.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data63.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... . 407 patterns found. (out of a total of 500 sites) . 77 sites without polymorphism (15.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18611.9311] [GTR parameters ] . ( 1 sec) [ -18277.0055] [Alpha ][ 0.500960] . ( 1 sec) [ -18203.6994] [ 3769] [depth= 7] . ( 1 sec) [ -18200.1300] [ 3791] [depth= 1] . ( 1 sec) [ -17588.6480] [ 3712] [depth= 3] . ( 1 sec) [ -17568.0338] [ 3698] [depth= 2] . ( 1 sec) [ -17539.8283] [ 3685] [depth= 3] . ( 1 sec) [ -17471.6200] [ 3654] [depth= 1] . ( 1 sec) [ -17381.3469] [ 3633] [depth= 6] . ( 2 sec) [ -17317.0042] [ 3620] [depth= 6] . ( 2 sec) [ -17212.7071] [ 3601] [depth= 1] . ( 2 sec) [ -17117.9097] [ 3550] [depth= 5] . ( 2 sec) [ -16987.7862] [ 3552] [depth= 1] . ( 2 sec) [ -16848.9728] [ 3478] [depth= 6] . ( 2 sec) [ -16621.7306] [ 3482] [depth= 2] . ( 2 sec) [ -16457.2896] [ 3481] [depth= 2] . ( 2 sec) [ -16344.7826] [ 3430] [depth= 5] . ( 2 sec) [ -16136.9722] [ 3422] [depth= 7] . ( 2 sec) [ -16072.3954] [ 3396] [depth= 4] . ( 2 sec) [ -16045.2801] [ 3392] [depth= 1] . ( 2 sec) [ -15830.1248] [ 3369] [depth= 13] . ( 2 sec) [ -15790.6368] [ 3366] [depth= 1] . ( 2 sec) [ -15772.8620] [ 3362] [depth= 2] . ( 2 sec) [ -15723.6532] [ 3343] [depth= 11] . ( 2 sec) [ -15651.3042] [ 3329] [depth= 8] . ( 2 sec) [ -14977.8663] [ 3241] [depth= 1] . ( 3 sec) [ -14701.5390] [ 3214] [depth= 6] . ( 3 sec) [ -14606.1650] [ 3190] [depth= 9] . ( 3 sec) [ -14093.3439] [ 3099] [depth= 1] . ( 3 sec) [ -13826.8062] [ 3015] [depth= 12] . ( 3 sec) [ -13825.5619] [ 3016] [depth= 1] . ( 3 sec) [ -13795.4880] [ 3012] [depth= 1] . ( 3 sec) [ -13027.2882] [ 2879] [depth= 14] . ( 3 sec) [ -12923.6438] [ 2852] [depth= 11] . ( 3 sec) [ -12589.4209] [ 2760] [depth= 1] . ( 3 sec) [ -12319.3843] [ 2678] [depth= 8] . ( 3 sec) [ -11915.1949] [ 2676] [depth= 1] . ( 3 sec) [ -11617.5554] [ 2670] [depth= 1] . ( 3 sec) [ -11493.6702] [ 2563] [depth= 12] . ( 3 sec) [ -11228.8955] [ 2454] [depth= 10] . ( 3 sec) [ -10956.9200] [ 2395] [depth= 10] . ( 3 sec) [ -10956.1593] [ 2395] [depth= 1] . ( 3 sec) [ -10461.2581] [ 2388] [depth= 4] . ( 4 sec) [ -10411.3854] [ 2375] [depth= 1] . ( 4 sec) [ -10321.2056] [ 2361] [depth= 5] . ( 4 sec) [ -10286.0178] [ 2370] [depth= 1] . ( 4 sec) [ -10274.4625] [ 2361] [depth= 1] . ( 4 sec) [ -10175.4229] [ 2315] [depth= 8] . ( 4 sec) [ -10164.9778] [ 2324] [depth= 1] . ( 4 sec) [ -10063.5140] [ 2328] [depth= 1] . ( 4 sec) [ -10062.4791] [ 2331] [depth= 1] . ( 4 sec) [ -9998.9509] [ 2312] [depth= 1] . ( 4 sec) [ -9952.6077] [ 2280] [depth= 1] . ( 4 sec) [ -9924.5663] [ 2266] [depth= 1] . ( 4 sec) [ -9912.0493] [ 2258] [depth= 7] . ( 4 sec) [ -9902.3167] [ 2240] [depth= 1] . ( 4 sec) [ -9782.3185] [ 2201] [depth= 6] . ( 5 sec) [ -9591.5338] [ 2136] [depth= 10] . ( 5 sec) [ -9517.6515] [ 2139] [depth= 1] . ( 5 sec) [ -9444.6453] [ 2136] [depth= 1] . ( 5 sec) [ -9443.7437] [ 2139] [depth= 1] . ( 5 sec) [ -9214.0605] [ 2014] [depth= 12] . ( 5 sec) [ -9020.1996] [ 2007] [depth= 8] . ( 5 sec) [ -9018.6236] [ 1997] [depth= 1] . ( 5 sec) [ -8964.5381] [ 1991] [depth= 1] . ( 5 sec) [ -8715.0179] [ 1905] [depth= 3] . ( 5 sec) [ -8688.0535] [ 1898] [depth= 1] . ( 5 sec) [ -8672.6515] [ 1884] [depth= 2] . ( 5 sec) [ -8599.5955] [ 1869] [depth= 1] . ( 5 sec) [ -8571.0878] [ 1866] [depth= 1] . ( 5 sec) [ -8567.5363] [ 1865] [depth= 2] . ( 5 sec) [ -8472.2511] [ 1829] [depth= 1] . ( 5 sec) [ -8452.6363] [ 1822] [depth= 1] . ( 5 sec) [ -8389.7142] [ 1796] [depth= 6] . ( 5 sec) [ -8352.5728] [ 1778] [depth= 1] . ( 6 sec) [ -8344.8482] [ 1783] [depth= 1] . ( 6 sec) [ -8233.5896] [Branch lengths ] . ( 7 sec) [ -8231.5165] [GTR parameters ] . ( 7 sec) [ -8203.2763] [Alpha ][ 0.880747] . ( 7 sec) [ -8203.1574] [ 1764] [depth= 1] . ( 7 sec) [ -8165.0695] [ 1749] [depth= 3] . ( 7 sec) [ -8149.5010] [ 1747] [depth= 1] . ( 7 sec) [ -8149.3706] [ 1746] [depth= 1] . ( 7 sec) [ -8144.6587] [ 1737] [depth= 1] . ( 7 sec) [ -8121.3921] [ 1729] [depth= 1] . ( 7 sec) [ -8116.8726] [ 1726] [depth= 2] . ( 8 sec) [ -8116.4794] [ 1719] [depth= 3] . ( 8 sec) [ -8116.2198] [ 1719] [depth= 1] . ( 8 sec) [ -8116.0731] [ 1717] [depth= 1] . ( 9 sec) [ -8116.0294] [ 1725] [depth= 1] . ( 9 sec) [ -8114.7776] [ 1726] [depth= 1] . ( 9 sec) [ -8114.0021] [ 1722] [depth= 1] . ( 9 sec) [ -8102.9407] [ 1714] [depth= 1] . ( 9 sec) [ -8101.8531] [ 1718] [depth= 1] . ( 10 sec) [ -8101.7008] [ 1718] [depth= 1] . ( 10 sec) [ -8097.2506] [ 1714] [depth= 1] . ( 10 sec) [ -8084.6053] [Branch lengths ] . ( 11 sec) [ -8084.5718] [GTR parameters ] . ( 11 sec) [ -8083.1068] [Alpha ][ 1.007809] . ( 11 sec) [ -8083.0583] [ 1716] [depth= 1] . ( 12 sec) [ -8082.8295] [ 1708] [depth= 1] . ( 14 sec) [ -8081.3707] [Branch lengths ] . ( 15 sec) [ -8081.3699] [GTR parameters ] . ( 15 sec) [ -8081.3573] [Alpha ][ 1.020805] . ( 18 sec) [ -8080.4546] [Branch lengths ] . ( 42 sec) [ -8076.5522] [Branch lengths ] . ( 42 sec) [ -8076.5522] [Topology ] . ( 43 sec) [ -8074.4655] [Topology ] . ( 44 sec) [ -8073.9301] [Topology ] . ( 45 sec) [ -8073.8142] [Topology ] . ( 46 sec) [ -8073.7894] [Topology ] . ( 47 sec) [ -8073.7839] [Topology ] . ( 48 sec) [ -8073.7825] [Topology ] . ( 48 sec) [ -8073.7750] [GTR parameters ] . ( 48 sec) [ -8073.7750] [Alpha ][ 1.020805] . ( 49 sec) [ -8073.7750] [Topology ] . ( 49 sec) [ -8073.7746] [Topology ] . ( 49 sec) [ -8073.7746] [GTR parameters ] . ( 49 sec) [ -8073.7746] [Alpha ][ 1.020805] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -8073.3830] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -8073.3819] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8073.381860. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19040.7861] [GTR parameters ] . ( 1 sec) [ -18690.0136] [Alpha ][ 0.500960] . ( 1 sec) [ -18592.7602] [ 3897] [depth= 3] . ( 1 sec) [ -18060.3338] [ 3845] [depth= 3] . ( 1 sec) [ -17941.1598] [ 3830] [depth= 3] . ( 1 sec) [ -17863.9485] [ 3825] [depth= 6] . ( 1 sec) [ -17643.8762] [ 3773] [depth= 2] . ( 1 sec) [ -17457.8635] [ 3763] [depth= 9] . ( 1 sec) [ -17411.1736] [ 3750] [depth= 1] . ( 1 sec) [ -17403.7779] [ 3738] [depth= 8] . ( 1 sec) [ -17248.5978] [ 3694] [depth= 4] . ( 1 sec) [ -17199.6179] [ 3689] [depth= 1] . ( 2 sec) [ -17152.7524] [ 3684] [depth= 3] . ( 2 sec) [ -17099.8225] [ 3681] [depth= 3] . ( 2 sec) [ -16549.6454] [ 3609] [depth= 9] . ( 2 sec) [ -16222.0616] [ 3612] [depth= 3] . ( 2 sec) [ -16065.0125] [ 3558] [depth= 11] . ( 2 sec) [ -15998.9580] [ 3461] [depth= 2] . ( 2 sec) [ -15922.1386] [ 3434] [depth= 7] . ( 2 sec) [ -15885.3494] [ 3416] [depth= 2] . ( 2 sec) [ -15342.3976] [ 3429] [depth= 1] . ( 2 sec) [ -14855.3895] [ 3406] [depth= 5] . ( 2 sec) [ -14813.5138] [ 3340] [depth= 1] . ( 2 sec) [ -14419.9853] [ 3294] [depth= 14] . ( 2 sec) [ -14121.0861] [ 3198] [depth= 12] . ( 2 sec) [ -14101.2500] [ 3208] [depth= 1] . ( 2 sec) [ -13856.6717] [ 3202] [depth= 3] . ( 2 sec) [ -13581.8402] [ 3157] [depth= 8] . ( 2 sec) [ -13339.4341] [ 3127] [depth= 11] . ( 2 sec) [ -13005.5060] [ 3016] [depth= 6] . ( 2 sec) [ -12957.7349] [ 2980] [depth= 1] . ( 2 sec) [ -12777.4725] [ 2957] [depth= 4] . ( 2 sec) [ -12573.8827] [ 2881] [depth= 14] . ( 3 sec) [ -12556.9305] [ 2883] [depth= 1] . ( 3 sec) [ -12502.8900] [ 2940] [depth= 1] . ( 3 sec) [ -12205.0446] [ 2795] [depth= 12] . ( 3 sec) [ -12132.8493] [ 2798] [depth= 2] . ( 3 sec) [ -12110.1869] [ 2804] [depth= 2] . ( 3 sec) [ -11899.9506] [ 2734] [depth= 3] . ( 3 sec) [ -11817.9329] [ 2701] [depth= 7] . ( 3 sec) [ -11802.8215] [ 2704] [depth= 1] . ( 3 sec) [ -11494.8179] [ 2654] [depth= 4] . ( 3 sec) [ -11475.0960] [ 2650] [depth= 4] . ( 3 sec) [ -11430.0306] [ 2648] [depth= 4] . ( 3 sec) [ -11416.7856] [ 2654] [depth= 1] . ( 3 sec) [ -11011.3969] [ 2516] [depth= 4] . ( 3 sec) [ -10999.0654] [ 2513] [depth= 1] . ( 3 sec) [ -10879.3028] [ 2482] [depth= 5] . ( 3 sec) [ -10870.6617] [ 2476] [depth= 4] . ( 3 sec) [ -10812.0883] [ 2471] [depth= 1] . ( 3 sec) [ -10795.9027] [ 2426] [depth= 1] . ( 3 sec) [ -10768.8111] [ 2423] [depth= 1] . ( 3 sec) [ -10733.3437] [ 2415] [depth= 1] . ( 3 sec) [ -10698.3399] [ 2412] [depth= 2] . ( 3 sec) [ -10666.0260] [ 2404] [depth= 2] . ( 3 sec) [ -10447.8033] [ 2316] [depth= 2] . ( 4 sec) [ -10440.0583] [ 2306] [depth= 1] . ( 4 sec) [ -10399.3214] [ 2307] [depth= 5] . ( 4 sec) [ -10290.2553] [ 2256] [depth= 5] . ( 4 sec) [ -10288.8592] [ 2253] [depth= 1] . ( 4 sec) [ -10041.3441] [ 2191] [depth= 4] . ( 4 sec) [ -9978.8573] [ 2182] [depth= 3] . ( 4 sec) [ -9661.8262] [ 2152] [depth= 5] . ( 4 sec) [ -9500.8002] [ 2110] [depth= 2] . ( 4 sec) [ -9485.0818] [ 2109] [depth= 4] . ( 4 sec) [ -9360.5191] [ 2079] [depth= 5] . ( 4 sec) [ -9236.4542] [ 2041] [depth= 2] . ( 4 sec) [ -9081.7421] [ 1987] [depth= 3] . ( 4 sec) [ -9059.6768] [ 1988] [depth= 1] . ( 4 sec) [ -9050.8912] [ 1970] [depth= 1] . ( 4 sec) [ -9034.5245] [ 1965] [depth= 1] . ( 4 sec) [ -9032.8191] [ 1968] [depth= 2] . ( 4 sec) [ -8972.4488] [ 1917] [depth= 3] . ( 4 sec) [ -8843.6182] [ 1876] [depth= 3] . ( 4 sec) [ -8817.6364] [ 1869] [depth= 1] . ( 5 sec) [ -8784.6847] [ 1868] [depth= 4] . ( 5 sec) [ -8767.8614] [ 1863] [depth= 1] . ( 5 sec) [ -8699.6778] [ 1819] [depth= 1] . ( 5 sec) [ -8606.7116] [ 1824] [depth= 1] . ( 5 sec) [ -8413.4288] [ 1800] [depth= 1] . ( 5 sec) [ -8381.8875] [ 1772] [depth= 1] . ( 5 sec) [ -8300.0805] [ 1742] [depth= 4] . ( 5 sec) [ -8299.9744] [ 1734] [depth= 5] . ( 5 sec) [ -8286.4329] [ 1735] [depth= 1] . ( 5 sec) [ -8283.2285] [ 1728] [depth= 1] . ( 5 sec) [ -8165.5757] [Branch lengths ] . ( 6 sec) [ -8159.8048] [GTR parameters ] . ( 6 sec) [ -8129.4502] [Alpha ][ 0.908760] . ( 6 sec) [ -8120.3413] [ 1710] [depth= 1] . ( 6 sec) [ -8119.9982] [ 1708] [depth= 1] . ( 6 sec) [ -8119.4650] [ 1715] [depth= 1] . ( 6 sec) [ -8112.5291] [ 1713] [depth= 2] . ( 7 sec) [ -8112.4487] [ 1713] [depth= 1] . ( 7 sec) [ -8112.3629] [ 1713] [depth= 1] . ( 7 sec) [ -8112.2500] [ 1706] [depth= 1] . ( 7 sec) [ -8112.2168] [ 1706] [depth= 1] . ( 7 sec) [ -8110.6501] [ 1707] [depth= 1] . ( 7 sec) [ -8106.9030] [ 1706] [depth= 1] . ( 8 sec) [ -8106.7954] [ 1706] [depth= 1] . ( 8 sec) [ -8103.6865] [ 1710] [depth= 1] . ( 8 sec) [ -8092.4692] [ 1702] [depth= 1] . ( 9 sec) [ -8083.8136] [Branch lengths ] . ( 10 sec) [ -8083.7555] [GTR parameters ] . ( 10 sec) [ -8082.9096] [Alpha ][ 1.007452] . ( 10 sec) [ -8082.5579] [ 1710] [depth= 1] . ( 12 sec) [ -8081.5183] [ 1708] [depth= 1] . ( 12 sec) [ -8079.4427] [ 1708] [depth= 1] . ( 13 sec) [ -8077.0475] [Branch lengths ] . ( 13 sec) [ -8077.0392] [GTR parameters ] . ( 14 sec) [ -8077.0267] [Alpha ][ 1.020471] . ( 17 sec) [ -8075.2076] [Branch lengths ] . ( 31 sec) [ -8074.8472] [ 1715] [depth= 2] . ( 39 sec) [ -8073.5167] [Branch lengths ] . ( 39 sec) [ -8073.5026] [GTR parameters ] . ( 39 sec) [ -8073.5026] [Alpha ][ 1.019451] . ( 61 sec) [ -8073.3719] [Branch lengths ] . ( 61 sec) [ -8073.3719] [Topology ] . ( 62 sec) [ -8073.3704] [Topology ] . ( 63 sec) [ -8073.3702] [Topology ] . ( 63 sec) [ -8073.3701] [GTR parameters ] . ( 63 sec) [ -8073.3701] [Alpha ][ 1.018431] . ( 63 sec) [ -8073.3701] [Topology ] . ( 64 sec) [ -8073.3700] [Topology ] . ( 64 sec) [ -8073.3700] [GTR parameters ] . ( 64 sec) [ -8073.3700] [Alpha ][ 1.018431] . Checking for NNIs, optimizing five branches... . ( 69 sec) [ -8073.3698] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8073.369850. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19090.5586] [GTR parameters ] . ( 1 sec) [ -18725.2317] [Alpha ][ 0.500960] . ( 1 sec) [ -18587.1225] [ 3907] [depth= 1] . ( 1 sec) [ -18173.2295] [ 3833] [depth= 8] . ( 1 sec) [ -18060.2087] [ 3815] [depth= 3] . ( 1 sec) [ -17935.5696] [ 3811] [depth= 3] . ( 1 sec) [ -17570.2804] [ 3747] [depth= 4] . ( 1 sec) [ -17309.5786] [ 3742] [depth= 3] . ( 1 sec) [ -16277.7858] [ 3582] [depth= 8] . ( 1 sec) [ -16257.2482] [ 3569] [depth= 5] . ( 1 sec) [ -15964.0471] [ 3471] [depth= 3] . ( 1 sec) [ -15891.9903] [ 3455] [depth= 13] . ( 1 sec) [ -15615.0865] [ 3449] [depth= 1] . ( 1 sec) [ -15584.9755] [ 3373] [depth= 8] . ( 1 sec) [ -15227.7995] [ 3368] [depth= 3] . ( 1 sec) [ -15209.6712] [ 3371] [depth= 1] . ( 1 sec) [ -15158.8287] [ 3365] [depth= 1] . ( 1 sec) [ -15137.1178] [ 3359] [depth= 2] . ( 1 sec) [ -14974.5690] [ 3346] [depth= 2] . ( 1 sec) [ -14889.7596] [ 3307] [depth= 2] . ( 1 sec) [ -14734.9882] [ 3298] [depth= 13] . ( 1 sec) [ -14519.9363] [ 3255] [depth= 10] . ( 1 sec) [ -13906.6990] [ 3079] [depth= 6] . ( 2 sec) [ -13703.9245] [ 3079] [depth= 14] . ( 2 sec) [ -13637.9055] [ 3027] [depth= 1] . ( 2 sec) [ -13432.5125] [ 2952] [depth= 9] . ( 2 sec) [ -13165.1500] [ 2901] [depth= 8] . ( 2 sec) [ -13164.2248] [ 2900] [depth= 2] . ( 2 sec) [ -13154.2494] [ 2896] [depth= 3] . ( 2 sec) [ -13137.8288] [ 2885] [depth= 14] . ( 2 sec) [ -13124.4493] [ 2879] [depth= 2] . ( 2 sec) [ -12660.2907] [ 2747] [depth= 10] . ( 2 sec) [ -12559.5873] [ 2662] [depth= 8] . ( 2 sec) [ -12171.8952] [ 2604] [depth= 7] . ( 2 sec) [ -11666.4455] [ 2615] [depth= 6] . ( 2 sec) [ -11663.1556] [ 2619] [depth= 1] . ( 2 sec) [ -11602.1224] [ 2611] [depth= 3] . ( 2 sec) [ -11587.1831] [ 2611] [depth= 1] . ( 2 sec) [ -11343.2134] [ 2493] [depth= 7] . ( 2 sec) [ -11333.5297] [ 2477] [depth= 1] . ( 2 sec) [ -11292.8371] [ 2476] [depth= 1] . ( 2 sec) [ -11279.1640] [ 2474] [depth= 2] . ( 2 sec) [ -11167.2347] [ 2463] [depth= 6] . ( 3 sec) [ -10943.6647] [ 2427] [depth= 6] . ( 3 sec) [ -10937.4151] [ 2415] [depth= 6] . ( 3 sec) [ -10924.6926] [ 2409] [depth= 2] . ( 3 sec) [ -10893.2477] [ 2406] [depth= 3] . ( 3 sec) [ -10860.6572] [ 2383] [depth= 4] . ( 3 sec) [ -10743.9532] [ 2373] [depth= 8] . ( 3 sec) [ -10661.9262] [ 2401] [depth= 12] . ( 3 sec) [ -10655.3577] [ 2395] [depth= 1] . ( 3 sec) [ -10556.8087] [ 2393] [depth= 1] . ( 3 sec) [ -10532.1139] [ 2389] [depth= 3] . ( 3 sec) [ -10432.1514] [ 2328] [depth= 2] . ( 3 sec) [ -10382.1681] [ 2323] [depth= 4] . ( 3 sec) [ -10222.1693] [ 2273] [depth= 7] . ( 3 sec) [ -10178.4425] [ 2255] [depth= 7] . ( 3 sec) [ -10072.4033] [ 2241] [depth= 6] . ( 3 sec) [ -9680.3758] [ 2148] [depth= 5] . ( 3 sec) [ -9675.8161] [ 2149] [depth= 1] . ( 3 sec) [ -9620.6928] [ 2099] [depth= 1] . ( 3 sec) [ -9601.6260] [ 2103] [depth= 2] . ( 3 sec) [ -9395.1447] [ 2060] [depth= 10] . ( 4 sec) [ -9291.1933] [ 2046] [depth= 3] . ( 4 sec) [ -9254.3753] [ 2056] [depth= 1] . ( 4 sec) [ -9236.7756] [ 2048] [depth= 1] . ( 4 sec) [ -9227.9928] [ 2038] [depth= 1] . ( 4 sec) [ -9160.0598] [ 2015] [depth= 1] . ( 4 sec) [ -9149.2376] [ 2009] [depth= 1] . ( 4 sec) [ -8983.5192] [ 2026] [depth= 1] . ( 4 sec) [ -8976.4610] [ 2009] [depth= 1] . ( 4 sec) [ -8874.3975] [ 1936] [depth= 6] . ( 4 sec) [ -8792.6617] [ 1914] [depth= 6] . ( 4 sec) [ -8786.7044] [ 1904] [depth= 1] . ( 4 sec) [ -8774.8346] [ 1914] [depth= 1] . ( 4 sec) [ -8757.9206] [ 1911] [depth= 2] . ( 4 sec) [ -8686.0557] [ 1908] [depth= 2] . ( 4 sec) [ -8630.0657] [ 1879] [depth= 3] . ( 4 sec) [ -8548.0744] [ 1855] [depth= 3] . ( 4 sec) [ -8495.5790] [ 1851] [depth= 2] . ( 4 sec) [ -8495.2727] [ 1846] [depth= 1] . ( 5 sec) [ -8372.5373] [Branch lengths ] . ( 5 sec) [ -8369.7701] [GTR parameters ] . ( 5 sec) [ -8341.6980] [Alpha ][ 0.874842] . ( 5 sec) [ -8242.5449] [ 1806] [depth= 7] . ( 5 sec) [ -8169.7758] [ 1745] [depth= 6] . ( 5 sec) [ -8168.5555] [ 1743] [depth= 1] . ( 5 sec) [ -8167.8334] [ 1736] [depth= 1] . ( 6 sec) [ -8166.0873] [ 1730] [depth= 1] . ( 6 sec) [ -8166.0249] [ 1730] [depth= 1] . ( 6 sec) [ -8161.5050] [ 1731] [depth= 3] . ( 6 sec) [ -8160.4561] [ 1729] [depth= 1] . ( 6 sec) [ -8160.4410] [ 1729] [depth= 1] . ( 6 sec) [ -8154.1288] [ 1728] [depth= 1] . ( 6 sec) [ -8153.9837] [ 1734] [depth= 1] . ( 6 sec) [ -8148.2151] [ 1727] [depth= 1] . ( 6 sec) [ -8147.9333] [ 1727] [depth= 2] . ( 6 sec) [ -8147.2487] [ 1727] [depth= 1] . ( 7 sec) [ -8147.1148] [ 1729] [depth= 1] . ( 7 sec) [ -8146.9465] [ 1729] [depth= 1] . ( 7 sec) [ -8141.1659] [ 1725] [depth= 1] . ( 7 sec) [ -8136.3166] [ 1727] [depth= 1] . ( 7 sec) [ -8135.6208] [ 1730] [depth= 2] . ( 7 sec) [ -8134.3869] [ 1724] [depth= 1] . ( 7 sec) [ -8129.1405] [ 1718] [depth= 1] . ( 8 sec) [ -8121.8073] [ 1708] [depth= 2] . ( 9 sec) [ -8098.4378] [Branch lengths ] . ( 9 sec) [ -8098.2044] [GTR parameters ] . ( 9 sec) [ -8097.0337] [Alpha ][ 0.985326] . ( 9 sec) [ -8096.9365] [ 1701] [depth= 1] . ( 12 sec) [ -8093.0069] [Branch lengths ] . ( 13 sec) [ -8093.0039] [GTR parameters ] . ( 13 sec) [ -8092.9469] [Alpha ][ 1.011443] . ( 16 sec) [ -8092.5523] [Branch lengths ] . ( 20 sec) [ -8092.2546] [ 1710] [depth= 1] . ( 30 sec) [ -8089.0028] [ 1708] [depth= 1] . ( 38 sec) [ -8088.3733] [Branch lengths ] . ( 38 sec) [ -8088.3649] [GTR parameters ] . ( 38 sec) [ -8088.3625] [Alpha ][ 1.017078] . ( 52 sec) [ -8087.9602] [ 1714] [depth= 3] . ( 60 sec) [ -8087.7789] [Branch lengths ] . ( 60 sec) [ -8087.7707] [GTR parameters ] . ( 60 sec) [ -8087.7704] [Alpha ][ 1.015045] . ( 60 sec) [ -8087.7704] [Topology ] . ( 61 sec) [ -8087.6370] [Topology ] . ( 62 sec) [ -8086.7318] [Topology ] . ( 62 sec) [ -8082.7269] [Topology ] . ( 63 sec) [ -8076.3839] [Topology ] . ( 64 sec) [ -8074.2567] [Topology ] . ( 64 sec) [ -8073.6477] [Topology ] . ( 65 sec) [ -8073.6266] [GTR parameters ] . ( 65 sec) [ -8073.6257] [Alpha ][ 1.018596] . ( 65 sec) [ -8073.6257] [Topology ] . ( 66 sec) [ -8073.4443] [Topology ] . ( 66 sec) [ -8073.3917] [Topology ] . ( 67 sec) [ -8073.3765] [Topology ] . ( 68 sec) [ -8073.3720] [Topology ] . ( 69 sec) [ -8073.3707] [Topology ] . ( 69 sec) [ -8073.3703] [Topology ] . ( 70 sec) [ -8073.3701] [GTR parameters ] . ( 70 sec) [ -8073.3701] [Alpha ][ 1.018596] . ( 70 sec) [ -8073.3701] [Topology ] . ( 70 sec) [ -8073.3700] [Topology ] . ( 70 sec) [ -8073.3699] [GTR parameters ] . ( 71 sec) [ -8073.3699] [Alpha ][ 1.018596] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -8073.3696] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8073.369649. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18346.5452] [GTR parameters ] . ( 1 sec) [ -18006.4465] [Alpha ][ 0.500960] . ( 1 sec) [ -17787.0725] [ 3761] [depth= 8] . ( 1 sec) [ -17365.5622] [ 3705] [depth= 9] . ( 1 sec) [ -17056.1549] [ 3642] [depth= 3] . ( 1 sec) [ -17042.6924] [ 3637] [depth= 1] . ( 1 sec) [ -16792.5661] [ 3563] [depth= 9] . ( 1 sec) [ -16613.9894] [ 3552] [depth= 3] . ( 1 sec) [ -16458.8277] [ 3545] [depth= 4] . ( 1 sec) [ -16181.4049] [ 3502] [depth= 5] . ( 1 sec) [ -15976.9387] [ 3484] [depth= 2] . ( 2 sec) [ -15876.3421] [ 3473] [depth= 4] . ( 2 sec) [ -15617.9320] [ 3478] [depth= 9] . ( 2 sec) [ -15298.5561] [ 3386] [depth= 10] . ( 2 sec) [ -15225.2430] [ 3354] [depth= 6] . ( 2 sec) [ -15145.8992] [ 3351] [depth= 5] . ( 2 sec) [ -14959.4523] [ 3352] [depth= 5] . ( 2 sec) [ -14868.4576] [ 3338] [depth= 14] . ( 2 sec) [ -14728.1127] [ 3336] [depth= 1] . ( 2 sec) [ -14477.1197] [ 3230] [depth= 19] . ( 2 sec) [ -14434.5888] [ 3221] [depth= 2] . ( 2 sec) [ -14374.0869] [ 3192] [depth= 9] . ( 2 sec) [ -14345.9579] [ 3194] [depth= 10] . ( 2 sec) [ -14171.0530] [ 3145] [depth= 1] . ( 2 sec) [ -14157.6821] [ 3145] [depth= 3] . ( 2 sec) [ -14103.4169] [ 3136] [depth= 4] . ( 2 sec) [ -14101.4273] [ 3136] [depth= 1] . ( 2 sec) [ -14077.7865] [ 3126] [depth= 1] . ( 2 sec) [ -13929.6406] [ 3082] [depth= 6] . ( 2 sec) [ -13543.5182] [ 2991] [depth= 16] . ( 2 sec) [ -13227.7795] [ 2896] [depth= 9] . ( 2 sec) [ -12404.2295] [ 2820] [depth= 8] . ( 2 sec) [ -12123.6651] [ 2777] [depth= 1] . ( 2 sec) [ -11945.3379] [ 2760] [depth= 6] . ( 3 sec) [ -11899.6972] [ 2727] [depth= 1] . ( 3 sec) [ -11894.6175] [ 2727] [depth= 1] . ( 3 sec) [ -11801.4442] [ 2718] [depth= 1] . ( 3 sec) [ -11772.2314] [ 2727] [depth= 1] . ( 3 sec) [ -11694.0680] [ 2665] [depth= 1] . ( 3 sec) [ -11574.5819] [ 2662] [depth= 4] . ( 3 sec) [ -11511.1513] [ 2650] [depth= 3] . ( 3 sec) [ -11469.8735] [ 2642] [depth= 1] . ( 3 sec) [ -11365.1627] [ 2625] [depth= 3] . ( 3 sec) [ -11311.1732] [ 2618] [depth= 1] . ( 3 sec) [ -11223.2246] [ 2573] [depth= 5] . ( 3 sec) [ -11188.6330] [ 2561] [depth= 1] . ( 3 sec) [ -11102.5445] [ 2547] [depth= 7] . ( 3 sec) [ -10976.1688] [ 2458] [depth= 5] . ( 3 sec) [ -10799.2842] [ 2448] [depth= 3] . ( 3 sec) [ -10779.0214] [ 2441] [depth= 1] . ( 3 sec) [ -10759.0077] [ 2414] [depth= 3] . ( 3 sec) [ -10585.9209] [ 2410] [depth= 2] . ( 3 sec) [ -10467.0772] [ 2384] [depth= 12] . ( 3 sec) [ -10233.3445] [ 2301] [depth= 1] . ( 3 sec) [ -10233.2868] [ 2296] [depth= 1] . ( 4 sec) [ -10189.2960] [ 2285] [depth= 1] . ( 4 sec) [ -10186.3823] [ 2273] [depth= 1] . ( 4 sec) [ -10127.5399] [ 2267] [depth= 1] . ( 4 sec) [ -9868.0994] [ 2265] [depth= 6] . ( 4 sec) [ -9829.9298] [ 2185] [depth= 1] . ( 4 sec) [ -9636.4911] [ 2106] [depth= 3] . ( 4 sec) [ -9612.1920] [ 2096] [depth= 5] . ( 4 sec) [ -9323.0215] [ 2040] [depth= 7] . ( 4 sec) [ -9289.5361] [ 2025] [depth= 3] . ( 4 sec) [ -9223.7065] [ 2006] [depth= 3] . ( 4 sec) [ -9209.1841] [ 2008] [depth= 1] . ( 4 sec) [ -9165.7754] [ 2004] [depth= 6] . ( 4 sec) [ -9157.8022] [ 2010] [depth= 1] . ( 4 sec) [ -9015.1673] [ 2000] [depth= 1] . ( 4 sec) [ -9013.9002] [ 2001] [depth= 1] . ( 4 sec) [ -8936.4963] [ 1986] [depth= 1] . ( 4 sec) [ -8911.0809] [ 1967] [depth= 1] . ( 4 sec) [ -8908.7910] [ 1972] [depth= 1] . ( 4 sec) [ -8904.6521] [ 2029] [depth= 1] . ( 4 sec) [ -8800.9158] [ 1950] [depth= 2] . ( 4 sec) [ -8735.5741] [ 1942] [depth= 3] . ( 5 sec) [ -8730.7139] [ 1947] [depth= 2] . ( 5 sec) [ -8711.6805] [ 1951] [depth= 3] . ( 5 sec) [ -8704.0760] [ 1911] [depth= 2] . ( 5 sec) [ -8597.8363] [ 1863] [depth= 2] . ( 5 sec) [ -8593.0053] [ 1860] [depth= 1] . ( 5 sec) [ -8420.1870] [Branch lengths ] . ( 6 sec) [ -8417.2494] [GTR parameters ] . ( 6 sec) [ -8390.6661] [Alpha ][ 0.850595] . ( 6 sec) [ -8227.2541] [ 1820] [depth= 4] . ( 6 sec) [ -8221.1334] [ 1819] [depth= 1] . ( 6 sec) [ -8221.0355] [ 1814] [depth= 1] . ( 6 sec) [ -8191.0039] [ 1793] [depth= 2] . ( 6 sec) [ -8189.4525] [ 1795] [depth= 1] . ( 6 sec) [ -8174.2193] [ 1785] [depth= 2] . ( 7 sec) [ -8174.0539] [ 1785] [depth= 1] . ( 7 sec) [ -8173.6720] [ 1788] [depth= 1] . ( 7 sec) [ -8172.7333] [ 1793] [depth= 1] . ( 7 sec) [ -8170.6601] [ 1790] [depth= 1] . ( 7 sec) [ -8170.4755] [ 1795] [depth= 1] . ( 7 sec) [ -8168.3705] [ 1792] [depth= 1] . ( 7 sec) [ -8167.8781] [ 1791] [depth= 2] . ( 7 sec) [ -8162.5397] [ 1791] [depth= 1] . ( 7 sec) [ -8161.1567] [ 1789] [depth= 2] . ( 8 sec) [ -8158.2778] [ 1784] [depth= 1] . ( 8 sec) [ -8150.1893] [ 1776] [depth= 2] . ( 8 sec) [ -8139.6727] [ 1764] [depth= 1] . ( 8 sec) [ -8133.5627] [ 1761] [depth= 1] . ( 8 sec) [ -8132.4460] [ 1746] [depth= 1] . ( 8 sec) [ -8132.2413] [ 1746] [depth= 1] . ( 8 sec) [ -8127.8738] [ 1740] [depth= 1] . ( 8 sec) [ -8100.3945] [ 1698] [depth= 2] . ( 8 sec) [ -8100.2005] [ 1698] [depth= 1] . ( 9 sec) [ -8099.3466] [ 1703] [depth= 1] . ( 9 sec) [ -8095.3641] [ 1698] [depth= 1] . ( 9 sec) [ -8083.9012] [Branch lengths ] . ( 10 sec) [ -8083.7327] [GTR parameters ] . ( 10 sec) [ -8081.4835] [Alpha ][ 1.003902] . ( 10 sec) [ -8079.7917] [ 1702] [depth= 1] . ( 12 sec) [ -8075.7357] [ 1706] [depth= 2] . ( 13 sec) [ -8073.9029] [Branch lengths ] . ( 14 sec) [ -8073.8936] [GTR parameters ] . ( 14 sec) [ -8073.8703] [Alpha ][ 1.021631] . ( 17 sec) [ -8073.7884] [Branch lengths ] . ( 33 sec) [ -8073.4208] [ 1715] [depth= 3] . ( 39 sec) [ -8073.3824] [Branch lengths ] . ( 39 sec) [ -8073.3731] [GTR parameters ] . ( 39 sec) [ -8073.3727] [Alpha ][ 1.019228] . ( 39 sec) [ -8073.3727] [Topology ] . ( 40 sec) [ -8073.3710] [Topology ] . ( 41 sec) [ -8073.3704] [Topology ] . ( 41 sec) [ -8073.3704] [GTR parameters ] . ( 41 sec) [ -8073.3704] [Alpha ][ 1.019228] . ( 41 sec) [ -8073.3704] [Topology ] . ( 42 sec) [ -8073.3701] [Topology ] . ( 42 sec) [ -8073.3701] [GTR parameters ] . ( 42 sec) [ -8073.3701] [Alpha ][ 1.019228] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -8073.3700] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8073.369951. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18588.9728] [GTR parameters ] . ( 1 sec) [ -18235.6039] [Alpha ][ 0.500960] . ( 1 sec) [ -18206.2432] [ 3963] [depth= 6] . ( 1 sec) [ -17966.7869] [ 3896] [depth= 11] . ( 1 sec) [ -17890.7005] [ 3885] [depth= 5] . ( 1 sec) [ -17882.4622] [ 3883] [depth= 1] . ( 1 sec) [ -17605.3749] [ 3811] [depth= 8] . ( 1 sec) [ -17465.5451] [ 3812] [depth= 7] . ( 1 sec) [ -17310.3594] [ 3785] [depth= 6] . ( 1 sec) [ -17240.5924] [ 3792] [depth= 1] . ( 1 sec) [ -16860.7013] [ 3739] [depth= 2] . ( 1 sec) [ -16618.0399] [ 3676] [depth= 11] . ( 1 sec) [ -16206.8454] [ 3520] [depth= 6] . ( 1 sec) [ -16069.8178] [ 3492] [depth= 12] . ( 1 sec) [ -15878.3476] [ 3434] [depth= 5] . ( 1 sec) [ -15761.0508] [ 3411] [depth= 1] . ( 1 sec) [ -15468.1213] [ 3393] [depth= 7] . ( 1 sec) [ -15449.4743] [ 3384] [depth= 1] . ( 1 sec) [ -15425.4804] [ 3371] [depth= 11] . ( 1 sec) [ -15363.5040] [ 3329] [depth= 1] . ( 1 sec) [ -15212.9318] [ 3325] [depth= 2] . ( 1 sec) [ -14946.1951] [ 3247] [depth= 10] . ( 1 sec) [ -14905.5829] [ 3235] [depth= 1] . ( 1 sec) [ -14855.8412] [ 3227] [depth= 5] . ( 2 sec) [ -14654.5286] [ 3178] [depth= 7] . ( 2 sec) [ -14654.3117] [ 3182] [depth= 1] . ( 2 sec) [ -14432.1171] [ 3165] [depth= 6] . ( 2 sec) [ -14361.9820] [ 3104] [depth= 1] . ( 2 sec) [ -14139.5992] [ 3038] [depth= 9] . ( 2 sec) [ -13306.2493] [ 2981] [depth= 3] . ( 2 sec) [ -13166.9420] [ 2986] [depth= 7] . ( 2 sec) [ -13066.5184] [ 2968] [depth= 3] . ( 2 sec) [ -12953.4594] [ 2926] [depth= 11] . ( 2 sec) [ -12914.1742] [ 2842] [depth= 1] . ( 2 sec) [ -12899.3240] [ 2821] [depth= 2] . ( 2 sec) [ -12866.0060] [ 2812] [depth= 10] . ( 2 sec) [ -12785.5936] [ 2809] [depth= 8] . ( 2 sec) [ -12513.0645] [ 2696] [depth= 1] . ( 2 sec) [ -12477.3952] [ 2682] [depth= 3] . ( 2 sec) [ -12277.9244] [ 2631] [depth= 9] . ( 2 sec) [ -12194.5744] [ 2616] [depth= 1] . ( 2 sec) [ -12186.5745] [ 2621] [depth= 1] . ( 2 sec) [ -12181.9329] [ 2614] [depth= 3] . ( 2 sec) [ -11932.9998] [ 2532] [depth= 7] . ( 2 sec) [ -11734.0422] [ 2446] [depth= 6] . ( 2 sec) [ -11615.1662] [ 2413] [depth= 1] . ( 3 sec) [ -11574.5766] [ 2404] [depth= 1] . ( 3 sec) [ -11565.0157] [ 2404] [depth= 1] . ( 3 sec) [ -11425.8603] [ 2403] [depth= 3] . ( 3 sec) [ -11361.5511] [ 2395] [depth= 5] . ( 3 sec) [ -11356.6764] [ 2389] [depth= 1] . ( 3 sec) [ -11349.2639] [ 2391] [depth= 2] . ( 3 sec) [ -11344.5727] [ 2390] [depth= 1] . ( 3 sec) [ -11316.4607] [ 2383] [depth= 1] . ( 3 sec) [ -11311.1568] [ 2378] [depth= 1] . ( 3 sec) [ -11156.5320] [ 2371] [depth= 2] . ( 3 sec) [ -11041.0190] [ 2316] [depth= 6] . ( 3 sec) [ -11003.8169] [ 2308] [depth= 1] . ( 3 sec) [ -10808.2354] [ 2209] [depth= 6] . ( 3 sec) [ -10758.2642] [ 2192] [depth= 3] . ( 3 sec) [ -10551.6305] [ 2147] [depth= 1] . ( 3 sec) [ -10523.0599] [ 2145] [depth= 1] . ( 3 sec) [ -10509.1089] [ 2144] [depth= 3] . ( 3 sec) [ -10505.3401] [ 2146] [depth= 1] . ( 3 sec) [ -10338.0738] [ 2043] [depth= 3] . ( 3 sec) [ -10328.0688] [ 2047] [depth= 1] . ( 3 sec) [ -10290.0357] [ 2038] [depth= 1] . ( 4 sec) [ -10256.2136] [ 2000] [depth= 4] . ( 4 sec) [ -9872.6210] [ 1916] [depth= 5] . ( 4 sec) [ -9819.2557] [ 1938] [depth= 1] . ( 4 sec) [ -9711.7097] [ 1960] [depth= 4] . ( 4 sec) [ -9703.7231] [ 1961] [depth= 2] . ( 4 sec) [ -9400.9352] [ 1784] [depth= 7] . ( 4 sec) [ -9366.2297] [ 1781] [depth= 1] . ( 4 sec) [ -9360.1072] [ 1777] [depth= 2] . ( 4 sec) [ -9346.6415] [ 1783] [depth= 1] . ( 4 sec) [ -9332.9071] [ 1777] [depth= 1] . ( 4 sec) [ -9279.6094] [ 1772] [depth= 3] . ( 4 sec) [ -8487.6319] [ 1768] [depth= 3] . ( 4 sec) [ -8469.7720] [ 1768] [depth= 1] . ( 4 sec) [ -8466.2570] [ 1747] [depth= 5] . ( 4 sec) [ -8461.2830] [ 1742] [depth= 1] . ( 4 sec) [ -8449.8606] [ 1749] [depth= 1] . ( 4 sec) [ -8393.3707] [ 1712] [depth= 1] . ( 5 sec) [ -8309.2936] [ 1711] [depth= 1] . ( 5 sec) [ -8168.3934] [Branch lengths ] . ( 5 sec) [ -8163.3361] [GTR parameters ] . ( 5 sec) [ -8129.3604] [Alpha ][ 0.936226] . ( 6 sec) [ -8129.2943] [ 1716] [depth= 1] . ( 6 sec) [ -8126.2685] [ 1712] [depth= 1] . ( 6 sec) [ -8114.2179] [ 1706] [depth= 1] . ( 6 sec) [ -8113.9077] [ 1706] [depth= 1] . ( 6 sec) [ -8112.2793] [ 1703] [depth= 1] . ( 7 sec) [ -8112.1910] [ 1703] [depth= 1] . ( 7 sec) [ -8107.1748] [ 1698] [depth= 1] . ( 7 sec) [ -8104.7947] [ 1705] [depth= 1] . ( 8 sec) [ -8104.6871] [ 1698] [depth= 1] . ( 8 sec) [ -8104.6267] [ 1698] [depth= 1] . ( 9 sec) [ -8100.9994] [ 1702] [depth= 1] . ( 9 sec) [ -8097.2515] [ 1706] [depth= 2] . ( 9 sec) [ -8089.5122] [Branch lengths ] . ( 9 sec) [ -8089.4205] [GTR parameters ] . ( 10 sec) [ -8088.9806] [Alpha ][ 1.008119] . ( 13 sec) [ -8086.0430] [Branch lengths ] . ( 23 sec) [ -8085.9446] [ 1706] [depth= 1] . ( 33 sec) [ -8085.5645] [ 1715] [depth= 3] . ( 35 sec) [ -8076.7018] [Branch lengths ] . ( 35 sec) [ -8076.6889] [GTR parameters ] . ( 35 sec) [ -8076.6825] [Alpha ][ 1.017339] . ( 39 sec) [ -8076.6381] [ 1715] [depth= 1] . ( 45 sec) [ -8076.4676] [ 1715] [depth= 1] . ( 57 sec) [ -8073.3746] [Branch lengths ] . ( 57 sec) [ -8073.3736] [GTR parameters ] . ( 57 sec) [ -8073.3735] [Alpha ][ 1.018507] . ( 79 sec) [ -8073.3702] [Branch lengths ] . ( 79 sec) [ -8073.3702] [Topology ] . ( 80 sec) [ -8073.3700] [Topology ] . ( 80 sec) [ -8073.3700] [GTR parameters ] . ( 80 sec) [ -8073.3700] [Alpha ][ 1.018507] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -8073.3699] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8073.369907. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8115.972555 . ( 0 sec) [ -8113.9827] [GTR parameters ] . ( 0 sec) [ -8113.8648] [Alpha ][ 1.041976] . ( 0 sec) [ -8113.8648] [Topology ] . ( 1 sec) [ -8081.6555] [Topology ] . ( 2 sec) [ -8076.8135] [Topology ] . ( 3 sec) [ -8075.2238] [Topology ] . ( 3 sec) [ -8074.5381] [Topology ] . ( 4 sec) [ -8074.2089] [Topology ] . ( 5 sec) [ -8074.0419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8074.041867 . ( 11 sec) [ -8074.0065] [GTR parameters ] . ( 11 sec) [ -8073.9835] [Alpha ][ 1.024630] . ( 11 sec) [ -8073.9835] [Topology ] . ( 12 sec) [ -8073.8911] [Topology ] . ( 13 sec) [ -8073.8417] [Topology ] . ( 13 sec) [ -8073.8141] [Topology ] . ( 14 sec) [ -8073.7984] [Topology ] . ( 15 sec) [ -8073.7893] [Topology ] . ( 16 sec) [ -8073.7839] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8073.783940 . ( 22 sec) [ -8073.7837] [GTR parameters ] . ( 22 sec) [ -8073.7832] [Alpha ][ 1.021692] . ( 22 sec) [ -8073.7832] [Topology ] . ( 22 sec) [ -8073.7798] [Topology ] . ( 23 sec) [ -8073.7777] [Topology ] . ( 24 sec) [ -8073.7764] [Topology ] . ( 25 sec) [ -8073.7756] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8073.775626 . ( 30 sec) [ -8073.7756] [GTR parameters ] . ( 30 sec) [ -8073.7756] [Alpha ][ 1.021692] . ( 30 sec) [ -8073.7756] [Topology ] . ( 31 sec) [ -8073.7751] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -8113.9827] [GTR parameters ] . ( 43 sec) [ -8113.8648] [Alpha ][ 1.041976] . ( 43 sec) [ -8112.9208] [ 1713] [depth= 1] . ( 43 sec) [ -8112.7853] [ 1714] [depth= 1] . ( 44 sec) [ -8111.9149] [ 1716] [depth= 1] . ( 44 sec) [ -8111.1914] [ 1714] [depth= 1] . ( 44 sec) [ -8111.1500] [ 1716] [depth= 1] . ( 44 sec) [ -8105.6202] [ 1715] [depth= 1] . ( 44 sec) [ -8105.5369] [ 1715] [depth= 1] . ( 44 sec) [ -8103.2695] [ 1716] [depth= 1] . ( 44 sec) [ -8099.2427] [ 1720] [depth= 1] . ( 44 sec) [ -8095.6583] [ 1716] [depth= 1] . ( 45 sec) [ -8093.3924] [ 1719] [depth= 1] . ( 45 sec) [ -8090.8734] [ 1716] [depth= 1] . ( 46 sec) [ -8090.7461] [ 1716] [depth= 1] . ( 46 sec) [ -8090.5215] [ 1716] [depth= 1] . ( 46 sec) [ -8074.6676] [Branch lengths ] . ( 47 sec) [ -8074.6182] [GTR parameters ] . ( 47 sec) [ -8074.5825] [Alpha ][ 1.020159] . ( 47 sec) [ -8074.4862] [ 1708] [depth= 1] . ( 50 sec) [ -8073.8581] [Branch lengths ] . ( 51 sec) [ -8073.8569] [GTR parameters ] . ( 51 sec) [ -8073.8566] [Alpha ][ 1.022149] . ( 60 sec) [ -8073.6190] [ 1714] [depth= 3] . ( 73 sec) [ -8073.3900] [Branch lengths ] . ( 74 sec) [ -8073.3810] [GTR parameters ] . ( 74 sec) [ -8073.3804] [Alpha ][ 1.019209] . ( 74 sec) [ -8073.3804] [Topology ] . ( 75 sec) [ -8073.3735] [Topology ] . ( 75 sec) [ -8073.3715] [Topology ] . ( 76 sec) [ -8073.3706] [Topology ] . ( 76 sec) [ -8073.3706] [GTR parameters ] . ( 76 sec) [ -8073.3706] [Alpha ][ 1.019209] . ( 76 sec) [ -8073.3706] [Topology ] . ( 77 sec) [ -8073.3702] [Topology ] . ( 77 sec) [ -8073.3702] [GTR parameters ] . ( 77 sec) [ -8073.3702] [Alpha ][ 1.019209] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -8073.3699] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8073.775106 . Log likelihood obtained after SPR moves : -8073.369886 . Log likelihood of the current tree: -8073.369886. . Printing the most likely tree in file 'data63.phy_phyml_tree.txt'... . Best log likelihood : -8073.369649 . Time used 0h1m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo