec) [ -16900.0429] [ 4303] [depth= 8] . ( 2 sec) [ -16765.5984] [ 4257] [depth= 2] . ( 2 sec) [ -16614.8976] [ 4241] [depth= 8] . ( 2 sec) [ -16529.7954] [ 4216] [depth= 1] . ( 2 sec) [ -16448.2602] [ 4174] [depth= 1] . ( 2 sec) [ -16357.8062] [ 4144] [depth= 2] . ( 2 sec) [ -16345.8735] [ 4139] [depth= 1] . ( 2 sec) [ -16145.7782] [ 4078] [depth= 6] . ( 2 sec) [ -15778.0407] [ 3918] [depth= 3] . ( 2 sec) [ -15712.9871] [ 3917] [depth= 1] . ( 3 sec) [ -15377.9036] [ 3801] [depth= 10] . ( 3 sec) [ -15257.0961] [ 3794] [depth= 2] . ( 3 sec) [ -15073.3083] [ 3770] [depth= 4] . ( 3 sec) [ -14886.2486] [ 3723] [depth= 1] . ( 3 sec) [ -14695.9130] [ 3628] [depth= 1] . ( 3 sec) [ -14652.4464] [ 3628] [depth= 1] . ( 3 sec) [ -14631.9128] [ 3615] [depth= 1] . ( 3 sec) [ -14601.3249] [ 3562] [depth= 2] . ( 3 sec) [ -14531.6710] [ 3563] [depth= 11] . ( 3 sec) [ -14512.9304] [ 3557] [depth= 1] . ( 3 sec) [ -14400.4499] [ 3541] [depth= 5] . ( 3 sec) [ -14398.8209] [ 3534] [depth= 1] . ( 3 sec) [ -14391.2948] [ 3571] [depth= 1] . ( 3 sec) [ -14267.7799] [ 3535] [depth= 2] . ( 4 sec) [ -14209.2615] [ 3518] [depth= 7] . ( 4 sec) [ -14114.0842] [ 3496] [depth= 1] . ( 4 sec) [ -14031.8359] [ 3469] [depth= 1] . ( 4 sec) [ -13950.5937] [ 3425] [depth= 1] . ( 4 sec) [ -13950.4704] [ 3426] [depth= 1] . ( 4 sec) [ -13930.0994] [ 3416] [depth= 1] . ( 4 sec) [ -13588.3750] [ 3244] [depth= 8] . ( 4 sec) [ -13586.6996] [ 3241] [depth= 1] . ( 4 sec) [ -13336.0565] [ 3163] [depth= 2] . ( 4 sec) [ -13010.7671] [ 3124] [depth= 7] . ( 4 sec) [ -12984.6096] [ 3117] [depth= 1] . ( 4 sec) [ -12981.7276] [ 3121] [depth= 8] . ( 4 sec) [ -12760.3234] [ 3011] [depth= 1] . ( 4 sec) [ -11892.7634] [ 2850] [depth= 3] . ( 5 sec) [ -11804.6144] [ 2853] [depth= 1] . ( 5 sec) [ -11668.5559] [ 2793] [depth= 6] . ( 5 sec) [ -11650.8755] [ 2785] [depth= 1] . ( 5 sec) [ -11596.1262] [ 2765] [depth= 6] . ( 5 sec) [ -11582.2255] [ 2750] [depth= 3] . ( 5 sec) [ -11577.9518] [ 2746] [depth= 1] . ( 5 sec) [ -11560.3359] [ 2747] [depth= 7] . ( 5 sec) [ -11518.7360] [ 2743] [depth= 7] . ( 5 sec) [ -11514.7806] [ 2723] [depth= 1] . ( 5 sec) [ -11450.2487] [ 2712] [depth= 3] . ( 5 sec) [ -11422.5381] [ 2710] [depth= 1] . ( 5 sec) [ -11363.9652] [ 2700] [depth= 1] . ( 6 sec) [ -11287.3415] [ 2694] [depth= 3] . ( 6 sec) [ -11261.1440] [ 2675] [depth= 1] . ( 6 sec) [ -11196.6762] [ 2663] [depth= 4] . ( 6 sec) [ -11083.3233] [ 2631] [depth= 3] . ( 6 sec) [ -11082.5384] [ 2633] [depth= 1] . ( 6 sec) [ -11076.9241] [ 2639] [depth= 1] . ( 6 sec) [ -11063.0894] [ 2627] [depth= 1] . ( 6 sec) [ -11020.3265] [ 2613] [depth= 3] . ( 6 sec) [ -11017.3337] [ 2610] [depth= 1] . ( 6 sec) [ -10881.5027] [ 2558] [depth= 3] . ( 6 sec) [ -10878.6143] [ 2552] [depth= 1] . ( 6 sec) [ -10782.9277] [ 2531] [depth= 1] . ( 6 sec) [ -10768.6952] [ 2525] [depth= 1] . ( 7 sec) [ -10767.3867] [ 2525] [depth= 1] . ( 7 sec) [ -10740.3045] [ 2526] [depth= 1] . ( 7 sec) [ -10581.9294] [Branch lengths ] . ( 8 sec) [ -10579.2986] [GTR parameters ] . ( 8 sec) [ -10553.4345] [Alpha ][ 0.824741] . ( 8 sec) [ -10546.0603] [ 2511] [depth= 1] . ( 9 sec) [ -10535.4891] [ 2505] [depth= 1] . ( 9 sec) [ -10535.2361] [ 2505] [depth= 1] . ( 9 sec) [ -10531.2953] [ 2470] [depth= 1] . ( 9 sec) [ -10526.8163] [ 2461] [depth= 1] . ( 9 sec) [ -10526.4258] [ 2466] [depth= 1] . ( 10 sec) [ -10518.8379] [ 2461] [depth= 1] . ( 10 sec) [ -10507.7539] [ 2459] [depth= 1] . ( 10 sec) [ -10506.9811] [ 2459] [depth= 1] . ( 10 sec) [ -10505.9444] [ 2459] [depth= 1] . ( 10 sec) [ -10504.9397] [ 2464] [depth= 1] . ( 11 sec) [ -10504.8060] [ 2467] [depth= 1] . ( 11 sec) [ -10502.0498] [ 2465] [depth= 2] . ( 12 sec) [ -10501.9513] [ 2464] [depth= 1] . ( 12 sec) [ -10501.9091] [ 2464] [depth= 1] . ( 13 sec) [ -10476.4669] [Branch lengths ] . ( 13 sec) [ -10476.4237] [GTR parameters ] . ( 14 sec) [ -10475.4084] [Alpha ][ 0.911294] . ( 14 sec) [ -10473.4398] [ 2458] [depth= 1] . ( 14 sec) [ -10473.4053] [ 2458] [depth= 1] . ( 14 sec) [ -10469.8209] [ 2453] [depth= 1] . ( 16 sec) [ -10469.7812] [ 2453] [depth= 1] . ( 18 sec) [ -10467.0250] [Branch lengths ] . ( 19 sec) [ -10467.0208] [GTR parameters ] . ( 19 sec) [ -10467.0162] [Alpha ][ 0.917442] . ( 23 sec) [ -10466.6629] [Branch lengths ] . ( 48 sec) [ -10466.5800] [Branch lengths ] . ( 49 sec) [ -10466.5800] [Topology ] . ( 50 sec) [ -10466.3472] [Topology ] . ( 50 sec) [ -10466.2860] [Topology ] . ( 52 sec) [ -10466.2789] [Topology ] . ( 53 sec) [ -10466.2763] [Topology ] . ( 54 sec) [ -10466.2750] [Topology ] . ( 55 sec) [ -10466.2742] [Topology ] . ( 56 sec) [ -10466.2732] [GTR parameters ] . ( 56 sec) [ -10466.2731] [Alpha ][ 0.918457] . ( 56 sec) [ -10466.2731] [Topology ] . ( 57 sec) [ -10466.2726] [Topology ] . ( 57 sec) [ -10466.2726] [GTR parameters ] . ( 57 sec) [ -10466.2726] [Alpha ][ 0.918457] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.272589. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -21612.1554] [GTR parameters ] . ( 2 sec) [ -21165.1064] [Alpha ][ 0.500960] . ( 2 sec) [ -20836.1456] [ 5135] [depth= 6] . ( 2 sec) [ -20655.1156] [ 5058] [depth= 11] . ( 2 sec) [ -20585.1521] [ 5043] [depth= 5] . ( 2 sec) [ -20547.0374] [ 5039] [depth= 1] . ( 2 sec) [ -20418.8086] [ 4977] [depth= 3] . ( 2 sec) [ -20413.0797] [ 4978] [depth= 1] . ( 3 sec) [ -20334.6331] [ 4943] [depth= 7] . ( 3 sec) [ -20231.7054] [ 4967] [depth= 1] . ( 3 sec) [ -19665.6924] [ 4883] [depth= 2] . ( 3 sec) [ -19431.4217] [ 4802] [depth= 3] . ( 3 sec) [ -19271.0668] [ 4694] [depth= 13] . ( 3 sec) [ -19213.0333] [ 4657] [depth= 8] . ( 3 sec) [ -19096.4056] [ 4630] [depth= 8] . ( 3 sec) [ -19050.5713] [ 4620] [depth= 1] . ( 3 sec) [ -18996.6176] [ 4554] [depth= 3] . ( 3 sec) [ -18927.9894] [ 4545] [depth= 3] . ( 3 sec) [ -18872.2424] [ 4521] [depth= 2] . ( 3 sec) [ -18735.1646] [ 4478] [depth= 7] . ( 3 sec) [ -18590.3092] [ 4370] [depth= 4] . ( 4 sec) [ -18135.9278] [ 4373] [depth= 7] . ( 4 sec) [ -18103.0844] [ 4362] [depth= 8] . ( 4 sec) [ -17997.3972] [ 4376] [depth= 5] . ( 4 sec) [ -17666.8174] [ 4266] [depth= 14] . ( 4 sec) [ -17462.1364] [ 4211] [depth= 14] . ( 4 sec) [ -17318.4807] [ 4183] [depth= 5] . ( 4 sec) [ -16910.6883] [ 4119] [depth= 7] . ( 4 sec) [ -16717.3458] [ 4024] [depth= 1] . ( 4 sec) [ -16714.8159] [ 4032] [depth= 1] . ( 4 sec) [ -16504.4971] [ 3989] [depth= 5] . ( 5 sec) [ -16482.4453] [ 3981] [depth= 1] . ( 5 sec) [ -16309.8925] [ 3972] [depth= 6] . ( 5 sec) [ -16211.9879] [ 3963] [depth= 1] . ( 5 sec) [ -16026.5806] [ 3921] [depth= 11] . ( 5 sec) [ -15753.9625] [ 3860] [depth= 1] . ( 5 sec) [ -15181.7416] [ 3705] [depth= 10] . ( 5 sec) [ -14929.8993] [ 3652] [depth= 7] . ( 5 sec) [ -14584.7241] [ 3563] [depth= 5] . ( 5 sec) [ -14546.8371] [ 3552] [depth= 1] . ( 5 sec) [ -14508.0574] [ 3537] [depth= 7] . ( 5 sec) [ -14504.5406] [ 3540] [depth= 1] . ( 6 sec) [ -14342.7540] [ 3421] [depth= 3] . ( 6 sec) [ -14092.3015] [ 3332] [depth= 1] . ( 6 sec) [ -13970.0863] [ 3330] [depth= 4] . ( 6 sec) [ -13939.4886] [ 3322] [depth= 4] . ( 6 sec) [ -13656.4267] [ 3286] [depth= 10] . ( 6 sec) [ -13297.4051] [ 3216] [depth= 9] . ( 6 sec) [ -13225.4667] [ 3218] [depth= 8] . ( 6 sec) [ -13148.7456] [ 3188] [depth= 4] . ( 6 sec) [ -12908.6298] [ 3128] [depth= 6] . ( 6 sec) [ -12766.2984] [ 3105] [depth= 3] . ( 6 sec) [ -12729.5429] [ 3099] [depth= 2] . ( 7 sec) [ -12684.1388] [ 3082] [depth= 5] . ( 7 sec) [ -12563.9770] [ 3029] [depth= 5] . ( 7 sec) [ -12535.5784] [ 3027] [depth= 1] . ( 7 sec) [ -12499.0767] [ 3016] [depth= 2] . ( 7 sec) [ -12497.1624] [ 3017] [depth= 1] . ( 7 sec) [ -12493.4782] [ 3017] [depth= 1] . ( 7 sec) [ -12165.2355] [ 3003] [depth= 6] . ( 7 sec) [ -12097.9954] [ 3018] [depth= 1] . ( 7 sec) [ -12055.5610] [ 3001] [depth= 8] . ( 7 sec) [ -12022.3026] [ 2976] [depth= 3] . ( 8 sec) [ -11950.8371] [ 2940] [depth= 2] . ( 8 sec) [ -11851.2732] [ 2919] [depth= 2] . ( 8 sec) [ -11805.5493] [ 2868] [depth= 1] . ( 8 sec) [ -11801.6289] [ 2856] [depth= 2] . ( 8 sec) [ -11369.0598] [ 2707] [depth= 4] . ( 8 sec) [ -11303.4654] [ 2697] [depth= 2] . ( 8 sec) [ -11143.9221] [ 2668] [depth= 1] . ( 8 sec) [ -11138.7216] [ 2666] [depth= 1] . ( 8 sec) [ -11137.9181] [ 2668] [depth= 1] . ( 8 sec) [ -11119.7677] [ 2673] [depth= 1] . ( 8 sec) [ -11119.0711] [ 2673] [depth= 1] . ( 9 sec) [ -11104.4827] [ 2668] [depth= 1] . ( 9 sec) [ -11098.9123] [ 2669] [depth= 1] . ( 9 sec) [ -10998.9415] [ 2621] [depth= 6] . ( 9 sec) [ -10983.8293] [ 2605] [depth= 1] . ( 9 sec) [ -10969.4065] [ 2606] [depth= 2] . ( 9 sec) [ -10895.1644] [ 2566] [depth= 1] . ( 9 sec) [ -10845.1350] [ 2551] [depth= 2] . ( 9 sec) [ -10843.6626] [ 2552] [depth= 1] . ( 9 sec) [ -10815.0297] [ 2519] [depth= 2] . ( 9 sec) [ -10814.5424] [ 2520] [depth= 1] . ( 9 sec) [ -10759.6522] [ 2522] [depth= 1] . ( 10 sec) [ -10569.7197] [Branch lengths ] . ( 11 sec) [ -10566.0465] [GTR parameters ] . ( 11 sec) [ -10537.7405] [Alpha ][ 0.849653] . ( 11 sec) [ -10536.6844] [ 2524] [depth= 1] . ( 11 sec) [ -10535.9419] [ 2525] [depth= 1] . ( 11 sec) [ -10525.8440] [ 2504] [depth= 2] . ( 12 sec) [ -10502.6559] [ 2492] [depth= 5] . ( 12 sec) [ -10496.6448] [ 2464] [depth= 3] . ( 12 sec) [ -10491.9165] [ 2460] [depth= 1] . ( 13 sec) [ -10486.2476] [ 2456] [depth= 1] . ( 13 sec) [ -10484.1689] [ 2453] [depth= 1] . ( 13 sec) [ -10483.5729] [ 2453] [depth= 1] . ( 14 sec) [ -10482.8449] [ 2453] [depth= 1] . ( 14 sec) [ -10482.7057] [ 2453] [depth= 1] . ( 15 sec) [ -10482.6287] [ 2453] [depth= 1] . ( 16 sec) [ -10469.4704] [Branch lengths ] . ( 16 sec) [ -10469.3906] [GTR parameters ] . ( 17 sec) [ -10468.8676] [Alpha ][ 0.912849] . ( 19 sec) [ -10468.8392] [ 2453] [depth= 1] . ( 20 sec) [ -10466.9974] [Branch lengths ] . ( 20 sec) [ -10466.9967] [GTR parameters ] . ( 20 sec) [ -10466.9939] [Alpha ][ 0.917671] . ( 24 sec) [ -10466.6465] [Branch lengths ] . ( 46 sec) [ -10466.5693] [Branch lengths ] . ( 46 sec) [ -10466.5693] [Topology ] . ( 47 sec) [ -10466.3448] [Topology ] . ( 48 sec) [ -10466.2830] [Topology ] . ( 49 sec) [ -10466.2767] [Topology ] . ( 50 sec) [ -10466.2748] [Topology ] . ( 50 sec) [ -10466.2739] [Topology ] . ( 51 sec) [ -10466.2730] [GTR parameters ] . ( 51 sec) [ -10466.2729] [Alpha ][ 0.918589] . ( 51 sec) [ -10466.2729] [Topology ] . ( 51 sec) [ -10466.2725] [Topology ] . ( 52 sec) [ -10466.2725] [GTR parameters ] . ( 52 sec) [ -10466.2725] [Alpha ][ 0.918589] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.272461. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10555.099857 . ( 1 sec) [ -10552.4569] [GTR parameters ] . ( 1 sec) [ -10551.5166] [Alpha ][ 0.903985] . ( 1 sec) [ -10551.5166] [Topology ] . ( 2 sec) [ -10484.8412] [Topology ] . ( 2 sec) [ -10473.4165] [Topology ] . ( 3 sec) [ -10469.6529] [Topology ] . ( 4 sec) [ -10468.0389] [Topology ] . ( 5 sec) [ -10467.2638] [Topology ] . ( 6 sec) [ -10466.8540] [Topology ] . ( 7 sec) [ -10466.6391] [Topology ] . ( 7 sec) [ -10466.5171] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.517115 . ( 14 sec) [ -10466.4575] [GTR parameters ] . ( 15 sec) [ -10466.4366] [Alpha ][ 0.917049] . ( 15 sec) [ -10466.4366] [Topology ] . ( 15 sec) [ -10466.3687] [Topology ] . ( 16 sec) [ -10466.3297] [Topology ] . ( 17 sec) [ -10466.3074] [Topology ] . ( 18 sec) [ -10466.2939] [Topology ] . ( 19 sec) [ -10466.2859] [Topology ] . ( 19 sec) [ -10466.2809] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.280895 . ( 26 sec) [ -10466.2807] [GTR parameters ] . ( 26 sec) [ -10466.2805] [Alpha ][ 0.918334] . ( 26 sec) [ -10466.2805] [Topology ] . ( 27 sec) [ -10466.2774] [Topology ] . ( 28 sec) [ -10466.2754] [Topology ] . ( 28 sec) [ -10466.2741] [Topology ] . ( 29 sec) [ -10466.2733] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.273300 . ( 36 sec) [ -10466.2733] [GTR parameters ] . ( 36 sec) [ -10466.2733] [Alpha ][ 0.918334] . ( 36 sec) [ -10466.2733] [Topology ] . ( 37 sec) [ -10466.2728] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -10552.4569] [GTR parameters ] . ( 52 sec) [ -10551.5166] [Alpha ][ 0.903985] . ( 52 sec) [ -10548.2201] [ 2456] [depth= 1] . ( 52 sec) [ -10544.6986] [ 2457] [depth= 1] . ( 53 sec) [ -10543.0224] [ 2456] [depth= 1] . ( 53 sec) [ -10543.0115] [ 2457] [depth= 1] . ( 53 sec) [ -10537.9108] [ 2471] [depth= 1] . ( 53 sec) [ -10533.7541] [ 2476] [depth= 1] . ( 53 sec) [ -10532.2155] [ 2474] [depth= 1] . ( 54 sec) [ -10531.9569] [ 2474] [depth= 1] . ( 54 sec) [ -10531.8595] [ 2474] [depth= 1] . ( 54 sec) [ -10531.2566] [ 2474] [depth= 1] . ( 54 sec) [ -10530.2162] [ 2474] [depth= 1] . ( 54 sec) [ -10530.1379] [ 2474] [depth= 1] . ( 54 sec) [ -10527.7675] [ 2477] [depth= 1] . ( 54 sec) [ -10524.4271] [ 2474] [depth= 1] . ( 54 sec) [ -10518.2294] [ 2474] [depth= 1] . ( 55 sec) [ -10516.9900] [ 2473] [depth= 1] . ( 55 sec) [ -10514.9712] [ 2474] [depth= 1] . ( 55 sec) [ -10514.2069] [ 2481] [depth= 1] . ( 55 sec) [ -10509.8468] [ 2474] [depth= 1] . ( 55 sec) [ -10509.4101] [ 2475] [depth= 1] . ( 55 sec) [ -10505.9143] [ 2474] [depth= 1] . ( 56 sec) [ -10474.8207] [Branch lengths ] . ( 56 sec) [ -10474.7433] [GTR parameters ] . ( 56 sec) [ -10474.7227] [Alpha ][ 0.917161] . ( 56 sec) [ -10473.2304] [ 2472] [depth= 1] . ( 56 sec) [ -10473.2158] [ 2473] [depth= 1] . ( 57 sec) [ -10472.6097] [ 2460] [depth= 1] . ( 57 sec) [ -10471.8746] [ 2459] [depth= 1] . ( 59 sec) [ -10467.1145] [Branch lengths ] . ( 60 sec) [ -10467.1076] [GTR parameters ] . ( 60 sec) [ -10467.1065] [Alpha ][ 0.920111] . ( 63 sec) [ -10466.5065] [Branch lengths ] . ( 85 sec) [ -10466.3403] [Branch lengths ] . ( 85 sec) [ -10466.3403] [Topology ] . ( 85 sec) [ -10466.3105] [Topology ] . ( 86 sec) [ -10466.2964] [Topology ] . ( 87 sec) [ -10466.2879] [Topology ] . ( 88 sec) [ -10466.2826] [Topology ] . ( 89 sec) [ -10466.2792] [Topology ] . ( 89 sec) [ -10466.2770] [Topology ] . ( 90 sec) [ -10466.2764] [GTR parameters ] . ( 90 sec) [ -10466.2762] [Alpha ][ 0.918674] . ( 90 sec) [ -10466.2762] [Topology ] . ( 91 sec) [ -10466.2747] [Topology ] . ( 91 sec) [ -10466.2737] [Topology ] . ( 92 sec) [ -10466.2737] [GTR parameters ] . ( 92 sec) [ -10466.2737] [Alpha ][ 0.918674] . ( 92 sec) [ -10466.2737] [Topology ] . ( 93 sec) [ -10466.2731] [Topology ] . ( 93 sec) [ -10466.2731] [GTR parameters ] . ( 93 sec) [ -10466.2731] [Alpha ][ 0.918674] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10466.272790 . Log likelihood obtained after SPR moves : -10466.273076 . Log likelihood of the current tree: -10466.272790. . Printing the most likely tree in file 'data35.phy_phyml_tree.txt'... . Best log likelihood : -10466.272461 . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo