.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data45.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... . 439 patterns found. (out of a total of 500 sites) . 55 sites without polymorphism (11.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21666.7602] [GTR parameters ] . ( 1 sec) [ -21235.8150] [Alpha ][ 0.500960] . ( 1 sec) [ -20860.2439] [ 4828] [depth= 8] . ( 1 sec) [ -20704.5046] [ 4827] [depth= 8] . ( 1 sec) [ -20513.1894] [ 4754] [depth= 1] . ( 1 sec) [ -20336.1839] [ 4733] [depth= 3] . ( 1 sec) [ -20040.1629] [ 4717] [depth= 7] . ( 1 sec) [ -20014.4570] [ 4718] [depth= 1] . ( 1 sec) [ -19800.8407] [ 4644] [depth= 6] . ( 1 sec) [ -19606.3463] [ 4656] [depth= 9] . ( 1 sec) [ -19108.1764] [ 4487] [depth= 19] . ( 1 sec) [ -18986.1498] [ 4408] [depth= 1] . ( 1 sec) [ -18847.8731] [ 4383] [depth= 7] . ( 1 sec) [ -18768.6369] [ 4351] [depth= 1] . ( 1 sec) [ -18463.2036] [ 4335] [depth= 5] . ( 1 sec) [ -18450.7681] [ 4342] [depth= 2] . ( 1 sec) [ -18263.1940] [ 4306] [depth= 8] . ( 1 sec) [ -17565.3616] [ 4293] [depth= 2] . ( 1 sec) [ -17448.3781] [ 4276] [depth= 2] . ( 1 sec) [ -17292.8005] [ 4224] [depth= 2] . ( 2 sec) [ -17242.4022] [ 4188] [depth= 5] . ( 2 sec) [ -17060.1751] [ 4174] [depth= 1] . ( 2 sec) [ -16970.3709] [ 4129] [depth= 1] . ( 2 sec) [ -16796.9340] [ 4087] [depth= 10] . ( 2 sec) [ -16701.0749] [ 4079] [depth= 1] . ( 2 sec) [ -16667.0654] [ 4075] [depth= 1] . ( 2 sec) [ -16317.0877] [ 4086] [depth= 15] . ( 2 sec) [ -16052.6529] [ 4012] [depth= 11] . ( 2 sec) [ -15589.0250] [ 3879] [depth= 3] . ( 2 sec) [ -15466.3160] [ 3783] [depth= 12] . ( 2 sec) [ -14821.1240] [ 3700] [depth= 13] . ( 2 sec) [ -14700.1496] [ 3650] [depth= 1] . ( 2 sec) [ -14667.6711] [ 3641] [depth= 1] . ( 2 sec) [ -14545.2465] [ 3621] [depth= 3] . ( 2 sec) [ -14433.8810] [ 3615] [depth= 2] . ( 2 sec) [ -14394.6929] [ 3590] [depth= 1] . ( 2 sec) [ -14333.3859] [ 3590] [depth= 1] . ( 2 sec) [ -14294.9536] [ 3579] [depth= 1] . ( 2 sec) [ -14250.8600] [ 3559] [depth= 3] . ( 2 sec) [ -14246.0179] [ 3560] [depth= 1] . ( 2 sec) [ -14104.0057] [ 3518] [depth= 9] . ( 2 sec) [ -13998.3849] [ 3474] [depth= 2] . ( 2 sec) [ -13991.0706] [ 3474] [depth= 2] . ( 3 sec) [ -13086.0099] [ 3271] [depth= 6] . ( 3 sec) [ -13053.0768] [ 3240] [depth= 1] . ( 3 sec) [ -12902.4839] [ 3180] [depth= 1] . ( 3 sec) [ -12576.0426] [ 3127] [depth= 14] . ( 3 sec) [ -12491.2938] [ 3090] [depth= 1] . ( 3 sec) [ -12310.9136] [ 3004] [depth= 11] . ( 3 sec) [ -12308.9981] [ 3003] [depth= 1] . ( 3 sec) [ -12002.0778] [ 2945] [depth= 5] . ( 3 sec) [ -11969.6111] [ 2949] [depth= 1] . ( 3 sec) [ -11969.1756] [ 2950] [depth= 1] . ( 3 sec) [ -11879.1346] [ 2935] [depth= 2] . ( 3 sec) [ -11666.5200] [ 2830] [depth= 9] . ( 3 sec) [ -11663.0808] [ 2834] [depth= 1] . ( 3 sec) [ -11662.3550] [ 2830] [depth= 1] . ( 3 sec) [ -11491.0705] [ 2770] [depth= 6] . ( 3 sec) [ -11362.8991] [ 2755] [depth= 4] . ( 3 sec) [ -11224.0393] [ 2678] [depth= 5] . ( 3 sec) [ -11223.1253] [ 2674] [depth= 1] . ( 4 sec) [ -11156.7356] [ 2582] [depth= 5] . ( 4 sec) [ -11152.0323] [ 2578] [depth= 1] . ( 4 sec) [ -11103.7681] [ 2557] [depth= 1] . ( 4 sec) [ -11092.0911] [ 2556] [depth= 1] . ( 4 sec) [ -11082.3146] [ 2564] [depth= 1] . ( 4 sec) [ -11074.4730] [ 2556] [depth= 1] . ( 4 sec) [ -11074.2449] [ 2564] [depth= 1] . ( 4 sec) [ -11055.4440] [ 2564] [depth= 1] . ( 4 sec) [ -11049.5271] [ 2565] [depth= 1] . ( 4 sec) [ -11002.0369] [ 2566] [depth= 2] . ( 4 sec) [ -10979.9011] [ 2568] [depth= 4] . ( 4 sec) [ -10969.8537] [ 2565] [depth= 3] . ( 4 sec) [ -10901.5813] [ 2540] [depth= 3] . ( 4 sec) [ -10899.4961] [ 2540] [depth= 1] . ( 4 sec) [ -10894.5339] [ 2541] [depth= 1] . ( 4 sec) [ -10823.8705] [ 2623] [depth= 4] . ( 4 sec) [ -10809.2180] [ 2618] [depth= 2] . ( 4 sec) [ -10799.6208] [ 2597] [depth= 1] . ( 4 sec) [ -10758.9824] [ 2589] [depth= 1] . ( 5 sec) [ -10721.6894] [ 2544] [depth= 1] . ( 5 sec) [ -10599.1270] [Branch lengths ] . ( 6 sec) [ -10593.8520] [GTR parameters ] . ( 6 sec) [ -10568.2684] [Alpha ][ 0.812716] . ( 6 sec) [ -10566.3738] [ 2548] [depth= 2] . ( 6 sec) [ -10563.0750] [ 2527] [depth= 5] . ( 6 sec) [ -10541.2880] [ 2518] [depth= 2] . ( 6 sec) [ -10538.8777] [ 2513] [depth= 1] . ( 6 sec) [ -10538.5347] [ 2514] [depth= 1] . ( 7 sec) [ -10535.3836] [ 2508] [depth= 1] . ( 7 sec) [ -10282.4057] [ 2407] [depth= 3] . ( 7 sec) [ -10276.4492] [ 2405] [depth= 1] . ( 7 sec) [ -10276.0844] [ 2405] [depth= 1] . ( 7 sec) [ -10273.9635] [ 2410] [depth= 1] . ( 7 sec) [ -10273.9483] [ 2411] [depth= 1] . ( 7 sec) [ -10263.2685] [ 2418] [depth= 1] . ( 8 sec) [ -10263.2198] [ 2417] [depth= 1] . ( 8 sec) [ -10263.1814] [ 2418] [depth= 1] . ( 8 sec) [ -10260.8736] [ 2418] [depth= 1] . ( 9 sec) [ -10258.4990] [ 2421] [depth= 1] . ( 9 sec) [ -10186.1462] [ 2374] [depth= 3] . ( 9 sec) [ -10186.1029] [ 2377] [depth= 1] . ( 10 sec) [ -10138.5500] [Branch lengths ] . ( 10 sec) [ -10137.7640] [GTR parameters ] . ( 10 sec) [ -10136.2825] [Alpha ][ 0.913709] . ( 11 sec) [ -10132.3966] [ 2362] [depth= 2] . ( 11 sec) [ -10132.2095] [ 2364] [depth= 1] . ( 11 sec) [ -10132.1349] [ 2361] [depth= 1] . ( 11 sec) [ -10132.0955] [ 2359] [depth= 1] . ( 12 sec) [ -10131.9094] [ 2355] [depth= 1] . ( 13 sec) [ -10131.4525] [ 2343] [depth= 1] . ( 13 sec) [ -10127.2471] [Branch lengths ] . ( 13 sec) [ -10127.2406] [GTR parameters ] . ( 14 sec) [ -10127.1780] [Alpha ][ 0.936405] . ( 16 sec) [ -10126.8226] [Branch lengths ] . ( 39 sec) [ -10126.7922] [Branch lengths ] . ( 39 sec) [ -10126.7922] [Topology ] . ( 40 sec) [ -10126.7598] [Topology ] . ( 40 sec) [ -10126.7419] [Topology ] . ( 41 sec) [ -10126.7389] [Topology ] . ( 42 sec) [ -10126.7379] [Topology ] . ( 42 sec) [ -10126.7375] [GTR parameters ] . ( 42 sec) [ -10126.7374] [Alpha ][ 0.935463] . ( 42 sec) [ -10126.7374] [Topology ] . ( 43 sec) [ -10126.7371] [Topology ] . ( 43 sec) [ -10126.7370] [GTR parameters ] . ( 43 sec) [ -10126.7370] [Alpha ][ 0.935463] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -10126.6377] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10126.637664. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21868.5654] [GTR parameters ] . ( 1 sec) [ -21451.2420] [Alpha ][ 0.500960] . ( 1 sec) [ -21183.4067] [ 4977] [depth= 3] . ( 1 sec) [ -20983.0129] [ 4885] [depth= 10] . ( 1 sec) [ -20607.7905] [ 4775] [depth= 4] . ( 1 sec) [ -20534.9956] [ 4771] [depth= 6] . ( 1 sec) [ -20375.6566] [ 4742] [depth= 1] . ( 1 sec) [ -20236.4712] [ 4726] [depth= 6] . ( 1 sec) [ -20128.6904] [ 4682] [depth= 1] . ( 1 sec) [ -19930.8802] [ 4668] [depth= 3] . ( 1 sec) [ -19775.0922] [ 4592] [depth= 4] . ( 1 sec) [ -19693.8461] [ 4575] [depth= 3] . ( 1 sec) [ -19386.9732] [ 4537] [depth= 10] . ( 1 sec) [ -19206.5074] [ 4525] [depth= 3] . ( 1 sec) [ -18978.9234] [ 4439] [depth= 1] . ( 1 sec) [ -18809.9050] [ 4403] [depth= 3] . ( 2 sec) [ -18182.5363] [ 4241] [depth= 16] . ( 2 sec) [ -17770.3176] [ 4100] [depth= 9] . ( 2 sec) [ -17174.1159] [ 4006] [depth= 5] . ( 2 sec) [ -17080.7439] [ 4008] [depth= 1] . ( 2 sec) [ -16768.9224] [ 4018] [depth= 1] . ( 2 sec) [ -16742.3650] [ 3948] [depth= 2] . ( 2 sec) [ -16622.8877] [ 3934] [depth= 2] . ( 2 sec) [ -15966.4278] [ 3834] [depth= 16] . ( 2 sec) [ -15537.6746] [ 3731] [depth= 3] . ( 2 sec) [ -15434.2909] [ 3707] [depth= 1] . ( 2 sec) [ -15016.0042] [ 3593] [depth= 15] . ( 2 sec) [ -14570.6192] [ 3484] [depth= 15] . ( 2 sec) [ -14181.6022] [ 3469] [depth= 10] . ( 2 sec) [ -14113.7907] [ 3475] [depth= 1] . ( 2 sec) [ -13885.5417] [ 3399] [depth= 17] . ( 2 sec) [ -13878.0755] [ 3396] [depth= 1] . ( 2 sec) [ -13855.8468] [ 3388] [depth= 2] . ( 2 sec) [ -13666.3968] [ 3326] [depth= 7] . ( 2 sec) [ -13302.5285] [ 3356] [depth= 3] . ( 3 sec) [ -13112.3479] [ 3296] [depth= 8] . ( 3 sec) [ -13066.6795] [ 3291] [depth= 3] . ( 3 sec) [ -12952.0981] [ 3246] [depth= 1] . ( 3 sec) [ -12828.2630] [ 3180] [depth= 9] . ( 3 sec) [ -12798.9503] [ 3153] [depth= 1] . ( 3 sec) [ -12750.7317] [ 3098] [depth= 1] . ( 3 sec) [ -12473.0042] [ 2944] [depth= 7] . ( 3 sec) [ -12238.2100] [ 2818] [depth= 2] . ( 3 sec) [ -12220.0245] [ 2826] [depth= 1] . ( 3 sec) [ -12165.2268] [ 2824] [depth= 3] . ( 3 sec) [ -12063.4755] [ 2807] [depth= 6] . ( 3 sec) [ -11889.4350] [ 2721] [depth= 3] . ( 3 sec) [ -11870.6249] [ 2717] [depth= 3] . ( 3 sec) [ -11861.3937] [ 2708] [depth= 1] . ( 3 sec) [ -11408.2135] [ 2702] [depth= 1] . ( 3 sec) [ -11401.6125] [ 2731] [depth= 1] . ( 3 sec) [ -11341.7433] [ 2736] [depth= 1] . ( 3 sec) [ -11325.9807] [ 2731] [depth= 1] . ( 3 sec) [ -11247.1708] [ 2712] [depth= 3] . ( 3 sec) [ -11205.7867] [ 2697] [depth= 1] . ( 3 sec) [ -11116.6260] [ 2680] [depth= 1] . ( 4 sec) [ -11023.3905] [ 2670] [depth= 1] . ( 4 sec) [ -11021.1364] [ 2682] [depth= 2] . ( 4 sec) [ -10929.7158] [ 2674] [depth= 4] . ( 4 sec) [ -10920.4582] [ 2649] [depth= 1] . ( 4 sec) [ -10906.8590] [ 2655] [depth= 1] . ( 4 sec) [ -10778.2187] [ 2552] [depth= 8] . ( 4 sec) [ -10717.9966] [ 2497] [depth= 1] . ( 4 sec) [ -10711.4808] [ 2495] [depth= 1] . ( 4 sec) [ -10682.2332] [ 2481] [depth= 7] . ( 4 sec) [ -10636.3967] [ 2481] [depth= 1] . ( 4 sec) [ -10543.9083] [ 2419] [depth= 4] . ( 4 sec) [ -10532.7974] [ 2409] [depth= 1] . ( 4 sec) [ -10445.6659] [ 2383] [depth= 1] . ( 4 sec) [ -10390.0493] [ 2368] [depth= 1] . ( 4 sec) [ -10367.0254] [ 2369] [depth= 1] . ( 4 sec) [ -10354.9712] [ 2372] [depth= 1] . ( 4 sec) [ -10350.9478] [ 2377] [depth= 1] . ( 5 sec) [ -10350.2054] [ 2378] [depth= 1] . ( 5 sec) [ -10340.3049] [ 2375] [depth= 3] . ( 5 sec) [ -10336.2179] [ 2372] [depth= 1] . ( 5 sec) [ -10318.6879] [ 2366] [depth= 1] . ( 5 sec) [ -10317.2483] [ 2371] [depth= 1] . ( 5 sec) [ -10316.5362] [ 2373] [depth= 2] . ( 5 sec) [ -10315.7119] [ 2373] [depth= 1] . ( 5 sec) [ -10206.0225] [Branch lengths ] . ( 6 sec) [ -10202.7598] [GTR parameters ] . ( 6 sec) [ -10169.8457] [Alpha ][ 0.878478] . ( 6 sec) [ -10168.5311] [ 2368] [depth= 1] . ( 6 sec) [ -10161.4709] [ 2365] [depth= 1] . ( 6 sec) [ -10159.9066] [ 2362] [depth= 1] . ( 7 sec) [ -10159.6093] [ 2356] [depth= 1] . ( 7 sec) [ -10158.1775] [ 2357] [depth= 1] . ( 7 sec) [ -10153.8331] [ 2345] [depth= 1] . ( 8 sec) [ -10153.0773] [ 2347] [depth= 1] . ( 8 sec) [ -10152.8788] [ 2350] [depth= 1] . ( 8 sec) [ -10152.7570] [ 2352] [depth= 1] . ( 8 sec) [ -10152.4746] [ 2352] [depth= 1] . ( 9 sec) [ -10152.3960] [ 2357] [depth= 1] . ( 9 sec) [ -10135.8806] [Branch lengths ] . ( 10 sec) [ -10135.5263] [GTR parameters ] . ( 10 sec) [ -10135.2807] [Alpha ][ 0.921607] . ( 10 sec) [ -10135.2651] [ 2355] [depth= 1] . ( 11 sec) [ -10135.2224] [ 2354] [depth= 1] . ( 11 sec) [ -10130.5786] [ 2350] [depth= 2] . ( 12 sec) [ -10130.0038] [ 2346] [depth= 1] . ( 13 sec) [ -10127.7855] [Branch lengths ] . ( 13 sec) [ -10127.7741] [GTR parameters ] . ( 13 sec) [ -10127.7654] [Alpha ][ 0.930105] . ( 14 sec) [ -10127.7371] [ 2342] [depth= 1] . ( 16 sec) [ -10126.9066] [Branch lengths ] . ( 16 sec) [ -10126.9047] [GTR parameters ] . ( 16 sec) [ -10126.9029] [Alpha ][ 0.933938] . ( 38 sec) [ -10126.8045] [Branch lengths ] . ( 38 sec) [ -10126.8045] [Topology ] . ( 39 sec) [ -10126.7641] [Topology ] . ( 40 sec) [ -10126.7439] [Topology ] . ( 41 sec) [ -10126.7401] [Topology ] . ( 42 sec) [ -10126.7389] [Topology ] . ( 42 sec) [ -10126.7384] [Topology ] . ( 42 sec) [ -10126.7377] [GTR parameters ] . ( 43 sec) [ -10126.7375] [Alpha ][ 0.935314] . ( 43 sec) [ -10126.7375] [Topology ] . ( 43 sec) [ -10126.7372] [Topology ] . ( 43 sec) [ -10126.7372] [GTR parameters ] . ( 44 sec) [ -10126.7372] [Alpha ][ 0.935314] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -10126.6374] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10126.637384. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22523.8023] [GTR parameters ] . ( 1 sec) [ -22068.6087] [Alpha ][ 0.500960] . ( 1 sec) [ -21743.7587] [ 5199] [depth= 8] . ( 1 sec) [ -21501.6520] [ 5122] [depth= 6] . ( 1 sec) [ -21463.4549] [ 5099] [depth= 3] . ( 1 sec) [ -21453.3437] [ 5098] [depth= 3] . ( 1 sec) [ -21196.3788] [ 5069] [depth= 3] . ( 2 sec) [ -21079.4655] [ 5069] [depth= 4] . ( 2 sec) [ -20572.2088] [ 4946] [depth= 7] . ( 2 sec) [ -20403.3453] [ 4909] [depth= 1] . ( 2 sec) [ -20233.5796] [ 4910] [depth= 2] . ( 2 sec) [ -20051.8443] [ 4827] [depth= 10] . ( 2 sec) [ -19772.6508] [ 4751] [depth= 2] . ( 2 sec) [ -19043.6126] [ 4625] [depth= 8] . ( 2 sec) [ -18738.3224] [ 4497] [depth= 10] . ( 2 sec) [ -18704.2580] [ 4492] [depth= 2] . ( 2 sec) [ -18582.1050] [ 4448] [depth= 1] . ( 2 sec) [ -18560.9411] [ 4441] [depth= 1] . ( 2 sec) [ -18529.0679] [ 4413] [depth= 1] . ( 2 sec) [ -18429.8309] [ 4394] [depth= 2] . ( 2 sec) [ -18148.4938] [ 4314] [depth= 9] . ( 2 sec) [ -17874.7379] [ 4190] [depth= 10] . ( 2 sec) [ -17597.1184] [ 4173] [depth= 2] . ( 2 sec) [ -17226.0688] [ 4141] [depth= 7] . ( 2 sec) [ -16950.9042] [ 4114] [depth= 4] . ( 2 sec) [ -16868.8984] [ 4077] [depth= 1] . ( 2 sec) [ -16173.8636] [ 3897] [depth= 10] . ( 3 sec) [ -16152.8268] [ 3902] [depth= 3] . ( 3 sec) [ -16077.2192] [ 3940] [depth= 1] . ( 3 sec) [ -15941.5230] [ 3900] [depth= 10] . ( 3 sec) [ -15790.3335] [ 3865] [depth= 1] . ( 3 sec) [ -15789.9279] [ 3860] [depth= 1] . ( 3 sec) [ -15689.0837] [ 3855] [depth= 1] . ( 3 sec) [ -15488.3711] [ 3785] [depth= 6] . ( 3 sec) [ -15422.4197] [ 3744] [depth= 4] . ( 3 sec) [ -15355.4110] [ 3740] [depth= 7] . ( 3 sec) [ -15246.1274] [ 3693] [depth= 1] . ( 3 sec) [ -15185.5755] [ 3677] [depth= 1] . ( 3 sec) [ -15173.7995] [ 3645] [depth= 1] . ( 3 sec) [ -14860.2062] [ 3545] [depth= 8] . ( 3 sec) [ -14860.0512] [ 3546] [depth= 1] . ( 3 sec) [ -14637.4716] [ 3435] [depth= 5] . ( 3 sec) [ -14481.4702] [ 3407] [depth= 6] . ( 3 sec) [ -14122.4376] [ 3389] [depth= 2] . ( 3 sec) [ -14040.6261] [ 3359] [depth= 1] . ( 4 sec) [ -13842.6522] [ 3231] [depth= 5] . ( 4 sec) [ -13537.2344] [ 3218] [depth= 3] . ( 4 sec) [ -13401.1454] [ 3162] [depth= 10] . ( 4 sec) [ -13351.6420] [ 3106] [depth= 1] . ( 4 sec) [ -13177.9845] [ 3071] [depth= 2] . ( 4 sec) [ -13170.0927] [ 3072] [depth= 1] . ( 4 sec) [ -13087.9376] [ 3041] [depth= 3] . ( 4 sec) [ -12932.9378] [ 2989] [depth= 1] . ( 4 sec) [ -12678.5564] [ 2928] [depth= 6] . ( 4 sec) [ -12671.2408] [ 2935] [depth= 2] . ( 4 sec) [ -12639.8657] [ 2903] [depth= 1] . ( 4 sec) [ -12464.3758] [ 2868] [depth= 7] . ( 4 sec) [ -12383.0129] [ 2861] [depth= 1] . ( 4 sec) [ -12052.8749] [ 2778] [depth= 2] . ( 4 sec) [ -11907.5385] [ 2778] [depth= 1] . ( 4 sec) [ -11845.0307] [ 2779] [depth= 1] . ( 4 sec) [ -11778.2989] [ 2753] [depth= 1] . ( 4 sec) [ -11698.6948] [ 2699] [depth= 5] . ( 5 sec) [ -11691.8773] [ 2682] [depth= 1] . ( 5 sec) [ -11495.4273] [ 2637] [depth= 1] . ( 5 sec) [ -11446.0715] [ 2639] [depth= 1] . ( 5 sec) [ -11230.4863] [ 2619] [depth= 1] . ( 5 sec) [ -10953.0390] [ 2503] [depth= 3] . ( 5 sec) [ -10847.3540] [ 2502] [depth= 2] . ( 5 sec) [ -10837.3540] [ 2513] [depth= 1] . ( 5 sec) [ -10830.4258] [ 2506] [depth= 2] . ( 5 sec) [ -10803.8703] [ 2504] [depth= 2] . ( 5 sec) [ -10734.6052] [ 2503] [depth= 6] . ( 5 sec) [ -10653.1386] [ 2424] [depth= 5] . ( 5 sec) [ -10646.0336] [ 2428] [depth= 1] . ( 5 sec) [ -10588.2592] [ 2415] [depth= 1] . ( 5 sec) [ -10586.8771] [ 2411] [depth= 1] . ( 5 sec) [ -10500.9169] [ 2392] [depth= 1] . ( 5 sec) [ -10436.5485] [ 2354] [depth= 1] . ( 5 sec) [ -10422.8102] [ 2353] [depth= 1] . ( 5 sec) [ -10422.5619] [ 2356] [depth= 1] . ( 6 sec) [ -10226.2999] [Branch lengths ] . ( 6 sec) [ -10222.1561] [GTR parameters ] . ( 6 sec) [ -10192.9415] [Alpha ][ 0.853376] . ( 6 sec) [ -10192.8638] [ 2357] [depth= 1] . ( 7 sec) [ -10192.3926] [ 2356] [depth= 1] . ( 7 sec) [ -10192.2550] [ 2357] [depth= 1] . ( 7 sec) [ -10191.8611] [ 2365] [depth= 1] . ( 7 sec) [ -10189.9748] [ 2362] [depth= 1] . ( 7 sec) [ -10187.7822] [ 2359] [depth= 1] . ( 7 sec) [ -10183.2732] [ 2351] [depth= 1] . ( 7 sec) [ -10169.9405] [ 2349] [depth= 1] . ( 7 sec) [ -10164.0428] [ 2344] [depth= 1] . ( 7 sec) [ -10163.5819] [ 2347] [depth= 1] . ( 8 sec) [ -10159.4966] [ 2344] [depth= 1] . ( 8 sec) [ -10159.3358] [ 2339] [depth= 1] . ( 8 sec) [ -10159.1719] [ 2339] [depth= 1] . ( 9 sec) [ -10157.6633] [ 2342] [depth= 1] . ( 9 sec) [ -10157.5474] [ 2343] [depth= 1] . ( 9 sec) [ -10157.1330] [ 2343] [depth= 1] . ( 9 sec) [ -10132.1766] [Branch lengths ] . ( 10 sec) [ -10131.9311] [GTR parameters ] . ( 10 sec) [ -10131.4294] [Alpha ][ 0.914433] . ( 11 sec) [ -10131.3778] [ 2343] [depth= 1] . ( 11 sec) [ -10131.2398] [ 2344] [depth= 1] . ( 12 sec) [ -10131.2052] [ 2343] [depth= 1] . ( 13 sec) [ -10127.3862] [Branch lengths ] . ( 13 sec) [ -10127.3721] [GTR parameters ] . ( 13 sec) [ -10127.3427] [Alpha ][ 0.930021] . ( 16 sec) [ -10126.8792] [Branch lengths ] . ( 38 sec) [ -10126.8086] [Branch lengths ] . ( 38 sec) [ -10126.8086] [Topology ] . ( 39 sec) [ -10126.7703] [Topology ] . ( 40 sec) [ -10126.7488] [Topology ] . ( 40 sec) [ -10126.7444] [Topology ] . ( 41 sec) [ -10126.7427] [Topology ] . ( 42 sec) [ -10126.7420] [Topology ] . ( 42 sec) [ -10126.7412] [GTR parameters ] . ( 42 sec) [ -10126.7380] [Alpha ][ 0.935104] . ( 42 sec) [ -10126.7380] [Topology ] . ( 43 sec) [ -10126.7374] [Topology ] . ( 43 sec) [ -10126.7374] [GTR parameters ] . ( 43 sec) [ -10126.7374] [Alpha ][ 0.935104] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -10126.6374] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10126.637431. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21856.4004] [GTR parameters ] . ( 0 sec) [ -21415.0278] [Alpha ][ 0.500960] . ( 0 sec) [ -21235.7919] [ 5002] [depth= 8] . ( 0 sec) [ -20818.4654] [ 4889] [depth= 8] . ( 1 sec) [ -20489.2660] [ 4849] [depth= 2] . ( 1 sec) [ -20343.7093] [ 4803] [depth= 1] . ( 1 sec) [ -20039.1105] [ 4723] [depth= 9] . ( 1 sec) [ -19905.1977] [ 4691] [depth= 1] . ( 1 sec) [ -19713.7718] [ 4666] [depth= 3] . ( 1 sec) [ -19482.7562] [ 4614] [depth= 4] . ( 1 sec) [ -19275.1694] [ 4591] [depth= 1] . ( 1 sec) [ -18949.0415] [ 4573] [depth= 4] . ( 1 sec) [ -18754.7993] [ 4545] [depth= 6] . ( 1 sec) [ -18559.0963] [ 4479] [depth= 4] . ( 1 sec) [ -18429.3215] [ 4473] [depth= 3] . ( 1 sec) [ -18368.2799] [ 4447] [depth= 2] . ( 1 sec) [ -18177.2911] [ 4416] [depth= 5] . ( 1 sec) [ -18013.4161] [ 4379] [depth= 16] . ( 1 sec) [ -17841.0086] [ 4395] [depth= 1] . ( 1 sec) [ -17481.6254] [ 4299] [depth= 2] . ( 1 sec) [ -17330.8426] [ 4238] [depth= 12] . ( 1 sec) [ -17184.9415] [ 4130] [depth= 7] . ( 1 sec) [ -16788.7081] [ 4092] [depth= 1] . ( 1 sec) [ -16664.9184] [ 4070] [depth= 3] . ( 1 sec) [ -16503.9198] [ 4047] [depth= 13] . ( 1 sec) [ -16222.3654] [ 3972] [depth= 9] . ( 1 sec) [ -16081.6006] [ 3941] [depth= 1] . ( 2 sec) [ -16033.3042] [ 3934] [depth= 11] . ( 2 sec) [ -15955.2034] [ 3928] [depth= 2] . ( 2 sec) [ -15806.2491] [ 3828] [depth= 10] . ( 2 sec) [ -15652.1860] [ 3834] [depth= 6] . ( 2 sec) [ -15430.9123] [ 3788] [depth= 1] . ( 2 sec) [ -15225.3209] [ 3800] [depth= 1] . ( 2 sec) [ -15197.3858] [ 3799] [depth= 2] . ( 2 sec) [ -14978.5325] [ 3681] [depth= 13] . ( 2 sec) [ -14693.7833] [ 3651] [depth= 1] . ( 2 sec) [ -14691.5043] [ 3627] [depth= 1] . ( 2 sec) [ -14534.8499] [ 3591] [depth= 1] . ( 2 sec) [ -14286.6700] [ 3446] [depth= 15] . ( 2 sec) [ -14285.6912] [ 3405] [depth= 3] . ( 2 sec) [ -14101.1299] [ 3398] [depth= 3] . ( 2 sec) [ -13884.9594] [ 3328] [depth= 1] . ( 2 sec) [ -13683.6086] [ 3320] [depth= 4] . ( 2 sec) [ -13629.4821] [ 3292] [depth= 2] . ( 2 sec) [ -13506.8858] [ 3282] [depth= 1] . ( 2 sec) [ -13420.6387] [ 3310] [depth= 11] . ( 2 sec) [ -13362.8542] [ 3299] [depth= 1] . ( 3 sec) [ -13258.8019] [ 3282] [depth= 10] . ( 3 sec) [ -13160.5313] [ 3265] [depth= 1] . ( 3 sec) [ -13158.7671] [ 3266] [depth= 1] . ( 3 sec) [ -12931.2209] [ 3184] [depth= 4] . ( 3 sec) [ -12842.4315] [ 3179] [depth= 5] . ( 3 sec) [ -12511.1279] [ 3047] [depth= 2] . ( 3 sec) [ -12504.2557] [ 3055] [depth= 2] . ( 3 sec) [ -12422.1326] [ 3042] [depth= 3] . ( 3 sec) [ -12259.5927] [ 2999] [depth= 1] . ( 3 sec) [ -12201.3874] [ 2923] [depth= 3] . ( 3 sec) [ -12056.5082] [ 2862] [depth= 6] . ( 3 sec) [ -11943.7245] [ 2826] [depth= 4] . ( 3 sec) [ -11905.6510] [ 2820] [depth= 1] . ( 3 sec) [ -11689.4409] [ 2768] [depth= 1] . ( 3 sec) [ -11653.2130] [ 2785] [depth= 6] . ( 3 sec) [ -11545.4116] [ 2770] [depth= 2] . ( 3 sec) [ -11498.5735] [ 2760] [depth= 2] . ( 3 sec) [ -11449.1874] [ 2734] [depth= 1] . ( 3 sec) [ -11297.5113] [ 2726] [depth= 1] . ( 4 sec) [ -11197.4573] [ 2678] [depth= 1] . ( 4 sec) [ -11086.2499] [ 2594] [depth= 8] . ( 4 sec) [ -11080.8383] [ 2597] [depth= 1] . ( 4 sec) [ -11047.4005] [ 2598] [depth= 1] . ( 4 sec) [ -10988.4568] [ 2533] [depth= 9] . ( 4 sec) [ -10955.1445] [ 2529] [depth= 1] . ( 4 sec) [ -10937.2774] [ 2525] [depth= 3] . ( 4 sec) [ -10933.5629] [ 2526] [depth= 1] . ( 4 sec) [ -10932.5624] [ 2523] [depth= 1] . ( 4 sec) [ -10889.2609] [ 2515] [depth= 1] . ( 4 sec) [ -10845.2729] [ 2489] [depth= 1] . ( 4 sec) [ -10844.9259] [ 2500] [depth= 1] . ( 4 sec) [ -10839.6105] [ 2501] [depth= 1] . ( 4 sec) [ -10833.4020] [ 2500] [depth= 1] . ( 4 sec) [ -10826.6041] [ 2499] [depth= 1] . ( 5 sec) [ -10601.2663] [Branch lengths ] . ( 5 sec) [ -10597.6156] [GTR parameters ] . ( 5 sec) [ -10572.4239] [Alpha ][ 0.812272] . ( 5 sec) [ -10529.2828] [ 2509] [depth= 1] . ( 5 sec) [ -10309.4820] [ 2407] [depth= 7] . ( 6 sec) [ -10309.3740] [ 2412] [depth= 1] . ( 6 sec) [ -10251.6631] [ 2383] [depth= 1] . ( 6 sec) [ -10249.9770] [ 2381] [depth= 1] . ( 6 sec) [ -10245.9566] [ 2378] [depth= 1] . ( 6 sec) [ -10245.3341] [ 2378] [depth= 1] . ( 6 sec) [ -10242.6141] [ 2376] [depth= 1] . ( 6 sec) [ -10238.5439] [ 2376] [depth= 1] . ( 6 sec) [ -10228.0747] [ 2373] [depth= 2] . ( 6 sec) [ -10195.8330] [ 2367] [depth= 1] . ( 7 sec) [ -10195.7413] [ 2368] [depth= 1] . ( 7 sec) [ -10190.5991] [ 2365] [depth= 1] . ( 7 sec) [ -10190.5503] [ 2369] [depth= 1] . ( 7 sec) [ -10186.4315] [ 2368] [depth= 1] . ( 7 sec) [ -10175.0300] [ 2356] [depth= 1] . ( 7 sec) [ -10174.3690] [ 2346] [depth= 1] . ( 8 sec) [ -10174.3110] [ 2346] [depth= 1] . ( 8 sec) [ -10174.2563] [ 2345] [depth= 1] . ( 9 sec) [ -10146.1994] [Branch lengths ] . ( 9 sec) [ -10145.5001] [GTR parameters ] . ( 9 sec) [ -10143.9177] [Alpha ][ 0.917522] . ( 12 sec) [ -10143.8989] [ 2346] [depth= 1] . ( 12 sec) [ -10127.0712] [Branch lengths ] . ( 13 sec) [ -10127.0685] [GTR parameters ] . ( 13 sec) [ -10127.0410] [Alpha ][ 0.932577] . ( 16 sec) [ -10126.7351] [Branch lengths ] . ( 37 sec) [ -10126.7078] [Branch lengths ] . ( 38 sec) [ -10126.7078] [Topology ] . ( 38 sec) [ -10126.7056] [Topology ] . ( 39 sec) [ -10126.7048] [Topology ] . ( 39 sec) [ -10126.7044] [GTR parameters ] . ( 39 sec) [ -10126.7039] [Alpha ][ 0.934443] . ( 39 sec) [ -10126.7039] [Topology ] . ( 40 sec) [ -10126.7034] [Topology ] . ( 40 sec) [ -10126.7034] [GTR parameters ] . ( 40 sec) [ -10126.7034] [Alpha ][ 0.934443] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -10126.6298] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10126.629752. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22567.7798] [GTR parameters ] . ( 0 sec) [ -22075.8713] [Alpha ][ 0.500960] . ( 1 sec) [ -21476.5784] [ 5176] [depth= 6] . ( 1 sec) [ -20939.5829] [ 5058] [depth= 11] . ( 1 sec) [ -20746.4896] [ 5011] [depth= 3] . ( 1 sec) [ -20689.1913] [ 5001] [depth= 2] . ( 1 sec) [ -20620.1005] [ 4988] [depth= 8] . ( 1 sec) [ -20510.8719] [ 4975] [depth= 5] . ( 1 sec) [ -20388.1191] [ 4953] [depth= 6] . ( 1 sec) [ -20176.8359] [ 4867] [depth= 1] . ( 1 sec) [ -19852.9088] [ 4813] [depth= 9] . ( 1 sec) [ -19675.1232] [ 4768] [depth= 1] . ( 1 sec) [ -18915.7996] [ 4636] [depth= 12] . ( 1 sec) [ -18507.5702] [ 4526] [depth= 8] . ( 1 sec) [ -18501.9401] [ 4532] [depth= 6] . ( 1 sec) [ -18350.9131] [ 4528] [depth= 11] . ( 1 sec) [ -18315.2487] [ 4519] [depth= 1] . ( 1 sec) [ -18145.7548] [ 4426] [depth= 8] . ( 1 sec) [ -18051.5402] [ 4419] [depth= 2] . ( 1 sec) [ -17872.0503] [ 4328] [depth= 8] . ( 1 sec) [ -17294.3569] [ 4160] [depth= 13] . ( 1 sec) [ -16985.4251] [ 4078] [depth= 10] . ( 1 sec) [ -16769.4259] [ 4019] [depth= 7] . ( 2 sec) [ -16728.0739] [ 4014] [depth= 1] . ( 2 sec) [ -16545.0816] [ 3950] [depth= 2] . ( 2 sec) [ -16183.9653] [ 3900] [depth= 7] . ( 2 sec) [ -16106.2545] [ 3870] [depth= 1] . ( 2 sec) [ -15675.7724] [ 3776] [depth= 10] . ( 2 sec) [ -15416.3423] [ 3729] [depth= 2] . ( 2 sec) [ -15352.4446] [ 3729] [depth= 8] . ( 2 sec) [ -15328.8409] [ 3721] [depth= 7] . ( 2 sec) [ -14823.0770] [ 3663] [depth= 1] . ( 2 sec) [ -14628.0314] [ 3579] [depth= 7] . ( 2 sec) [ -14441.9967] [ 3508] [depth= 8] . ( 2 sec) [ -14278.5005] [ 3401] [depth= 10] . ( 2 sec) [ -14175.9858] [ 3361] [depth= 1] . ( 2 sec) [ -13890.8718] [ 3299] [depth= 11] . ( 2 sec) [ -13553.9818] [ 3227] [depth= 11] . ( 2 sec) [ -13445.2477] [ 3173] [depth= 1] . ( 2 sec) [ -13380.4880] [ 3162] [depth= 1] . ( 2 sec) [ -13313.7164] [ 3155] [depth= 1] . ( 2 sec) [ -13280.7453] [ 3112] [depth= 1] . ( 2 sec) [ -12931.9750] [ 2982] [depth= 4] . ( 3 sec) [ -12826.2385] [ 2938] [depth= 3] . ( 3 sec) [ -12508.7663] [ 2840] [depth= 9] . ( 3 sec) [ -12499.2375] [ 2833] [depth= 2] . ( 3 sec) [ -12402.8778] [ 2810] [depth= 3] . ( 3 sec) [ -12293.2913] [ 2756] [depth= 2] . ( 3 sec) [ -12281.2024] [ 2757] [depth= 1] . ( 3 sec) [ -12250.6390] [ 2739] [depth= 1] . ( 3 sec) [ -11603.0582] [ 2652] [depth= 5] . ( 3 sec) [ -11570.1478] [ 2664] [depth= 4] . ( 3 sec) [ -11549.2566] [ 2669] [depth= 1] . ( 3 sec) [ -11543.9738] [ 2673] [depth= 1] . ( 3 sec) [ -11532.5735] [ 2670] [depth= 1] . ( 3 sec) [ -11524.7757] [ 2668] [depth= 1] . ( 3 sec) [ -11521.4593] [ 2641] [depth= 3] . ( 3 sec) [ -11481.3643] [ 2627] [depth= 5] . ( 3 sec) [ -11473.1606] [ 2626] [depth= 1] . ( 3 sec) [ -11448.2847] [ 2624] [depth= 1] . ( 3 sec) [ -11442.5675] [ 2621] [depth= 1] . ( 3 sec) [ -11266.1599] [ 2561] [depth= 3] . ( 3 sec) [ -11263.9491] [ 2561] [depth= 1] . ( 3 sec) [ -11182.8228] [ 2548] [depth= 1] . ( 4 sec) [ -11173.0449] [ 2547] [depth= 1] . ( 4 sec) [ -10772.8933] [ 2453] [depth= 4] . ( 4 sec) [ -10743.2195] [ 2448] [depth= 3] . ( 4 sec) [ -10687.8017] [ 2471] [depth= 2] . ( 4 sec) [ -10634.7373] [ 2447] [depth= 1] . ( 4 sec) [ -10633.9841] [ 2448] [depth= 1] . ( 4 sec) [ -10625.8295] [ 2453] [depth= 1] . ( 4 sec) [ -10603.6202] [ 2455] [depth= 1] . ( 4 sec) [ -10520.2686] [ 2421] [depth= 2] . ( 4 sec) [ -10514.4867] [ 2416] [depth= 1] . ( 4 sec) [ -10485.2135] [ 2417] [depth= 1] . ( 4 sec) [ -10482.5019] [ 2418] [depth= 1] . ( 5 sec) [ -10256.8072] [Branch lengths ] . ( 5 sec) [ -10253.1007] [GTR parameters ] . ( 5 sec) [ -10224.7373] [Alpha ][ 0.845893] . ( 5 sec) [ -10224.3472] [ 2419] [depth= 1] . ( 6 sec) [ -10219.9488] [ 2414] [depth= 1] . ( 6 sec) [ -10157.5190] [ 2351] [depth= 6] . ( 6 sec) [ -10154.2059] [ 2350] [depth= 1] . ( 6 sec) [ -10152.7720] [ 2349] [depth= 1] . ( 6 sec) [ -10147.7172] [ 2342] [depth= 1] . ( 7 sec) [ -10147.3205] [ 2341] [depth= 1] . ( 7 sec) [ -10147.1372] [ 2342] [depth= 1] . ( 7 sec) [ -10146.8916] [ 2345] [depth= 1] . ( 7 sec) [ -10146.1077] [ 2357] [depth= 1] . ( 7 sec) [ -10145.9263] [ 2345] [depth= 1] . ( 8 sec) [ -10145.3859] [ 2344] [depth= 1] . ( 9 sec) [ -10129.2466] [Branch lengths ] . ( 9 sec) [ -10129.2308] [GTR parameters ] . ( 9 sec) [ -10128.4829] [Alpha ][ 0.920065] . ( 9 sec) [ -10128.3453] [ 2346] [depth= 1] . ( 11 sec) [ -10128.3222] [ 2345] [depth= 1] . ( 12 sec) [ -10126.9343] [Branch lengths ] . ( 12 sec) [ -10126.9325] [GTR parameters ] . ( 12 sec) [ -10126.9175] [Alpha ][ 0.931207] . ( 15 sec) [ -10126.7297] [Branch lengths ] . ( 37 sec) [ -10126.6948] [Branch lengths ] . ( 37 sec) [ -10126.6948] [Topology ] . ( 38 sec) [ -10126.6564] [Topology ] . ( 39 sec) [ -10126.6372] [Topology ] . ( 40 sec) [ -10126.6334] [Topology ] . ( 40 sec) [ -10126.6320] [Topology ] . ( 41 sec) [ -10126.6315] [Topology ] . ( 41 sec) [ -10126.6308] [GTR parameters ] . ( 41 sec) [ -10126.6294] [Alpha ][ 0.934541] . ( 42 sec) [ -10126.6294] [Topology ] . ( 42 sec) [ -10126.6291] [Topology ] . ( 42 sec) [ -10126.6291] [GTR parameters ] . ( 43 sec) [ -10126.6291] [Alpha ][ 0.934541] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10126.629066. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10249.134706 . ( 1 sec) [ -10245.1148] [GTR parameters ] . ( 1 sec) [ -10243.8466] [Alpha ][ 0.889997] . ( 1 sec) [ -10243.8466] [Topology ] . ( 2 sec) [ -10164.4022] [Topology ] . ( 3 sec) [ -10138.0065] [Topology ] . ( 4 sec) [ -10131.1905] [Topology ] . ( 4 sec) [ -10129.1012] [Topology ] . ( 5 sec) [ -10128.1641] [Topology ] . ( 6 sec) [ -10127.6945] [Topology ] . ( 7 sec) [ -10127.4437] [Topology ] . ( 8 sec) [ -10127.3062] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10127.306184 . ( 14 sec) [ -10127.0631] [GTR parameters ] . ( 14 sec) [ -10126.8625] [Alpha ][ 0.929574] . ( 14 sec) [ -10126.8625] [Topology ] . ( 15 sec) [ -10126.7541] [Topology ] . ( 16 sec) [ -10126.6997] [Topology ] . ( 17 sec) [ -10126.6700] [Topology ] . ( 18 sec) [ -10126.6535] [Topology ] . ( 19 sec) [ -10126.6444] [Topology ] . ( 19 sec) [ -10126.6392] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10126.639199 . ( 26 sec) [ -10126.6387] [GTR parameters ] . ( 26 sec) [ -10126.6362] [Alpha ][ 0.934120] . ( 26 sec) [ -10126.6362] [Topology ] . ( 26 sec) [ -10126.6329] [Topology ] . ( 27 sec) [ -10126.6311] [Topology ] . ( 28 sec) [ -10126.6301] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10126.630135 . ( 34 sec) [ -10126.6301] [GTR parameters ] . ( 34 sec) [ -10126.6301] [Alpha ][ 0.934120] . ( 34 sec) [ -10126.6301] [Topology ] . ( 35 sec) [ -10126.6295] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -10245.1148] [GTR parameters ] . ( 48 sec) [ -10243.8466] [Alpha ][ 0.889997] . ( 49 sec) [ -10238.6405] [ 2364] [depth= 1] . ( 49 sec) [ -10231.1171] [ 2361] [depth= 2] . ( 49 sec) [ -10217.1031] [ 2351] [depth= 1] . ( 49 sec) [ -10208.8573] [ 2363] [depth= 1] . ( 49 sec) [ -10208.4418] [ 2365] [depth= 1] . ( 49 sec) [ -10208.4284] [ 2364] [depth= 1] . ( 49 sec) [ -10207.8106] [ 2369] [depth= 1] . ( 50 sec) [ -10201.9318] [ 2364] [depth= 1] . ( 50 sec) [ -10195.7216] [ 2363] [depth= 1] . ( 50 sec) [ -10187.8812] [ 2364] [depth= 1] . ( 50 sec) [ -10185.9883] [ 2369] [depth= 1] . ( 50 sec) [ -10185.3439] [ 2370] [depth= 1] . ( 50 sec) [ -10183.7502] [ 2373] [depth= 2] . ( 50 sec) [ -10178.9131] [ 2366] [depth= 3] . ( 51 sec) [ -10173.1634] [ 2372] [depth= 1] . ( 51 sec) [ -10172.3758] [ 2373] [depth= 1] . ( 51 sec) [ -10171.6514] [ 2372] [depth= 1] . ( 51 sec) [ -10169.8675] [ 2373] [depth= 1] . ( 51 sec) [ -10169.1876] [ 2377] [depth= 1] . ( 51 sec) [ -10168.4663] [ 2380] [depth= 1] . ( 52 sec) [ -10146.7781] [Branch lengths ] . ( 52 sec) [ -10146.5599] [GTR parameters ] . ( 52 sec) [ -10146.3890] [Alpha ][ 0.926299] . ( 52 sec) [ -10141.9730] [ 2370] [depth= 1] . ( 53 sec) [ -10141.9341] [ 2371] [depth= 1] . ( 53 sec) [ -10141.9009] [ 2370] [depth= 1] . ( 54 sec) [ -10141.0617] [ 2365] [depth= 1] . ( 54 sec) [ -10140.4559] [ 2366] [depth= 1] . ( 54 sec) [ -10137.6579] [ 2371] [depth= 1] . ( 54 sec) [ -10137.5992] [ 2371] [depth= 1] . ( 55 sec) [ -10136.2718] [ 2363] [depth= 1] . ( 55 sec) [ -10135.3541] [ 2365] [depth= 1] . ( 56 sec) [ -10128.2168] [Branch lengths ] . ( 56 sec) [ -10128.1278] [GTR parameters ] . ( 56 sec) [ -10128.1261] [Alpha ][ 0.930112] . ( 60 sec) [ -10127.6984] [Branch lengths ] . ( 67 sec) [ -10127.6260] [ 2350] [depth= 1] . ( 75 sec) [ -10127.3138] [ 2346] [depth= 1] . ( 81 sec) [ -10126.8579] [Branch lengths ] . ( 81 sec) [ -10126.8555] [GTR parameters ] . ( 81 sec) [ -10126.8528] [Alpha ][ 0.934841] . ( 81 sec) [ -10126.8528] [Topology ] . ( 82 sec) [ -10126.7864] [Topology ] . ( 83 sec) [ -10126.7550] [Topology ] . ( 84 sec) [ -10126.7457] [Topology ] . ( 84 sec) [ -10126.7415] [Topology ] . ( 85 sec) [ -10126.7395] [Topology ] . ( 86 sec) [ -10126.7385] [Topology ] . ( 87 sec) [ -10126.7379] [Topology ] . ( 87 sec) [ -10126.7377] [GTR parameters ] . ( 87 sec) [ -10126.7376] [Alpha ][ 0.935776] . ( 87 sec) [ -10126.7376] [Topology ] . ( 88 sec) [ -10126.7373] [Topology ] . ( 88 sec) [ -10126.7373] [GTR parameters ] . ( 88 sec) [ -10126.7373] [Alpha ][ 0.935776] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -10126.6375] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10126.629534 . Log likelihood obtained after SPR moves : -10126.637464 . Log likelihood of the current tree: -10126.629534. . Printing the most likely tree in file 'data45.phy_phyml_tree.txt'... . Best log likelihood : -10126.629066 . Time used 0h1m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo