.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data64.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... . 433 patterns found. (out of a total of 500 sites) . 61 sites without polymorphism (12.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18501.5442] [GTR parameters ] . ( 1 sec) [ -18218.8828] [Alpha ][ 0.500960] . ( 1 sec) [ -17983.8445] [ 3974] [depth= 6] . ( 1 sec) [ -17727.7401] [ 3931] [depth= 4] . ( 1 sec) [ -17619.7113] [ 3923] [depth= 3] . ( 1 sec) [ -17278.4031] [ 3911] [depth= 7] . ( 1 sec) [ -17036.8191] [ 3887] [depth= 4] . ( 1 sec) [ -17001.5247] [ 3893] [depth= 5] . ( 1 sec) [ -16963.7927] [ 3874] [depth= 9] . ( 1 sec) [ -16727.5176] [ 3799] [depth= 15] . ( 1 sec) [ -16470.9881] [ 3763] [depth= 5] . ( 1 sec) [ -16145.2959] [ 3659] [depth= 10] . ( 1 sec) [ -16130.5276] [ 3727] [depth= 16] . ( 1 sec) [ -15902.4142] [ 3684] [depth= 3] . ( 1 sec) [ -15787.8822] [ 3670] [depth= 3] . ( 1 sec) [ -15767.9734] [ 3638] [depth= 3] . ( 1 sec) [ -15520.9720] [ 3613] [depth= 11] . ( 1 sec) [ -15301.0747] [ 3522] [depth= 4] . ( 1 sec) [ -15286.2113] [ 3548] [depth= 8] . ( 1 sec) [ -15105.2071] [ 3541] [depth= 3] . ( 1 sec) [ -15022.0685] [ 3506] [depth= 1] . ( 1 sec) [ -14795.7226] [ 3455] [depth= 7] . ( 1 sec) [ -14644.5699] [ 3453] [depth= 1] . ( 2 sec) [ -14198.3111] [ 3410] [depth= 10] . ( 2 sec) [ -14134.9141] [ 3400] [depth= 3] . ( 2 sec) [ -14134.4078] [ 3396] [depth= 1] . ( 2 sec) [ -14046.6114] [ 3372] [depth= 6] . ( 2 sec) [ -13998.0057] [ 3358] [depth= 7] . ( 2 sec) [ -13823.4542] [ 3235] [depth= 13] . ( 2 sec) [ -13656.8290] [ 3172] [depth= 4] . ( 2 sec) [ -13493.9314] [ 3142] [depth= 4] . ( 2 sec) [ -13099.4567] [ 3032] [depth= 4] . ( 2 sec) [ -12871.5675] [ 2975] [depth= 13] . ( 2 sec) [ -12581.1130] [ 2964] [depth= 1] . ( 2 sec) [ -12468.6137] [ 2866] [depth= 5] . ( 2 sec) [ -12343.1571] [ 2803] [depth= 5] . ( 2 sec) [ -12266.1848] [ 2785] [depth= 10] . ( 2 sec) [ -11970.9465] [ 2698] [depth= 11] . ( 2 sec) [ -11753.9274] [ 2663] [depth= 6] . ( 2 sec) [ -11650.4091] [ 2638] [depth= 16] . ( 2 sec) [ -11507.7255] [ 2580] [depth= 5] . ( 2 sec) [ -11505.3810] [ 2584] [depth= 1] . ( 2 sec) [ -11505.1794] [ 2586] [depth= 1] . ( 3 sec) [ -11500.1788] [ 2579] [depth= 2] . ( 3 sec) [ -11474.9589] [ 2590] [depth= 12] . ( 3 sec) [ -11292.2012] [ 2552] [depth= 12] . ( 3 sec) [ -11153.9284] [ 2499] [depth= 8] . ( 3 sec) [ -11063.5320] [ 2484] [depth= 2] . ( 3 sec) [ -10920.4263] [ 2460] [depth= 2] . ( 3 sec) [ -10649.0436] [ 2414] [depth= 6] . ( 3 sec) [ -10595.9318] [ 2398] [depth= 1] . ( 3 sec) [ -10593.2263] [ 2403] [depth= 1] . ( 3 sec) [ -10486.6910] [ 2387] [depth= 2] . ( 3 sec) [ -10389.0950] [ 2365] [depth= 6] . ( 3 sec) [ -10374.7171] [ 2367] [depth= 1] . ( 3 sec) [ -10372.0186] [ 2368] [depth= 1] . ( 3 sec) [ -10368.0163] [ 2365] [depth= 1] . ( 3 sec) [ -10292.7748] [ 2311] [depth= 1] . ( 3 sec) [ -10219.8279] [ 2302] [depth= 1] . ( 3 sec) [ -10194.5647] [ 2288] [depth= 4] . ( 4 sec) [ -10122.0854] [ 2288] [depth= 1] . ( 4 sec) [ -10041.3132] [ 2247] [depth= 1] . ( 4 sec) [ -10036.4274] [ 2245] [depth= 1] . ( 4 sec) [ -10035.1120] [ 2249] [depth= 1] . ( 4 sec) [ -10014.4284] [ 2245] [depth= 1] . ( 4 sec) [ -10000.6354] [ 2247] [depth= 1] . ( 4 sec) [ -9999.5456] [ 2249] [depth= 1] . ( 4 sec) [ -9943.5614] [ 2220] [depth= 4] . ( 4 sec) [ -9810.2898] [ 2164] [depth= 1] . ( 4 sec) [ -9808.2323] [ 2162] [depth= 1] . ( 4 sec) [ -9807.9863] [ 2166] [depth= 1] . ( 4 sec) [ -9794.0974] [ 2165] [depth= 1] . ( 5 sec) [ -9701.7446] [Branch lengths ] . ( 5 sec) [ -9700.2101] [GTR parameters ] . ( 5 sec) [ -9645.8169] [Alpha ][ 1.000222] . ( 5 sec) [ -9644.7505] [ 2162] [depth= 1] . ( 6 sec) [ -9643.4443] [ 2160] [depth= 1] . ( 6 sec) [ -9641.6477] [ 2156] [depth= 1] . ( 6 sec) [ -9641.3959] [ 2161] [depth= 1] . ( 6 sec) [ -9635.2830] [ 2145] [depth= 1] . ( 7 sec) [ -9634.0532] [ 2141] [depth= 1] . ( 7 sec) [ -9583.7941] [ 2116] [depth= 5] . ( 7 sec) [ -9583.3396] [ 2116] [depth= 1] . ( 9 sec) [ -9574.3171] [Branch lengths ] . ( 9 sec) [ -9574.0673] [GTR parameters ] . ( 9 sec) [ -9572.4630] [Alpha ][ 1.143379] . ( 12 sec) [ -9571.0637] [Branch lengths ] . ( 27 sec) [ -9570.7303] [ 2122] [depth= 1] . ( 32 sec) [ -9570.5172] [Branch lengths ] . ( 33 sec) [ -9570.5146] [GTR parameters ] . ( 33 sec) [ -9570.4873] [Alpha ][ 1.164042] . ( 33 sec) [ -9570.4873] [Topology ] . ( 34 sec) [ -9570.4813] [Topology ] . ( 34 sec) [ -9570.4794] [Topology ] . ( 35 sec) [ -9570.4786] [Topology ] . ( 35 sec) [ -9570.4786] [GTR parameters ] . ( 35 sec) [ -9570.4785] [Alpha ][ 1.165206] . ( 35 sec) [ -9570.4785] [Topology ] . ( 36 sec) [ -9570.4780] [Topology ] . ( 36 sec) [ -9570.4780] [GTR parameters ] . ( 36 sec) [ -9570.4780] [Alpha ][ 1.165206] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -9570.4779] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9570.477917. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18662.0544] [GTR parameters ] . ( 1 sec) [ -18345.1223] [Alpha ][ 0.500960] . ( 1 sec) [ -18054.7361] [ 4067] [depth= 9] . ( 1 sec) [ -17555.8006] [ 4037] [depth= 4] . ( 1 sec) [ -17400.2351] [ 4021] [depth= 4] . ( 1 sec) [ -17303.8654] [ 4000] [depth= 8] . ( 1 sec) [ -16952.1333] [ 3953] [depth= 6] . ( 1 sec) [ -16915.6851] [ 3946] [depth= 5] . ( 1 sec) [ -16889.5614] [ 3955] [depth= 1] . ( 1 sec) [ -16726.0808] [ 3936] [depth= 4] . ( 2 sec) [ -16609.8932] [ 3865] [depth= 2] . ( 2 sec) [ -16510.9621] [ 3855] [depth= 6] . ( 2 sec) [ -16329.8783] [ 3821] [depth= 3] . ( 2 sec) [ -16274.0921] [ 3810] [depth= 4] . ( 2 sec) [ -15915.8301] [ 3755] [depth= 8] . ( 2 sec) [ -15835.2979] [ 3746] [depth= 4] . ( 2 sec) [ -15564.1358] [ 3703] [depth= 6] . ( 2 sec) [ -15431.2690] [ 3654] [depth= 1] . ( 2 sec) [ -15406.5973] [ 3649] [depth= 2] . ( 2 sec) [ -15203.6257] [ 3598] [depth= 13] . ( 2 sec) [ -15131.6295] [ 3584] [depth= 2] . ( 2 sec) [ -15024.6225] [ 3581] [depth= 2] . ( 2 sec) [ -14806.5738] [ 3534] [depth= 6] . ( 2 sec) [ -14626.6318] [ 3443] [depth= 1] . ( 2 sec) [ -14232.6807] [ 3326] [depth= 9] . ( 2 sec) [ -14184.1064] [ 3271] [depth= 4] . ( 2 sec) [ -14100.0055] [ 3269] [depth= 1] . ( 2 sec) [ -14028.4938] [ 3226] [depth= 1] . ( 2 sec) [ -13965.3443] [ 3220] [depth= 1] . ( 2 sec) [ -13836.3931] [ 3173] [depth= 1] . ( 2 sec) [ -13833.7609] [ 3179] [depth= 1] . ( 2 sec) [ -13560.1145] [ 3163] [depth= 4] . ( 3 sec) [ -13485.5228] [ 3146] [depth= 1] . ( 3 sec) [ -13431.2293] [ 3149] [depth= 1] . ( 3 sec) [ -13284.3112] [ 3145] [depth= 8] . ( 3 sec) [ -13217.9844] [ 3108] [depth= 9] . ( 3 sec) [ -13097.1011] [ 3081] [depth= 2] . ( 3 sec) [ -13069.0008] [ 3080] [depth= 3] . ( 3 sec) [ -13062.6204] [ 3076] [depth= 4] . ( 3 sec) [ -13017.5378] [ 3038] [depth= 8] . ( 3 sec) [ -13015.1519] [ 3039] [depth= 1] . ( 3 sec) [ -12977.3993] [ 3037] [depth= 1] . ( 3 sec) [ -12941.7867] [ 3034] [depth= 1] . ( 3 sec) [ -12829.8575] [ 2982] [depth= 12] . ( 3 sec) [ -12810.4271] [ 2975] [depth= 2] . ( 3 sec) [ -12695.2113] [ 2896] [depth= 2] . ( 3 sec) [ -12679.6487] [ 2892] [depth= 1] . ( 3 sec) [ -12531.5073] [ 2870] [depth= 5] . ( 3 sec) [ -12525.0589] [ 2869] [depth= 2] . ( 3 sec) [ -12465.1409] [ 2821] [depth= 3] . ( 4 sec) [ -12445.0066] [ 2823] [depth= 1] . ( 4 sec) [ -12369.0159] [ 2782] [depth= 3] . ( 4 sec) [ -12117.4606] [ 2761] [depth= 2] . ( 4 sec) [ -12023.1838] [ 2734] [depth= 3] . ( 4 sec) [ -11972.6704] [ 2726] [depth= 1] . ( 4 sec) [ -11909.4274] [ 2738] [depth= 1] . ( 4 sec) [ -11832.9750] [ 2684] [depth= 1] . ( 4 sec) [ -11580.0924] [ 2628] [depth= 4] . ( 4 sec) [ -11475.1445] [ 2617] [depth= 1] . ( 4 sec) [ -11466.4503] [ 2613] [depth= 1] . ( 4 sec) [ -11427.8324] [ 2584] [depth= 1] . ( 4 sec) [ -11276.2645] [ 2552] [depth= 7] . ( 4 sec) [ -11266.7817] [ 2545] [depth= 2] . ( 4 sec) [ -10951.1254] [ 2470] [depth= 3] . ( 4 sec) [ -10868.1495] [ 2424] [depth= 1] . ( 4 sec) [ -10671.9120] [ 2385] [depth= 2] . ( 4 sec) [ -10646.5815] [ 2387] [depth= 1] . ( 5 sec) [ -10640.8575] [ 2390] [depth= 1] . ( 5 sec) [ -10584.7799] [ 2388] [depth= 1] . ( 5 sec) [ -10570.3380] [ 2383] [depth= 2] . ( 5 sec) [ -10536.5144] [ 2366] [depth= 3] . ( 5 sec) [ -10512.7035] [ 2367] [depth= 1] . ( 5 sec) [ -10451.3566] [ 2363] [depth= 1] . ( 5 sec) [ -10312.0828] [ 2307] [depth= 3] . ( 5 sec) [ -10290.7582] [ 2307] [depth= 1] . ( 5 sec) [ -10261.0524] [ 2313] [depth= 5] . ( 5 sec) [ -10195.7384] [ 2288] [depth= 3] . ( 5 sec) [ -10146.1850] [ 2290] [depth= 1] . ( 5 sec) [ -10144.6559] [ 2288] [depth= 1] . ( 5 sec) [ -10132.5150] [ 2268] [depth= 2] . ( 5 sec) [ -10064.4089] [ 2232] [depth= 2] . ( 6 sec) [ -9905.9470] [Branch lengths ] . ( 6 sec) [ -9904.8722] [GTR parameters ] . ( 6 sec) [ -9857.1379] [Alpha ][ 0.999962] . ( 6 sec) [ -9856.0054] [ 2226] [depth= 1] . ( 6 sec) [ -9788.4581] [ 2176] [depth= 1] . ( 6 sec) [ -9775.0191] [ 2188] [depth= 4] . ( 6 sec) [ -9752.3487] [ 2192] [depth= 1] . ( 6 sec) [ -9751.8899] [ 2188] [depth= 2] . ( 7 sec) [ -9749.6455] [ 2189] [depth= 1] . ( 7 sec) [ -9749.3388] [ 2190] [depth= 1] . ( 7 sec) [ -9748.2065] [ 2190] [depth= 1] . ( 7 sec) [ -9711.8168] [ 2183] [depth= 3] . ( 7 sec) [ -9710.2786] [ 2177] [depth= 1] . ( 7 sec) [ -9708.8043] [ 2172] [depth= 2] . ( 7 sec) [ -9708.0492] [ 2172] [depth= 1] . ( 8 sec) [ -9706.9571] [ 2172] [depth= 1] . ( 8 sec) [ -9701.1049] [ 2159] [depth= 1] . ( 8 sec) [ -9698.2845] [ 2163] [depth= 1] . ( 9 sec) [ -9680.0917] [ 2161] [depth= 2] . ( 9 sec) [ -9679.2326] [ 2166] [depth= 1] . ( 9 sec) [ -9655.6012] [ 2142] [depth= 1] . ( 9 sec) [ -9655.2578] [ 2145] [depth= 1] . ( 10 sec) [ -9652.6005] [ 2143] [depth= 1] . ( 10 sec) [ -9611.2475] [Branch lengths ] . ( 10 sec) [ -9611.0129] [GTR parameters ] . ( 11 sec) [ -9609.7156] [Alpha ][ 1.128551] . ( 11 sec) [ -9576.2160] [ 2121] [depth= 2] . ( 13 sec) [ -9576.1743] [ 2121] [depth= 1] . ( 14 sec) [ -9571.1375] [Branch lengths ] . ( 14 sec) [ -9571.0821] [GTR parameters ] . ( 14 sec) [ -9571.0450] [Alpha ][ 1.152581] . ( 18 sec) [ -9570.5713] [Branch lengths ] . ( 37 sec) [ -9570.5017] [Branch lengths ] . ( 37 sec) [ -9570.5017] [Topology ] . ( 38 sec) [ -9570.4941] [Topology ] . ( 39 sec) [ -9570.4912] [Topology ] . ( 40 sec) [ -9570.4898] [Topology ] . ( 41 sec) [ -9570.4890] [Topology ] . ( 41 sec) [ -9570.4889] [GTR parameters ] . ( 41 sec) [ -9570.4797] [Alpha ][ 1.164587] . ( 41 sec) [ -9570.4797] [Topology ] . ( 42 sec) [ -9570.4785] [Topology ] . ( 43 sec) [ -9570.4781] [Topology ] . ( 43 sec) [ -9570.4781] [GTR parameters ] . ( 43 sec) [ -9570.4781] [Alpha ][ 1.164587] . ( 43 sec) [ -9570.4781] [Topology ] . ( 44 sec) [ -9570.4779] [Topology ] . ( 44 sec) [ -9570.4778] [GTR parameters ] . ( 44 sec) [ -9570.4778] [Alpha ][ 1.165751] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9570.477836. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19285.9640] [GTR parameters ] . ( 1 sec) [ -18967.2773] [Alpha ][ 0.500960] . ( 1 sec) [ -18778.7027] [ 4202] [depth= 6] . ( 1 sec) [ -18647.5732] [ 4155] [depth= 6] . ( 1 sec) [ -18483.2613] [ 4150] [depth= 4] . ( 1 sec) [ -18350.7738] [ 4150] [depth= 1] . ( 1 sec) [ -18036.0452] [ 4118] [depth= 5] . ( 1 sec) [ -17895.2827] [ 4116] [depth= 3] . ( 1 sec) [ -17753.2330] [ 4009] [depth= 1] . ( 2 sec) [ -17633.3404] [ 3973] [depth= 6] . ( 2 sec) [ -17102.2418] [ 3807] [depth= 15] . ( 2 sec) [ -16982.6211] [ 3823] [depth= 15] . ( 2 sec) [ -16977.1580] [ 3791] [depth= 5] . ( 2 sec) [ -16766.8014] [ 3785] [depth= 1] . ( 2 sec) [ -16400.5340] [ 3675] [depth= 17] . ( 2 sec) [ -16388.5444] [ 3669] [depth= 8] . ( 2 sec) [ -16149.9494] [ 3649] [depth= 3] . ( 2 sec) [ -16060.2092] [ 3619] [depth= 7] . ( 2 sec) [ -15879.9896] [ 3631] [depth= 3] . ( 2 sec) [ -15810.9490] [ 3551] [depth= 3] . ( 2 sec) [ -15741.7924] [ 3560] [depth= 1] . ( 2 sec) [ -15437.6679] [ 3446] [depth= 4] . ( 2 sec) [ -15339.8505] [ 3428] [depth= 6] . ( 2 sec) [ -15028.6404] [ 3348] [depth= 2] . ( 2 sec) [ -14775.8711] [ 3271] [depth= 8] . ( 2 sec) [ -14386.6204] [ 3238] [depth= 13] . ( 2 sec) [ -14347.1344] [ 3213] [depth= 1] . ( 2 sec) [ -14303.4701] [ 3212] [depth= 1] . ( 2 sec) [ -14261.4127] [ 3199] [depth= 1] . ( 2 sec) [ -14247.4177] [ 3210] [depth= 1] . ( 2 sec) [ -13976.7994] [ 3125] [depth= 7] . ( 3 sec) [ -13855.7889] [ 3078] [depth= 7] . ( 3 sec) [ -13748.1044] [ 3019] [depth= 6] . ( 3 sec) [ -13707.7961] [ 3019] [depth= 1] . ( 3 sec) [ -13647.3326] [ 2992] [depth= 2] . ( 3 sec) [ -13415.7197] [ 2944] [depth= 6] . ( 3 sec) [ -13250.4604] [ 2919] [depth= 6] . ( 3 sec) [ -13186.0197] [ 2922] [depth= 1] . ( 3 sec) [ -13014.4017] [ 2854] [depth= 9] . ( 3 sec) [ -12858.9922] [ 2827] [depth= 8] . ( 3 sec) [ -12804.3089] [ 2788] [depth= 1] . ( 3 sec) [ -12516.2347] [ 2681] [depth= 8] . ( 3 sec) [ -11940.9298] [ 2631] [depth= 5] . ( 3 sec) [ -11746.3106] [ 2582] [depth= 5] . ( 3 sec) [ -11744.0684] [ 2583] [depth= 1] . ( 3 sec) [ -11688.2750] [ 2582] [depth= 2] . ( 3 sec) [ -11622.5916] [ 2581] [depth= 2] . ( 3 sec) [ -11601.8753] [ 2581] [depth= 1] . ( 3 sec) [ -11535.3988] [ 2541] [depth= 4] . ( 3 sec) [ -11493.0677] [ 2545] [depth= 1] . ( 3 sec) [ -11484.5507] [ 2539] [depth= 1] . ( 4 sec) [ -11484.1342] [ 2544] [depth= 1] . ( 4 sec) [ -11382.9108] [ 2529] [depth= 9] . ( 4 sec) [ -11164.0260] [ 2463] [depth= 10] . ( 4 sec) [ -11008.0528] [ 2422] [depth= 3] . ( 4 sec) [ -11000.3858] [ 2426] [depth= 1] . ( 4 sec) [ -10930.9339] [ 2422] [depth= 1] . ( 4 sec) [ -10819.9060] [ 2380] [depth= 5] . ( 4 sec) [ -10724.8411] [ 2303] [depth= 9] . ( 4 sec) [ -10480.1583] [ 2329] [depth= 1] . ( 4 sec) [ -10449.4317] [ 2303] [depth= 1] . ( 4 sec) [ -10419.7099] [ 2298] [depth= 2] . ( 4 sec) [ -10380.6564] [ 2288] [depth= 5] . ( 4 sec) [ -10377.9460] [ 2287] [depth= 1] . ( 4 sec) [ -10358.4685] [ 2303] [depth= 5] . ( 4 sec) [ -10356.9621] [ 2302] [depth= 1] . ( 4 sec) [ -10295.5009] [ 2280] [depth= 1] . ( 4 sec) [ -10207.3769] [ 2239] [depth= 6] . ( 4 sec) [ -10204.5885] [ 2237] [depth= 1] . ( 4 sec) [ -10181.5460] [ 2234] [depth= 1] . ( 5 sec) [ -10139.1451] [ 2216] [depth= 2] . ( 5 sec) [ -10135.8684] [ 2216] [depth= 1] . ( 5 sec) [ -10132.0678] [ 2216] [depth= 1] . ( 5 sec) [ -10097.3765] [ 2212] [depth= 3] . ( 5 sec) [ -10049.0192] [ 2187] [depth= 1] . ( 5 sec) [ -10040.0947] [ 2205] [depth= 1] . ( 5 sec) [ -9945.3298] [ 2195] [depth= 1] . ( 5 sec) [ -9864.2991] [ 2171] [depth= 2] . ( 5 sec) [ -9808.0943] [ 2155] [depth= 2] . ( 5 sec) [ -9780.6445] [ 2165] [depth= 1] . ( 5 sec) [ -9778.4252] [ 2164] [depth= 1] . ( 6 sec) [ -9700.1792] [Branch lengths ] . ( 6 sec) [ -9698.8736] [GTR parameters ] . ( 6 sec) [ -9657.6563] [Alpha ][ 0.966923] . ( 6 sec) [ -9656.1787] [ 2161] [depth= 1] . ( 6 sec) [ -9655.9703] [ 2162] [depth= 1] . ( 7 sec) [ -9654.2512] [ 2162] [depth= 1] . ( 7 sec) [ -9654.0552] [ 2158] [depth= 1] . ( 7 sec) [ -9644.7791] [ 2149] [depth= 1] . ( 7 sec) [ -9641.5329] [ 2147] [depth= 1] . ( 8 sec) [ -9641.3156] [ 2137] [depth= 1] . ( 8 sec) [ -9640.5117] [ 2137] [depth= 1] . ( 8 sec) [ -9609.1314] [ 2115] [depth= 4] . ( 9 sec) [ -9608.8463] [ 2116] [depth= 2] . ( 10 sec) [ -9592.6634] [Branch lengths ] . ( 10 sec) [ -9592.4994] [GTR parameters ] . ( 10 sec) [ -9590.9090] [Alpha ][ 1.105234] . ( 11 sec) [ -9590.7875] [ 2116] [depth= 1] . ( 12 sec) [ -9590.6897] [ 2116] [depth= 1] . ( 13 sec) [ -9586.6657] [Branch lengths ] . ( 14 sec) [ -9586.6649] [GTR parameters ] . ( 14 sec) [ -9586.5731] [Alpha ][ 1.141180] . ( 17 sec) [ -9580.1970] [Branch lengths ] . ( 18 sec) [ -9580.1023] [ 2122] [depth= 1] . ( 20 sec) [ -9579.8827] [ 2122] [depth= 1] . ( 26 sec) [ -9579.8695] [ 2122] [depth= 1] . ( 36 sec) [ -9571.5970] [Branch lengths ] . ( 37 sec) [ -9571.5945] [GTR parameters ] . ( 37 sec) [ -9571.5489] [Alpha ][ 1.166796] . ( 40 sec) [ -9571.4039] [ 2122] [depth= 1] . ( 46 sec) [ -9571.3526] [ 2122] [depth= 1] . ( 56 sec) [ -9570.4828] [Branch lengths ] . ( 57 sec) [ -9570.4827] [GTR parameters ] . ( 57 sec) [ -9570.4826] [Alpha ][ 1.165629] . ( 77 sec) [ -9570.4781] [Branch lengths ] . ( 77 sec) [ -9570.4781] [Topology ] . ( 77 sec) [ -9570.4778] [Topology ] . ( 78 sec) [ -9570.4777] [GTR parameters ] . ( 78 sec) [ -9570.4777] [Alpha ][ 1.165629] . Checking for NNIs, optimizing five branches... . ( 84 sec) [ -9570.4776] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9570.477624. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19185.5710] [GTR parameters ] . ( 1 sec) [ -18883.4249] [Alpha ][ 0.500960] . ( 1 sec) [ -18716.4995] [ 4147] [depth= 9] . ( 1 sec) [ -18284.4565] [ 4102] [depth= 9] . ( 1 sec) [ -17984.1340] [ 4061] [depth= 8] . ( 1 sec) [ -17833.5512] [ 4020] [depth= 1] . ( 1 sec) [ -17630.8335] [ 3997] [depth= 9] . ( 1 sec) [ -17486.4724] [ 3991] [depth= 3] . ( 1 sec) [ -17144.0475] [ 3986] [depth= 5] . ( 1 sec) [ -17018.0353] [ 3946] [depth= 2] . ( 1 sec) [ -16946.1859] [ 3940] [depth= 2] . ( 1 sec) [ -16782.0574] [ 3927] [depth= 5] . ( 2 sec) [ -16667.4333] [ 3924] [depth= 1] . ( 2 sec) [ -16600.5279] [ 3899] [depth= 6] . ( 2 sec) [ -16490.6214] [ 3869] [depth= 3] . ( 2 sec) [ -16417.5643] [ 3842] [depth= 2] . ( 2 sec) [ -16315.6036] [ 3839] [depth= 1] . ( 2 sec) [ -15947.2491] [ 3761] [depth= 10] . ( 2 sec) [ -15864.8561] [ 3762] [depth= 1] . ( 2 sec) [ -15729.5810] [ 3759] [depth= 14] . ( 2 sec) [ -15620.0337] [ 3751] [depth= 1] . ( 2 sec) [ -15460.1213] [ 3670] [depth= 11] . ( 2 sec) [ -15459.5966] [ 3664] [depth= 1] . ( 2 sec) [ -15456.9770] [ 3670] [depth= 1] . ( 2 sec) [ -15284.7381] [ 3635] [depth= 1] . ( 2 sec) [ -15192.2156] [ 3619] [depth= 3] . ( 2 sec) [ -14667.4533] [ 3459] [depth= 10] . ( 2 sec) [ -14662.4499] [ 3460] [depth= 1] . ( 2 sec) [ -14617.0548] [ 3454] [depth= 8] . ( 2 sec) [ -14562.0401] [ 3450] [depth= 4] . ( 2 sec) [ -14381.9546] [ 3364] [depth= 12] . ( 2 sec) [ -14219.9889] [ 3357] [depth= 1] . ( 2 sec) [ -14108.3532] [ 3293] [depth= 1] . ( 2 sec) [ -14041.5007] [ 3285] [depth= 1] . ( 3 sec) [ -13885.0468] [ 3233] [depth= 8] . ( 3 sec) [ -13527.4718] [ 3109] [depth= 10] . ( 3 sec) [ -13521.7022] [ 3111] [depth= 1] . ( 3 sec) [ -13498.5619] [ 3104] [depth= 1] . ( 3 sec) [ -13395.0784] [ 3075] [depth= 1] . ( 3 sec) [ -13161.7659] [ 3019] [depth= 5] . ( 3 sec) [ -13160.1385] [ 3026] [depth= 1] . ( 3 sec) [ -12817.5485] [ 3008] [depth= 4] . ( 3 sec) [ -12727.1226] [ 2989] [depth= 7] . ( 3 sec) [ -12712.4813] [ 2992] [depth= 7] . ( 3 sec) [ -12515.9904] [ 2911] [depth= 9] . ( 3 sec) [ -12506.7483] [ 2905] [depth= 1] . ( 3 sec) [ -12422.5448] [ 2891] [depth= 8] . ( 3 sec) [ -12223.6296] [ 2841] [depth= 1] . ( 3 sec) [ -12210.9896] [ 2839] [depth= 3] . ( 3 sec) [ -12140.7562] [ 2844] [depth= 5] . ( 3 sec) [ -12137.6173] [ 2832] [depth= 2] . ( 4 sec) [ -11796.2038] [ 2772] [depth= 2] . ( 4 sec) [ -11724.6343] [ 2732] [depth= 5] . ( 4 sec) [ -11640.8722] [ 2717] [depth= 1] . ( 4 sec) [ -11564.3569] [ 2706] [depth= 5] . ( 4 sec) [ -11562.5222] [ 2703] [depth= 1] . ( 4 sec) [ -11459.6570] [ 2675] [depth= 4] . ( 4 sec) [ -11444.1056] [ 2651] [depth= 4] . ( 4 sec) [ -11426.5430] [ 2676] [depth= 1] . ( 4 sec) [ -11203.9912] [ 2649] [depth= 1] . ( 4 sec) [ -10764.0341] [ 2480] [depth= 10] . ( 4 sec) [ -10686.2835] [ 2436] [depth= 3] . ( 4 sec) [ -10644.5314] [ 2406] [depth= 1] . ( 4 sec) [ -10427.3813] [ 2411] [depth= 10] . ( 4 sec) [ -10393.6416] [ 2355] [depth= 5] . ( 4 sec) [ -10327.5718] [ 2334] [depth= 4] . ( 4 sec) [ -10311.5096] [ 2322] [depth= 1] . ( 4 sec) [ -10189.5518] [ 2272] [depth= 9] . ( 4 sec) [ -10188.8395] [ 2278] [depth= 1] . ( 4 sec) [ -10143.0503] [ 2246] [depth= 1] . ( 5 sec) [ -10131.0377] [ 2244] [depth= 2] . ( 5 sec) [ -10109.9625] [ 2249] [depth= 1] . ( 5 sec) [ -10101.5094] [ 2247] [depth= 1] . ( 5 sec) [ -10087.7359] [ 2252] [depth= 1] . ( 5 sec) [ -10082.5708] [ 2247] [depth= 1] . ( 5 sec) [ -10082.3364] [ 2248] [depth= 1] . ( 5 sec) [ -10076.0593] [ 2246] [depth= 3] . ( 5 sec) [ -10063.2746] [ 2243] [depth= 2] . ( 5 sec) [ -10060.7853] [ 2247] [depth= 1] . ( 5 sec) [ -10008.2561] [ 2222] [depth= 3] . ( 5 sec) [ -9985.8625] [ 2216] [depth= 1] . ( 5 sec) [ -9972.8840] [ 2218] [depth= 1] . ( 5 sec) [ -9969.1536] [ 2216] [depth= 1] . ( 6 sec) [ -9811.7203] [Branch lengths ] . ( 6 sec) [ -9809.6427] [GTR parameters ] . ( 6 sec) [ -9761.4307] [Alpha ][ 1.000548] . ( 6 sec) [ -9756.5855] [ 2213] [depth= 1] . ( 6 sec) [ -9712.3472] [ 2188] [depth= 1] . ( 7 sec) [ -9691.7836] [ 2167] [depth= 1] . ( 7 sec) [ -9648.8141] [ 2146] [depth= 2] . ( 7 sec) [ -9636.8146] [ 2149] [depth= 2] . ( 7 sec) [ -9636.5552] [ 2151] [depth= 1] . ( 7 sec) [ -9635.9786] [ 2149] [depth= 1] . ( 7 sec) [ -9635.4257] [ 2150] [depth= 1] . ( 8 sec) [ -9634.4528] [ 2149] [depth= 1] . ( 9 sec) [ -9606.1772] [ 2119] [depth= 2] . ( 9 sec) [ -9602.8860] [ 2120] [depth= 1] . ( 9 sec) [ -9601.9525] [ 2119] [depth= 1] . ( 9 sec) [ -9590.1405] [ 2122] [depth= 2] . ( 10 sec) [ -9589.7915] [ 2122] [depth= 1] . ( 10 sec) [ -9574.2159] [Branch lengths ] . ( 10 sec) [ -9573.8871] [GTR parameters ] . ( 10 sec) [ -9572.5125] [Alpha ][ 1.133085] . ( 14 sec) [ -9570.8350] [Branch lengths ] . ( 34 sec) [ -9570.5924] [Branch lengths ] . ( 34 sec) [ -9570.5924] [Topology ] . ( 35 sec) [ -9570.5656] [Topology ] . ( 36 sec) [ -9570.5554] [Topology ] . ( 36 sec) [ -9570.5504] [Topology ] . ( 37 sec) [ -9570.5477] [Topology ] . ( 38 sec) [ -9570.5464] [Topology ] . ( 39 sec) [ -9570.5456] [Topology ] . ( 39 sec) [ -9570.5453] [GTR parameters ] . ( 39 sec) [ -9570.4840] [Alpha ][ 1.162811] . ( 39 sec) [ -9570.4840] [Topology ] . ( 40 sec) [ -9570.4800] [Topology ] . ( 41 sec) [ -9570.4790] [Topology ] . ( 41 sec) [ -9570.4785] [Topology ] . ( 42 sec) [ -9570.4785] [GTR parameters ] . ( 42 sec) [ -9570.4781] [Alpha ][ 1.164922] . ( 42 sec) [ -9570.4781] [Topology ] . ( 43 sec) [ -9570.4778] [Topology ] . ( 43 sec) [ -9570.4778] [GTR parameters ] . ( 43 sec) [ -9570.4778] [Alpha ][ 1.164922] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9570.477836. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18972.0755] [GTR parameters ] . ( 1 sec) [ -18687.5524] [Alpha ][ 0.500960] . ( 1 sec) [ -18403.5996] [ 4179] [depth= 8] . ( 1 sec) [ -17659.4902] [ 4136] [depth= 7] . ( 1 sec) [ -17515.7089] [ 4127] [depth= 6] . ( 1 sec) [ -17452.5800] [ 4125] [depth= 6] . ( 1 sec) [ -17274.4465] [ 4087] [depth= 3] . ( 1 sec) [ -17218.2572] [ 4088] [depth= 5] . ( 1 sec) [ -17149.9869] [ 4062] [depth= 14] . ( 1 sec) [ -17030.2070] [ 4058] [depth= 1] . ( 1 sec) [ -16700.8169] [ 3949] [depth= 19] . ( 1 sec) [ -16507.7939] [ 3935] [depth= 2] . ( 1 sec) [ -16300.5617] [ 3867] [depth= 15] . ( 1 sec) [ -16210.8836] [ 3834] [depth= 1] . ( 1 sec) [ -15838.5820] [ 3797] [depth= 10] . ( 1 sec) [ -15809.8326] [ 3793] [depth= 1] . ( 1 sec) [ -15708.9780] [ 3771] [depth= 10] . ( 1 sec) [ -15542.7480] [ 3755] [depth= 7] . ( 2 sec) [ -15500.5606] [ 3758] [depth= 1] . ( 2 sec) [ -15385.5818] [ 3729] [depth= 7] . ( 2 sec) [ -15009.1350] [ 3648] [depth= 9] . ( 2 sec) [ -14925.6301] [ 3641] [depth= 1] . ( 2 sec) [ -14889.8814] [ 3637] [depth= 10] . ( 2 sec) [ -14826.7412] [ 3607] [depth= 3] . ( 2 sec) [ -14456.3395] [ 3570] [depth= 9] . ( 2 sec) [ -14280.0799] [ 3521] [depth= 1] . ( 2 sec) [ -14229.5061] [ 3516] [depth= 7] . ( 2 sec) [ -14163.1342] [ 3479] [depth= 1] . ( 2 sec) [ -13834.5033] [ 3375] [depth= 6] . ( 2 sec) [ -13748.1292] [ 3366] [depth= 9] . ( 2 sec) [ -13601.2863] [ 3306] [depth= 11] . ( 2 sec) [ -13361.7512] [ 3166] [depth= 13] . ( 2 sec) [ -13276.1904] [ 3127] [depth= 11] . ( 2 sec) [ -13269.4061] [ 3189] [depth= 10] . ( 2 sec) [ -13152.4323] [ 3123] [depth= 3] . ( 2 sec) [ -13134.0998] [ 3111] [depth= 1] . ( 2 sec) [ -13042.9546] [ 2986] [depth= 8] . ( 2 sec) [ -12778.0299] [ 2988] [depth= 1] . ( 3 sec) [ -12765.1486] [ 2985] [depth= 1] . ( 3 sec) [ -12591.6022] [ 2899] [depth= 10] . ( 3 sec) [ -12439.6686] [ 2813] [depth= 3] . ( 3 sec) [ -12413.0339] [ 2810] [depth= 7] . ( 3 sec) [ -12400.6325] [ 2803] [depth= 1] . ( 3 sec) [ -12312.9345] [ 2804] [depth= 1] . ( 3 sec) [ -12288.7408] [ 2803] [depth= 1] . ( 3 sec) [ -12288.1602] [ 2805] [depth= 1] . ( 3 sec) [ -12265.1779] [ 2839] [depth= 7] . ( 3 sec) [ -12263.4399] [ 2837] [depth= 1] . ( 3 sec) [ -12243.0429] [ 2836] [depth= 1] . ( 3 sec) [ -12238.2253] [ 2837] [depth= 1] . ( 3 sec) [ -12174.7808] [ 2840] [depth= 1] . ( 3 sec) [ -12113.8546] [ 2821] [depth= 2] . ( 3 sec) [ -11976.6969] [ 2766] [depth= 4] . ( 3 sec) [ -11838.1075] [ 2732] [depth= 1] . ( 3 sec) [ -11689.3695] [ 2728] [depth= 5] . ( 3 sec) [ -11527.7505] [ 2683] [depth= 1] . ( 3 sec) [ -11478.9283] [ 2655] [depth= 4] . ( 4 sec) [ -11444.3210] [ 2657] [depth= 6] . ( 4 sec) [ -11429.4301] [ 2642] [depth= 2] . ( 4 sec) [ -11422.7572] [ 2621] [depth= 1] . ( 4 sec) [ -11380.9187] [ 2597] [depth= 5] . ( 4 sec) [ -11347.5567] [ 2587] [depth= 7] . ( 4 sec) [ -11165.2521] [ 2548] [depth= 1] . ( 4 sec) [ -11083.9395] [ 2510] [depth= 11] . ( 4 sec) [ -11048.3910] [ 2488] [depth= 1] . ( 4 sec) [ -11006.3046] [ 2482] [depth= 2] . ( 4 sec) [ -10985.0925] [ 2479] [depth= 1] . ( 4 sec) [ -10831.9269] [ 2427] [depth= 6] . ( 4 sec) [ -10767.6265] [ 2407] [depth= 1] . ( 4 sec) [ -10759.8767] [ 2407] [depth= 1] . ( 4 sec) [ -10759.1804] [ 2405] [depth= 1] . ( 4 sec) [ -10723.5868] [ 2379] [depth= 1] . ( 4 sec) [ -10712.9914] [ 2382] [depth= 1] . ( 4 sec) [ -10652.1347] [ 2402] [depth= 2] . ( 4 sec) [ -10594.4424] [ 2391] [depth= 1] . ( 4 sec) [ -10580.0736] [ 2383] [depth= 6] . ( 5 sec) [ -10568.2004] [ 2381] [depth= 2] . ( 5 sec) [ -10544.7704] [ 2376] [depth= 3] . ( 5 sec) [ -10379.1666] [ 2408] [depth= 1] . ( 5 sec) [ -10377.3672] [ 2412] [depth= 1] . ( 5 sec) [ -10342.7764] [ 2362] [depth= 14] . ( 5 sec) [ -10340.8463] [ 2359] [depth= 1] . ( 5 sec) [ -10269.4868] [ 2323] [depth= 8] . ( 5 sec) [ -10194.7903] [ 2292] [depth= 1] . ( 5 sec) [ -10129.4160] [ 2274] [depth= 4] . ( 5 sec) [ -10128.0756] [ 2275] [depth= 1] . ( 5 sec) [ -10126.5576] [ 2280] [depth= 1] . ( 5 sec) [ -10102.8358] [ 2269] [depth= 1] . ( 5 sec) [ -9935.1724] [Branch lengths ] . ( 6 sec) [ -9933.9234] [GTR parameters ] . ( 6 sec) [ -9897.4208] [Alpha ][ 0.919481] . ( 6 sec) [ -9895.7292] [ 2266] [depth= 1] . ( 6 sec) [ -9862.4240] [ 2221] [depth= 10] . ( 6 sec) [ -9860.7838] [ 2219] [depth= 1] . ( 6 sec) [ -9859.2443] [ 2215] [depth= 1] . ( 6 sec) [ -9857.6718] [ 2210] [depth= 1] . ( 6 sec) [ -9854.4423] [ 2210] [depth= 1] . ( 7 sec) [ -9851.8106] [ 2212] [depth= 1] . ( 7 sec) [ -9849.8744] [ 2208] [depth= 1] . ( 7 sec) [ -9836.7285] [ 2205] [depth= 1] . ( 7 sec) [ -9833.4960] [ 2210] [depth= 1] . ( 7 sec) [ -9826.9561] [ 2198] [depth= 2] . ( 7 sec) [ -9724.3258] [ 2173] [depth= 2] . ( 8 sec) [ -9692.1528] [ 2154] [depth= 2] . ( 8 sec) [ -9690.6109] [ 2155] [depth= 1] . ( 8 sec) [ -9668.8834] [ 2142] [depth= 1] . ( 8 sec) [ -9666.5602] [ 2155] [depth= 1] . ( 8 sec) [ -9657.4468] [ 2160] [depth= 1] . ( 8 sec) [ -9655.2187] [ 2171] [depth= 1] . ( 8 sec) [ -9644.9677] [ 2160] [depth= 1] . ( 8 sec) [ -9640.8672] [ 2158] [depth= 1] . ( 9 sec) [ -9639.6157] [ 2153] [depth= 1] . ( 9 sec) [ -9638.5890] [ 2152] [depth= 1] . ( 9 sec) [ -9635.8007] [ 2147] [depth= 1] . ( 9 sec) [ -9601.0591] [ 2112] [depth= 5] . ( 9 sec) [ -9600.6213] [ 2116] [depth= 1] . ( 9 sec) [ -9598.8776] [ 2115] [depth= 1] . ( 10 sec) [ -9579.2951] [Branch lengths ] . ( 10 sec) [ -9579.0831] [GTR parameters ] . ( 10 sec) [ -9575.2435] [Alpha ][ 1.130881] . ( 10 sec) [ -9574.0615] [ 2111] [depth= 1] . ( 13 sec) [ -9571.2103] [Branch lengths ] . ( 13 sec) [ -9571.2057] [GTR parameters ] . ( 14 sec) [ -9571.1571] [Alpha ][ 1.157314] . ( 17 sec) [ -9570.6745] [Branch lengths ] . ( 36 sec) [ -9570.5402] [Branch lengths ] . ( 36 sec) [ -9570.5402] [Topology ] . ( 37 sec) [ -9570.5144] [Topology ] . ( 38 sec) [ -9570.5011] [Topology ] . ( 39 sec) [ -9570.4926] [Topology ] . ( 40 sec) [ -9570.4868] [Topology ] . ( 40 sec) [ -9570.4841] [Topology ] . ( 41 sec) [ -9570.4831] [Topology ] . ( 41 sec) [ -9570.4824] [GTR parameters ] . ( 41 sec) [ -9570.4787] [Alpha ][ 1.164924] . ( 41 sec) [ -9570.4787] [Topology ] . ( 42 sec) [ -9570.4780] [Topology ] . ( 42 sec) [ -9570.4780] [GTR parameters ] . ( 42 sec) [ -9570.4780] [Alpha ][ 1.164924] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9570.478027. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9633.594476 . ( 0 sec) [ -9633.1925] [GTR parameters ] . ( 1 sec) [ -9631.5367] [Alpha ][ 1.149448] . ( 1 sec) [ -9631.5367] [Topology ] . ( 1 sec) [ -9584.1716] [Topology ] . ( 2 sec) [ -9574.1907] [Topology ] . ( 3 sec) [ -9571.8821] [Topology ] . ( 4 sec) [ -9571.1460] [Topology ] . ( 5 sec) [ -9570.8312] [Topology ] . ( 5 sec) [ -9570.6829] [Topology ] . ( 6 sec) [ -9570.6084] [Topology ] . ( 7 sec) [ -9570.5694] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.569422 . ( 14 sec) [ -9570.5359] [GTR parameters ] . ( 14 sec) [ -9570.5256] [Alpha ][ 1.162201] . ( 14 sec) [ -9570.5256] [Topology ] . ( 15 sec) [ -9570.5023] [Topology ] . ( 16 sec) [ -9570.4906] [Topology ] . ( 16 sec) [ -9570.4847] [Topology ] . ( 17 sec) [ -9570.4816] [Topology ] . ( 18 sec) [ -9570.4800] [Topology ] . ( 19 sec) [ -9570.4792] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.479199 . ( 25 sec) [ -9570.4792] [GTR parameters ] . ( 25 sec) [ -9570.4787] [Alpha ][ 1.164851] . ( 25 sec) [ -9570.4787] [Topology ] . ( 26 sec) [ -9570.4782] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.478181 . ( 33 sec) [ -9570.4782] [GTR parameters ] . ( 33 sec) [ -9570.4782] [Alpha ][ 1.164851] . ( 33 sec) [ -9570.4782] [Topology ] . ( 33 sec) [ -9570.4779] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -9633.1925] [GTR parameters ] . ( 47 sec) [ -9631.5367] [Alpha ][ 1.149448] . ( 47 sec) [ -9630.8308] [ 2120] [depth= 1] . ( 47 sec) [ -9628.5460] [ 2119] [depth= 1] . ( 47 sec) [ -9627.9684] [ 2120] [depth= 1] . ( 47 sec) [ -9626.3291] [ 2120] [depth= 1] . ( 48 sec) [ -9624.9462] [ 2121] [depth= 1] . ( 48 sec) [ -9622.4295] [ 2120] [depth= 1] . ( 48 sec) [ -9618.5712] [ 2121] [depth= 1] . ( 48 sec) [ -9613.9623] [ 2116] [depth= 1] . ( 48 sec) [ -9612.3173] [ 2116] [depth= 1] . ( 48 sec) [ -9611.5887] [ 2116] [depth= 1] . ( 48 sec) [ -9611.1207] [ 2116] [depth= 1] . ( 49 sec) [ -9609.9239] [ 2115] [depth= 1] . ( 49 sec) [ -9608.7957] [ 2120] [depth= 2] . ( 49 sec) [ -9607.4962] [ 2121] [depth= 1] . ( 49 sec) [ -9607.4603] [ 2121] [depth= 1] . ( 49 sec) [ -9607.4126] [ 2116] [depth= 1] . ( 49 sec) [ -9607.3899] [ 2119] [depth= 1] . ( 50 sec) [ -9579.1170] [Branch lengths ] . ( 51 sec) [ -9579.0908] [GTR parameters ] . ( 51 sec) [ -9579.0906] [Alpha ][ 1.147681] . ( 52 sec) [ -9577.7436] [ 2124] [depth= 1] . ( 53 sec) [ -9576.0336] [ 2121] [depth= 1] . ( 53 sec) [ -9575.8884] [ 2122] [depth= 1] . ( 53 sec) [ -9575.8388] [ 2117] [depth= 1] . ( 54 sec) [ -9570.8584] [Branch lengths ] . ( 55 sec) [ -9570.8509] [GTR parameters ] . ( 55 sec) [ -9570.8385] [Alpha ][ 1.161660] . ( 58 sec) [ -9570.4958] [Branch lengths ] . ( 78 sec) [ -9570.4804] [Branch lengths ] . ( 78 sec) [ -9570.4804] [Topology ] . ( 78 sec) [ -9570.4793] [Topology ] . ( 79 sec) [ -9570.4790] [Topology ] . ( 79 sec) [ -9570.4789] [GTR parameters ] . ( 79 sec) [ -9570.4782] [Alpha ][ 1.164980] . ( 79 sec) [ -9570.4782] [Topology ] . ( 80 sec) [ -9570.4779] [Topology ] . ( 80 sec) [ -9570.4779] [GTR parameters ] . ( 80 sec) [ -9570.4779] [Alpha ][ 1.164980] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -9570.4778] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9570.477914 . Log likelihood obtained after SPR moves : -9570.477755 . Log likelihood of the current tree: -9570.477755. . Printing the most likely tree in file 'data64.phy_phyml_tree.txt'... . Best log likelihood : -9570.477624 . Time used 0h1m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo