.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data73.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... . 372 patterns found. (out of a total of 500 sites) . 117 sites without polymorphism (23.40%). . [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)... . ( 0 sec) [ -20342.9112] [GTR parameters ] . ( 1 sec) [ -19945.3261] [Alpha ][ 0.500960] . ( 1 sec) [ -19506.8811] [ 3307] [depth= 4] . ( 1 sec) [ -19183.5333] [ 3229] [depth= 6] . ( 1 sec) [ -19150.0330] [ 3227] [depth= 1] . ( 1 sec) [ -19121.7534] [ 3226] [depth= 2] . ( 1 sec) [ -19087.6285] [ 3196] [depth= 2] . ( 1 sec) [ -19005.2015] [ 3188] [depth= 5] . ( 1 sec) [ -19004.6061] [ 3188] [depth= 1] . ( 1 sec) [ -18999.7341] [ 3188] [depth= 1] . ( 1 sec) [ -18673.2963] [ 3146] [depth= 5] . ( 1 sec) [ -18323.1398] [ 3038] [depth= 1] . ( 1 sec) [ -18022.9869] [ 2999] [depth= 16] . ( 1 sec) [ -17934.3433] [ 2936] [depth= 2] . ( 1 sec) [ -17786.7821] [ 2938] [depth= 1] . ( 1 sec) [ -17189.7673] [ 2814] [depth= 5] . ( 1 sec) [ -17060.8315] [ 2786] [depth= 3] . ( 1 sec) [ -16861.8540] [ 2776] [depth= 1] . ( 1 sec) [ -16683.3950] [ 2657] [depth= 2] . ( 1 sec) [ -16653.3286] [ 2652] [depth= 8] . ( 1 sec) [ -16338.3358] [ 2613] [depth= 8] . ( 1 sec) [ -16154.5818] [ 2619] [depth= 1] . ( 1 sec) [ -16060.5163] [ 2622] [depth= 1] . ( 1 sec) [ -13118.6171] [ 2614] [depth= 6] . ( 1 sec) [ -13114.9515] [ 2610] [depth= 1] . ( 1 sec) [ -12736.8237] [ 2556] [depth= 2] . ( 2 sec) [ -12482.9227] [ 2480] [depth= 4] . ( 2 sec) [ -12224.0652] [ 2384] [depth= 7] . ( 2 sec) [ -12008.6049] [ 2331] [depth= 7] . ( 2 sec) [ -11883.7733] [ 2327] [depth= 1] . ( 2 sec) [ -11690.7395] [ 2303] [depth= 3] . ( 2 sec) [ -11386.8436] [ 2261] [depth= 10] . ( 2 sec) [ -11223.0929] [ 2204] [depth= 5] . ( 2 sec) [ -11180.8255] [ 2194] [depth= 1] . ( 2 sec) [ -11000.0885] [ 2154] [depth= 9] . ( 2 sec) [ -10426.2953] [ 2121] [depth= 5] . ( 2 sec) [ -10333.7844] [ 2111] [depth= 3] . ( 2 sec) [ -10329.5979] [ 2113] [depth= 1] . ( 2 sec) [ -10100.7708] [ 2070] [depth= 3] . ( 2 sec) [ -10059.1214] [ 2048] [depth= 6] . ( 2 sec) [ -10028.4524] [ 2033] [depth= 1] . ( 2 sec) [ -9952.2200] [ 2012] [depth= 7] . ( 2 sec) [ -9909.6340] [ 1998] [depth= 1] . ( 2 sec) [ -9628.4534] [ 1901] [depth= 5] . ( 2 sec) [ -9275.6941] [ 1842] [depth= 5] . ( 2 sec) [ -9266.7699] [ 1845] [depth= 1] . ( 2 sec) [ -9103.9367] [ 1813] [depth= 9] . ( 2 sec) [ -9092.8671] [ 1821] [depth= 2] . ( 2 sec) [ -8828.9397] [ 1756] [depth= 9] . ( 2 sec) [ -8785.0931] [ 1714] [depth= 1] . ( 3 sec) [ -8746.7266] [ 1711] [depth= 4] . ( 3 sec) [ -8746.2420] [ 1710] [depth= 1] . ( 3 sec) [ -8684.4291] [ 1675] [depth= 6] . ( 3 sec) [ -8680.3086] [ 1672] [depth= 1] . ( 3 sec) [ -8538.8366] [ 1635] [depth= 3] . ( 3 sec) [ -8526.6135] [ 1630] [depth= 3] . ( 3 sec) [ -8503.6031] [ 1629] [depth= 2] . ( 3 sec) [ -8369.9878] [ 1620] [depth= 3] . ( 3 sec) [ -8267.3621] [ 1587] [depth= 7] . ( 3 sec) [ -8261.6920] [ 1578] [depth= 1] . ( 3 sec) [ -8260.1039] [ 1578] [depth= 1] . ( 3 sec) [ -8223.1609] [ 1573] [depth= 1] . ( 3 sec) [ -7775.4823] [ 1565] [depth= 4] . ( 3 sec) [ -7657.3391] [ 1536] [depth= 3] . ( 3 sec) [ -7657.1014] [ 1540] [depth= 1] . ( 3 sec) [ -7638.0818] [ 1531] [depth= 3] . ( 3 sec) [ -7636.6478] [ 1528] [depth= 1] . ( 3 sec) [ -7607.3036] [ 1529] [depth= 1] . ( 3 sec) [ -7582.5059] [ 1527] [depth= 1] . ( 3 sec) [ -7577.0241] [ 1527] [depth= 1] . ( 4 sec) [ -7569.9037] [ 1516] [depth= 3] . ( 4 sec) [ -7569.1581] [ 1521] [depth= 1] . ( 4 sec) [ -7557.8740] [ 1535] [depth= 1] . ( 4 sec) [ -7513.7406] [ 1530] [depth= 1] . ( 4 sec) [ -7409.9797] [ 1537] [depth= 5] . ( 4 sec) [ -7399.3384] [ 1543] [depth= 1] . ( 4 sec) [ -7378.8039] [ 1536] [depth= 1] . ( 4 sec) [ -7373.2801] [ 1528] [depth= 2] . ( 4 sec) [ -7339.7791] [ 1522] [depth= 3] . ( 4 sec) [ -7339.2076] [ 1511] [depth= 1] . ( 4 sec) [ -7160.6522] [Branch lengths ] . ( 5 sec) [ -7158.6454] [GTR parameters ] . ( 5 sec) [ -7141.6517] [Alpha ][ 0.780776] . ( 5 sec) [ -7141.6383] [ 1511] [depth= 1] . ( 5 sec) [ -7137.6034] [ 1495] [depth= 1] . ( 6 sec) [ -7137.3112] [ 1494] [depth= 1] . ( 6 sec) [ -7068.2583] [ 1452] [depth= 5] . ( 6 sec) [ -7040.5772] [ 1446] [depth= 4] . ( 6 sec) [ -7036.1675] [ 1447] [depth= 1] . ( 6 sec) [ -7027.3934] [ 1436] [depth= 3] . ( 6 sec) [ -7023.2368] [ 1436] [depth= 1] . ( 6 sec) [ -7022.4818] [ 1434] [depth= 1] . ( 6 sec) [ -7022.1537] [ 1435] [depth= 1] . ( 6 sec) [ -7020.6657] [ 1439] [depth= 1] . ( 6 sec) [ -6998.6520] [ 1431] [depth= 2] . ( 6 sec) [ -6987.4803] [ 1433] [depth= 1] . ( 7 sec) [ -6986.8032] [ 1429] [depth= 2] . ( 7 sec) [ -6984.8167] [ 1427] [depth= 1] . ( 7 sec) [ -6984.2708] [ 1430] [depth= 1] . ( 7 sec) [ -6938.2947] [ 1403] [depth= 1] . ( 7 sec) [ -6937.1679] [ 1400] [depth= 1] . ( 7 sec) [ -6936.5999] [ 1399] [depth= 1] . ( 7 sec) [ -6936.4516] [ 1401] [depth= 1] . ( 7 sec) [ -6936.2796] [ 1400] [depth= 1] . ( 7 sec) [ -6936.0442] [ 1400] [depth= 2] . ( 8 sec) [ -6927.7617] [ 1407] [depth= 6] . ( 8 sec) [ -6927.6458] [ 1405] [depth= 1] . ( 8 sec) [ -6927.2766] [ 1410] [depth= 1] . ( 8 sec) [ -6900.7472] [ 1390] [depth= 2] . ( 8 sec) [ -6878.1731] [ 1376] [depth= 3] . ( 8 sec) [ -6874.9419] [ 1373] [depth= 1] . ( 8 sec) [ -6874.4277] [ 1377] [depth= 1] . ( 8 sec) [ -6865.0864] [ 1376] [depth= 1] . ( 10 sec) [ -6861.9375] [ 1376] [depth= 1] . ( 10 sec) [ -6860.0650] [ 1377] [depth= 1] . ( 10 sec) [ -6859.8040] [ 1373] [depth= 1] . ( 11 sec) [ -6845.5567] [Branch lengths ] . ( 11 sec) [ -6845.3933] [GTR parameters ] . ( 11 sec) [ -6843.7341] [Alpha ][ 0.910108] . ( 13 sec) [ -6843.2714] [ 1377] [depth= 1] . ( 15 sec) [ -6843.0371] [ 1378] [depth= 1] . ( 16 sec) [ -6841.8461] [Branch lengths ] . ( 16 sec) [ -6841.8369] [GTR parameters ] . ( 16 sec) [ -6841.8369] [Alpha ][ 0.910108] . ( 22 sec) [ -6841.3392] [Branch lengths ] . ( 43 sec) [ -6840.5861] [Branch lengths ] . ( 43 sec) [ -6840.5861] [Topology ] . ( 44 sec) [ -6840.5132] [Topology ] . ( 44 sec) [ -6840.4843] [Topology ] . ( 45 sec) [ -6840.4656] [Topology ] . ( 46 sec) [ -6840.4515] [Topology ] . ( 47 sec) [ -6840.4387] [Topology ] . ( 47 sec) [ -6840.4261] [Topology ] . ( 48 sec) [ -6840.4252] [GTR parameters ] . ( 48 sec) [ -6840.4251] [Alpha ][ 0.911018] . ( 48 sec) [ -6840.4251] [Topology ] . ( 49 sec) [ -6840.4119] [Topology ] . ( 49 sec) [ -6840.3979] [Topology ] . ( 50 sec) [ -6840.3823] [Topology ] . ( 51 sec) [ -6840.3669] [Topology ] . ( 51 sec) [ -6840.3550] [Topology ] . ( 52 sec) [ -6840.3504] [Topology ] . ( 52 sec) [ -6840.3504] [GTR parameters ] . ( 52 sec) [ -6840.3504] [Alpha ][ 0.911018] . ( 52 sec) [ -6840.3504] [Topology ] . ( 53 sec) [ -6840.3493] [Topology ] . ( 54 sec) [ -6840.3491] [Topology ] . ( 54 sec) [ -6840.3491] [GTR parameters ] . ( 54 sec) [ -6840.3491] [Alpha ][ 0.911018] . ( 54 sec) [ -6840.3491] [Topology ] . ( 55 sec) [ -6840.3490] [Topology ] . ( 55 sec) [ -6840.3490] [GTR parameters ] . ( 55 sec) [ -6840.3490] [Alpha ][ 0.911018] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6840.348987. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18994.7947] [GTR parameters ] . ( 0 sec) [ -18607.7407] [Alpha ][ 0.500960] . ( 0 sec) [ -18322.7712] [ 3434] [depth= 4] . ( 0 sec) [ -17975.6371] [ 3361] [depth= 11] . ( 0 sec) [ -17940.5127] [ 3337] [depth= 4] . ( 1 sec) [ -17777.0128] [ 3311] [depth= 7] . ( 1 sec) [ -17234.6821] [ 3268] [depth= 6] . ( 1 sec) [ -16925.8638] [ 3265] [depth= 8] . ( 1 sec) [ -16783.4350] [ 3258] [depth= 1] . ( 1 sec) [ -16643.9474] [ 3251] [depth= 3] . ( 1 sec) [ -16631.0718] [ 3220] [depth= 2] . ( 1 sec) [ -16461.7166] [ 3195] [depth= 5] . ( 1 sec) [ -16417.9528] [ 3187] [depth= 2] . ( 1 sec) [ -16204.6814] [ 3182] [depth= 5] . ( 1 sec) [ -15745.8748] [ 3097] [depth= 7] . ( 1 sec) [ -15652.8687] [ 3102] [depth= 1] . ( 1 sec) [ -15378.6064] [ 3038] [depth= 10] . ( 1 sec) [ -15294.9574] [ 3014] [depth= 10] . ( 1 sec) [ -15288.8221] [ 3019] [depth= 1] . ( 1 sec) [ -14939.3867] [ 2949] [depth= 5] . ( 1 sec) [ -14789.8012] [ 2929] [depth= 9] . ( 1 sec) [ -14470.5112] [ 2930] [depth= 1] . ( 1 sec) [ -14232.7090] [ 2879] [depth= 11] . ( 1 sec) [ -14225.8462] [ 2858] [depth= 1] . ( 1 sec) [ -13947.7351] [ 2782] [depth= 12] . ( 1 sec) [ -13821.9815] [ 2752] [depth= 10] . ( 1 sec) [ -13201.3535] [ 2778] [depth= 1] . ( 1 sec) [ -12998.7299] [ 2693] [depth= 3] . ( 1 sec) [ -12845.0209] [ 2691] [depth= 7] . ( 2 sec) [ -12790.6751] [ 2683] [depth= 5] . ( 2 sec) [ -12782.7997] [ 2682] [depth= 1] . ( 2 sec) [ -12677.8261] [ 2676] [depth= 1] . ( 2 sec) [ -12665.3695] [ 2672] [depth= 2] . ( 2 sec) [ -12577.6107] [ 2649] [depth= 1] . ( 2 sec) [ -12546.1980] [ 2638] [depth= 1] . ( 2 sec) [ -12469.0509] [ 2601] [depth= 1] . ( 2 sec) [ -12451.4416] [ 2603] [depth= 1] . ( 2 sec) [ -12284.1113] [ 2548] [depth= 1] . ( 2 sec) [ -12262.7001] [ 2546] [depth= 1] . ( 2 sec) [ -12150.5383] [ 2528] [depth= 6] . ( 2 sec) [ -12111.4770] [ 2531] [depth= 1] . ( 2 sec) [ -12076.8542] [ 2502] [depth= 14] . ( 2 sec) [ -12018.8463] [ 2384] [depth= 3] . ( 2 sec) [ -11936.6079] [ 2374] [depth= 3] . ( 2 sec) [ -11873.8182] [ 2335] [depth= 7] . ( 2 sec) [ -11866.4310] [ 2332] [depth= 1] . ( 2 sec) [ -11783.2536] [ 2264] [depth= 3] . ( 2 sec) [ -11563.0089] [ 2249] [depth= 4] . ( 2 sec) [ -10757.8764] [ 2178] [depth= 4] . ( 2 sec) [ -10757.6051] [ 2180] [depth= 1] . ( 2 sec) [ -10476.0571] [ 2180] [depth= 2] . ( 2 sec) [ -10442.0166] [ 2166] [depth= 15] . ( 2 sec) [ -10422.8424] [ 2165] [depth= 4] . ( 3 sec) [ -10407.4743] [ 2152] [depth= 1] . ( 3 sec) [ -10218.2650] [ 2149] [depth= 1] . ( 3 sec) [ -9552.0951] [ 2069] [depth= 2] . ( 3 sec) [ -9450.1428] [ 1987] [depth= 3] . ( 3 sec) [ -9431.4058] [ 1984] [depth= 1] . ( 3 sec) [ -9428.8116] [ 1999] [depth= 1] . ( 3 sec) [ -9390.2486] [ 1984] [depth= 1] . ( 3 sec) [ -9366.8494] [ 1978] [depth= 1] . ( 3 sec) [ -9296.4329] [ 1975] [depth= 1] . ( 3 sec) [ -9260.7472] [ 1971] [depth= 3] . ( 3 sec) [ -9209.8172] [ 1961] [depth= 6] . ( 3 sec) [ -9203.1825] [ 1960] [depth= 1] . ( 3 sec) [ -9145.6370] [ 1947] [depth= 12] . ( 3 sec) [ -9130.5903] [ 1955] [depth= 1] . ( 3 sec) [ -8925.8941] [ 1942] [depth= 1] . ( 3 sec) [ -8767.9010] [ 1901] [depth= 11] . ( 3 sec) [ -8605.5396] [ 1896] [depth= 2] . ( 3 sec) [ -8402.2460] [ 1762] [depth= 1] . ( 3 sec) [ -8240.9109] [ 1751] [depth= 4] . ( 3 sec) [ -8174.1724] [ 1703] [depth= 1] . ( 3 sec) [ -7925.4811] [ 1696] [depth= 2] . ( 4 sec) [ -7860.6330] [ 1676] [depth= 1] . ( 4 sec) [ -7821.5226] [ 1612] [depth= 1] . ( 4 sec) [ -7751.0831] [ 1600] [depth= 5] . ( 4 sec) [ -7747.6065] [ 1606] [depth= 1] . ( 4 sec) [ -7665.3287] [ 1536] [depth= 1] . ( 4 sec) [ -7525.7051] [ 1510] [depth= 3] . ( 4 sec) [ -7476.6351] [ 1493] [depth= 1] . ( 4 sec) [ -7472.8761] [ 1493] [depth= 1] . ( 4 sec) [ -7317.3890] [ 1431] [depth= 4] . ( 4 sec) [ -7277.8321] [ 1434] [depth= 2] . ( 4 sec) [ -7277.1082] [ 1434] [depth= 1] . ( 4 sec) [ -7050.3092] [Branch lengths ] . ( 5 sec) [ -7041.9815] [GTR parameters ] . ( 5 sec) [ -7019.9300] [Alpha ][ 0.832384] . ( 5 sec) [ -7019.8686] [ 1434] [depth= 1] . ( 5 sec) [ -7019.7316] [ 1431] [depth= 1] . ( 5 sec) [ -7019.6626] [ 1431] [depth= 1] . ( 5 sec) [ -6985.9085] [ 1431] [depth= 1] . ( 5 sec) [ -6922.4389] [ 1378] [depth= 2] . ( 5 sec) [ -6900.5932] [ 1368] [depth= 1] . ( 5 sec) [ -6898.9261] [ 1371] [depth= 2] . ( 5 sec) [ -6896.4602] [ 1368] [depth= 1] . ( 5 sec) [ -6879.7827] [ 1375] [depth= 1] . ( 6 sec) [ -6879.7710] [ 1375] [depth= 1] . ( 6 sec) [ -6876.5768] [ 1375] [depth= 1] . ( 6 sec) [ -6876.2838] [ 1376] [depth= 1] . ( 6 sec) [ -6869.6951] [ 1369] [depth= 1] . ( 6 sec) [ -6863.7880] [ 1379] [depth= 1] . ( 7 sec) [ -6857.3685] [ 1378] [depth= 1] . ( 7 sec) [ -6857.3213] [ 1381] [depth= 1] . ( 8 sec) [ -6849.8364] [Branch lengths ] . ( 9 sec) [ -6849.1705] [GTR parameters ] . ( 9 sec) [ -6848.6750] [Alpha ][ 0.904688] . ( 9 sec) [ -6848.6404] [ 1381] [depth= 1] . ( 10 sec) [ -6848.5322] [ 1378] [depth= 1] . ( 10 sec) [ -6846.3338] [ 1374] [depth= 4] . ( 10 sec) [ -6842.9109] [ 1378] [depth= 1] . ( 11 sec) [ -6841.6391] [ 1378] [depth= 1] . ( 13 sec) [ -6840.6357] [Branch lengths ] . ( 14 sec) [ -6840.6014] [GTR parameters ] . ( 14 sec) [ -6840.5941] [Alpha ][ 0.914281] . ( 18 sec) [ -6840.4732] [Branch lengths ] . ( 38 sec) [ -6840.4227] [Branch lengths ] . ( 38 sec) [ -6840.4227] [Topology ] . ( 39 sec) [ -6840.4031] [Topology ] . ( 39 sec) [ -6840.3882] [Topology ] . ( 40 sec) [ -6840.3722] [Topology ] . ( 41 sec) [ -6840.3579] [Topology ] . ( 42 sec) [ -6840.3520] [Topology ] . ( 42 sec) [ -6840.3505] [Topology ] . ( 43 sec) [ -6840.3501] [GTR parameters ] . ( 43 sec) [ -6840.3493] [Alpha ][ 0.910956] . ( 43 sec) [ -6840.3493] [Topology ] . ( 43 sec) [ -6840.3490] [Topology ] . ( 43 sec) [ -6840.3490] [GTR parameters ] . ( 43 sec) [ -6840.3490] [Alpha ][ 0.910956] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6840.348958. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21014.2084] [GTR parameters ] . ( 0 sec) [ -20582.8596] [Alpha ][ 0.500960] . ( 0 sec) [ -20372.7976] [ 3479] [depth= 1] . ( 0 sec) [ -19939.1000] [ 3415] [depth= 4] . ( 0 sec) [ -19887.6548] [ 3399] [depth= 2] . ( 0 sec) [ -19703.6526] [ 3396] [depth= 2] . ( 0 sec) [ -19393.6126] [ 3359] [depth= 6] . ( 0 sec) [ -19346.8741] [ 3365] [depth= 3] . ( 0 sec) [ -17009.4765] [ 3308] [depth= 10] . ( 0 sec) [ -16708.1486] [ 3289] [depth= 6] . ( 0 sec) [ -16272.6316] [ 3195] [depth= 9] . ( 0 sec) [ -16143.6254] [ 3208] [depth= 16] . ( 0 sec) [ -15122.5628] [ 3123] [depth= 10] . ( 1 sec) [ -14703.9980] [ 3107] [depth= 15] . ( 1 sec) [ -14547.9611] [ 3023] [depth= 9] . ( 1 sec) [ -14547.7167] [ 3016] [depth= 4] . ( 1 sec) [ -14310.7836] [ 2980] [depth= 12] . ( 1 sec) [ -14288.2779] [ 2967] [depth= 1] . ( 1 sec) [ -13935.7883] [ 2929] [depth= 1] . ( 1 sec) [ -13864.7801] [ 2919] [depth= 9] . ( 1 sec) [ -13376.7234] [ 2883] [depth= 6] . ( 1 sec) [ -13040.4810] [ 2795] [depth= 1] . ( 1 sec) [ -12588.8957] [ 2694] [depth= 7] . ( 1 sec) [ -12426.8687] [ 2623] [depth= 1] . ( 1 sec) [ -12219.6016] [ 2594] [depth= 7] . ( 1 sec) [ -11884.8033] [ 2511] [depth= 10] . ( 1 sec) [ -11512.3781] [ 2446] [depth= 12] . ( 1 sec) [ -11377.9718] [ 2413] [depth= 6] . ( 1 sec) [ -11272.3890] [ 2414] [depth= 1] . ( 1 sec) [ -11071.4389] [ 2311] [depth= 4] . ( 1 sec) [ -11059.9779] [ 2312] [depth= 1] . ( 1 sec) [ -11059.2973] [ 2311] [depth= 1] . ( 1 sec) [ -10972.2851] [ 2308] [depth= 1] . ( 1 sec) [ -10968.6408] [ 2308] [depth= 2] . ( 1 sec) [ -10859.3328] [ 2224] [depth= 10] . ( 1 sec) [ -10732.2430] [ 2234] [depth= 1] . ( 2 sec) [ -10697.9838] [ 2223] [depth= 1] . ( 2 sec) [ -10672.5456] [ 2221] [depth= 1] . ( 2 sec) [ -10624.4925] [ 2113] [depth= 1] . ( 2 sec) [ -10548.5771] [ 2108] [depth= 7] . ( 2 sec) [ -10187.1719] [ 2056] [depth= 5] . ( 2 sec) [ -10152.8469] [ 2051] [depth= 1] . ( 2 sec) [ -10056.4654] [ 2034] [depth= 1] . ( 2 sec) [ -9770.6438] [ 1990] [depth= 7] . ( 2 sec) [ -9757.2140] [ 2025] [depth= 2] . ( 2 sec) [ -9516.5853] [ 1970] [depth= 5] . ( 2 sec) [ -9416.2618] [ 1965] [depth= 1] . ( 2 sec) [ -9312.4017] [ 1952] [depth= 1] . ( 2 sec) [ -9070.0955] [ 1850] [depth= 3] . ( 2 sec) [ -9050.9738] [ 1846] [depth= 3] . ( 2 sec) [ -9005.5552] [ 1834] [depth= 2] . ( 2 sec) [ -8833.9977] [ 1832] [depth= 3] . ( 2 sec) [ -8674.4656] [ 1733] [depth= 9] . ( 2 sec) [ -8588.4210] [ 1728] [depth= 1] . ( 2 sec) [ -8559.1760] [ 1726] [depth= 2] . ( 2 sec) [ -8539.5912] [ 1709] [depth= 1] . ( 2 sec) [ -8530.6819] [ 1708] [depth= 5] . ( 2 sec) [ -8438.5182] [ 1701] [depth= 2] . ( 2 sec) [ -8378.1952] [ 1645] [depth= 6] . ( 3 sec) [ -8369.7906] [ 1641] [depth= 2] . ( 3 sec) [ -8280.4426] [ 1646] [depth= 1] . ( 3 sec) [ -8216.4121] [ 1645] [depth= 2] . ( 3 sec) [ -8188.5989] [ 1646] [depth= 2] . ( 3 sec) [ -8187.5076] [ 1646] [depth= 1] . ( 3 sec) [ -8109.4693] [ 1642] [depth= 2] . ( 3 sec) [ -7997.4889] [ 1645] [depth= 1] . ( 3 sec) [ -7976.4997] [ 1640] [depth= 1] . ( 3 sec) [ -7822.0724] [ 1570] [depth= 8] . ( 3 sec) [ -7822.0124] [ 1574] [depth= 1] . ( 3 sec) [ -7817.7486] [ 1567] [depth= 2] . ( 3 sec) [ -7789.0085] [ 1542] [depth= 2] . ( 3 sec) [ -7695.2078] [ 1553] [depth= 1] . ( 3 sec) [ -7677.1571] [ 1562] [depth= 3] . ( 3 sec) [ -7673.3000] [ 1562] [depth= 1] . ( 3 sec) [ -7518.6825] [ 1525] [depth= 5] . ( 3 sec) [ -7492.3158] [ 1515] [depth= 3] . ( 3 sec) [ -7483.8779] [ 1512] [depth= 1] . ( 3 sec) [ -7446.8617] [ 1499] [depth= 3] . ( 3 sec) [ -7435.3095] [ 1498] [depth= 1] . ( 3 sec) [ -7392.1935] [ 1484] [depth= 2] . ( 3 sec) [ -7383.4607] [ 1479] [depth= 1] . ( 3 sec) [ -7380.3984] [ 1482] [depth= 1] . ( 3 sec) [ -7380.1684] [ 1479] [depth= 1] . ( 4 sec) [ -7308.3295] [ 1441] [depth= 2] . ( 4 sec) [ -7303.7771] [ 1439] [depth= 1] . ( 4 sec) [ -7296.9676] [ 1441] [depth= 1] . ( 4 sec) [ -7294.5903] [ 1441] [depth= 1] . ( 4 sec) [ -7040.9159] [Branch lengths ] . ( 5 sec) [ -7035.6252] [GTR parameters ] . ( 5 sec) [ -7010.4228] [Alpha ][ 0.860564] . ( 5 sec) [ -7003.5473] [ 1437] [depth= 1] . ( 5 sec) [ -7003.4726] [ 1438] [depth= 1] . ( 5 sec) [ -7003.4566] [ 1438] [depth= 1] . ( 5 sec) [ -7000.8507] [ 1436] [depth= 1] . ( 5 sec) [ -6963.8355] [ 1421] [depth= 3] . ( 5 sec) [ -6963.4296] [ 1424] [depth= 1] . ( 6 sec) [ -6961.8837] [ 1427] [depth= 1] . ( 6 sec) [ -6961.8570] [ 1424] [depth= 1] . ( 6 sec) [ -6961.4477] [ 1426] [depth= 1] . ( 6 sec) [ -6961.0595] [ 1424] [depth= 1] . ( 6 sec) [ -6960.4121] [ 1422] [depth= 1] . ( 6 sec) [ -6960.3988] [ 1422] [depth= 1] . ( 6 sec) [ -6960.1184] [ 1420] [depth= 1] . ( 6 sec) [ -6959.9579] [ 1421] [depth= 1] . ( 6 sec) [ -6871.0576] [ 1386] [depth= 1] . ( 6 sec) [ -6864.1799] [ 1384] [depth= 1] . ( 7 sec) [ -6863.9375] [ 1386] [depth= 1] . ( 7 sec) [ -6863.2639] [ 1385] [depth= 1] . ( 7 sec) [ -6862.3561] [ 1390] [depth= 1] . ( 7 sec) [ -6859.4715] [ 1387] [depth= 1] . ( 7 sec) [ -6859.4408] [ 1385] [depth= 1] . ( 7 sec) [ -6859.3387] [ 1385] [depth= 1] . ( 8 sec) [ -6859.0333] [ 1384] [depth= 1] . ( 8 sec) [ -6846.0286] [Branch lengths ] . ( 9 sec) [ -6845.6033] [GTR parameters ] . ( 9 sec) [ -6845.3094] [Alpha ][ 0.917115] . ( 9 sec) [ -6845.2707] [ 1384] [depth= 1] . ( 9 sec) [ -6845.2063] [ 1384] [depth= 1] . ( 9 sec) [ -6845.1574] [ 1382] [depth= 1] . ( 10 sec) [ -6844.9443] [ 1379] [depth= 1] . ( 10 sec) [ -6844.8879] [ 1379] [depth= 1] . ( 11 sec) [ -6844.4457] [ 1379] [depth= 1] . ( 13 sec) [ -6841.9158] [Branch lengths ] . ( 13 sec) [ -6841.8993] [GTR parameters ] . ( 13 sec) [ -6841.8992] [Alpha ][ 0.918032] . ( 17 sec) [ -6841.2310] [Branch lengths ] . ( 27 sec) [ -6841.0965] [ 1378] [depth= 1] . ( 37 sec) [ -6840.3972] [Branch lengths ] . ( 38 sec) [ -6840.3967] [GTR parameters ] . ( 38 sec) [ -6840.3934] [Alpha ][ 0.911303] . ( 38 sec) [ -6840.3934] [Topology ] . ( 38 sec) [ -6840.3625] [Topology ] . ( 39 sec) [ -6840.3542] [Topology ] . ( 40 sec) [ -6840.3509] [Topology ] . ( 41 sec) [ -6840.3496] [Topology ] . ( 41 sec) [ -6840.3491] [Topology ] . ( 41 sec) [ -6840.3490] [GTR parameters ] . ( 41 sec) [ -6840.3490] [Alpha ][ 0.911303] . ( 41 sec) [ -6840.3490] [Topology ] . ( 42 sec) [ -6840.3488] [Topology ] . ( 42 sec) [ -6840.3488] [GTR parameters ] . ( 42 sec) [ -6840.3488] [Alpha ][ 0.911303] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6840.348799. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22453.4798] [GTR parameters ] . ( 1 sec) [ -22023.9439] [Alpha ][ 0.500960] . ( 1 sec) [ -21669.7478] [ 3443] [depth= 10] . ( 1 sec) [ -20924.3947] [ 3383] [depth= 3] . ( 1 sec) [ -20712.3596] [ 3343] [depth= 7] . ( 1 sec) [ -20491.0547] [ 3309] [depth= 1] . ( 1 sec) [ -20388.9410] [ 3247] [depth= 8] . ( 2 sec) [ -20229.2074] [ 3216] [depth= 3] . ( 2 sec) [ -20179.1425] [ 3209] [depth= 2] . ( 2 sec) [ -19549.1134] [ 3172] [depth= 7] . ( 2 sec) [ -19479.7924] [ 3169] [depth= 3] . ( 2 sec) [ -19100.2356] [ 3142] [depth= 7] . ( 2 sec) [ -18979.6606] [ 3137] [depth= 5] . ( 2 sec) [ -18824.7197] [ 3133] [depth= 2] . ( 2 sec) [ -18764.8833] [ 3128] [depth= 4] . ( 2 sec) [ -18543.3913] [ 3078] [depth= 1] . ( 2 sec) [ -18536.9324] [ 3078] [depth= 1] . ( 2 sec) [ -18502.1699] [ 3060] [depth= 10] . ( 2 sec) [ -18444.3401] [ 3060] [depth= 2] . ( 2 sec) [ -18158.1953] [ 2933] [depth= 3] . ( 2 sec) [ -17978.8068] [ 2926] [depth= 1] . ( 2 sec) [ -17828.1446] [ 2893] [depth= 4] . ( 2 sec) [ -17632.0165] [ 2845] [depth= 18] . ( 2 sec) [ -17515.1455] [ 2844] [depth= 1] . ( 2 sec) [ -17429.5762] [ 2831] [depth= 2] . ( 2 sec) [ -17377.7286] [ 2812] [depth= 13] . ( 2 sec) [ -17153.5426] [ 2745] [depth= 7] . ( 2 sec) [ -16949.6059] [ 2663] [depth= 15] . ( 2 sec) [ -16600.9456] [ 2622] [depth= 7] . ( 2 sec) [ -16325.5335] [ 2564] [depth= 5] . ( 2 sec) [ -16044.1467] [ 2537] [depth= 8] . ( 2 sec) [ -15684.6891] [ 2453] [depth= 4] . ( 3 sec) [ -15679.5325] [ 2444] [depth= 1] . ( 3 sec) [ -15649.8488] [ 2430] [depth= 1] . ( 3 sec) [ -14815.3592] [ 2315] [depth= 16] . ( 3 sec) [ -14814.1980] [ 2315] [depth= 1] . ( 3 sec) [ -13981.7274] [ 2217] [depth= 12] . ( 3 sec) [ -13631.0401] [ 2140] [depth= 1] . ( 3 sec) [ -13630.9362] [ 2140] [depth= 1] . ( 3 sec) [ -13577.2829] [ 2114] [depth= 1] . ( 3 sec) [ -13576.6461] [ 2116] [depth= 2] . ( 3 sec) [ -13545.5703] [ 2100] [depth= 6] . ( 3 sec) [ -13366.4138] [ 2042] [depth= 1] . ( 3 sec) [ -13314.6417] [ 2027] [depth= 9] . ( 3 sec) [ -13295.5202] [ 2022] [depth= 1] . ( 3 sec) [ -13138.2224] [ 1973] [depth= 5] . ( 3 sec) [ -13088.4096] [ 2006] [depth= 1] . ( 3 sec) [ -12930.2792] [ 1968] [depth= 10] . ( 3 sec) [ -9412.2942] [ 1895] [depth= 8] . ( 3 sec) [ -9121.7957] [ 1883] [depth= 2] . ( 3 sec) [ -9005.0968] [ 1834] [depth= 7] . ( 3 sec) [ -8904.1793] [ 1821] [depth= 2] . ( 3 sec) [ -8403.0001] [ 1679] [depth= 2] . ( 3 sec) [ -8355.7393] [ 1681] [depth= 1] . ( 4 sec) [ -8347.1974] [ 1667] [depth= 3] . ( 4 sec) [ -8345.9059] [ 1668] [depth= 1] . ( 4 sec) [ -8297.5953] [ 1671] [depth= 1] . ( 4 sec) [ -8265.3943] [ 1662] [depth= 2] . ( 4 sec) [ -8222.4977] [ 1660] [depth= 1] . ( 4 sec) [ -8032.9970] [ 1654] [depth= 3] . ( 4 sec) [ -8030.1166] [ 1651] [depth= 2] . ( 4 sec) [ -7971.6176] [ 1639] [depth= 1] . ( 4 sec) [ -7968.7702] [ 1638] [depth= 1] . ( 4 sec) [ -7929.3025] [ 1595] [depth= 1] . ( 4 sec) [ -7874.6283] [ 1597] [depth= 1] . ( 4 sec) [ -7840.5618] [ 1594] [depth= 1] . ( 4 sec) [ -7768.5545] [ 1599] [depth= 1] . ( 4 sec) [ -7685.2663] [ 1521] [depth= 4] . ( 4 sec) [ -7681.6210] [ 1518] [depth= 1] . ( 4 sec) [ -7681.4747] [ 1517] [depth= 1] . ( 4 sec) [ -7588.8555] [ 1508] [depth= 3] . ( 5 sec) [ -7581.0072] [ 1507] [depth= 1] . ( 5 sec) [ -7568.0739] [ 1512] [depth= 1] . ( 5 sec) [ -7554.4663] [ 1507] [depth= 1] . ( 5 sec) [ -7441.7099] [ 1490] [depth= 1] . ( 5 sec) [ -7272.1408] [ 1455] [depth= 4] . ( 5 sec) [ -7143.0772] [ 1417] [depth= 2] . ( 5 sec) [ -7142.2359] [ 1428] [depth= 1] . ( 5 sec) [ -7134.0147] [ 1427] [depth= 1] . ( 5 sec) [ -7129.6161] [ 1425] [depth= 1] . ( 5 sec) [ -7129.3574] [ 1426] [depth= 1] . ( 5 sec) [ -7075.5393] [ 1406] [depth= 1] . ( 5 sec) [ -6955.6237] [Branch lengths ] . ( 6 sec) [ -6951.3168] [GTR parameters ] . ( 6 sec) [ -6929.7252] [Alpha ][ 0.854309] . ( 6 sec) [ -6929.7023] [ 1406] [depth= 1] . ( 6 sec) [ -6921.1369] [ 1394] [depth= 1] . ( 6 sec) [ -6898.5569] [ 1384] [depth= 3] . ( 6 sec) [ -6897.2033] [ 1382] [depth= 3] . ( 6 sec) [ -6895.9377] [ 1385] [depth= 1] . ( 6 sec) [ -6895.8488] [ 1385] [depth= 1] . ( 6 sec) [ -6895.7584] [ 1385] [depth= 1] . ( 6 sec) [ -6895.4769] [ 1385] [depth= 1] . ( 7 sec) [ -6895.3112] [ 1386] [depth= 1] . ( 7 sec) [ -6894.0572] [ 1385] [depth= 1] . ( 7 sec) [ -6892.0095] [ 1387] [depth= 1] . ( 7 sec) [ -6891.9579] [ 1387] [depth= 1] . ( 7 sec) [ -6880.6852] [ 1376] [depth= 1] . ( 7 sec) [ -6880.6594] [ 1376] [depth= 1] . ( 7 sec) [ -6874.9461] [ 1377] [depth= 3] . ( 8 sec) [ -6869.7017] [ 1380] [depth= 2] . ( 8 sec) [ -6866.7955] [ 1380] [depth= 1] . ( 8 sec) [ -6865.8423] [ 1382] [depth= 1] . ( 8 sec) [ -6865.4693] [ 1386] [depth= 1] . ( 8 sec) [ -6864.7426] [ 1385] [depth= 1] . ( 8 sec) [ -6864.5691] [ 1386] [depth= 1] . ( 8 sec) [ -6861.7713] [ 1382] [depth= 2] . ( 9 sec) [ -6860.9777] [ 1385] [depth= 1] . ( 9 sec) [ -6859.4417] [ 1383] [depth= 1] . ( 9 sec) [ -6844.4396] [Branch lengths ] . ( 10 sec) [ -6844.2045] [GTR parameters ] . ( 10 sec) [ -6844.0340] [Alpha ][ 0.898089] . ( 10 sec) [ -6844.0236] [ 1383] [depth= 1] . ( 10 sec) [ -6843.9421] [ 1381] [depth= 1] . ( 10 sec) [ -6843.6768] [ 1381] [depth= 1] . ( 12 sec) [ -6843.2167] [ 1378] [depth= 1] . ( 14 sec) [ -6840.7243] [Branch lengths ] . ( 14 sec) [ -6840.7201] [GTR parameters ] . ( 14 sec) [ -6840.7173] [Alpha ][ 0.904008] . ( 19 sec) [ -6840.4264] [Branch lengths ] . ( 39 sec) [ -6840.3610] [Branch lengths ] . ( 39 sec) [ -6840.3610] [Topology ] . ( 39 sec) [ -6840.3564] [Topology ] . ( 40 sec) [ -6840.3550] [Topology ] . ( 41 sec) [ -6840.3544] [Topology ] . ( 41 sec) [ -6840.3532] [GTR parameters ] . ( 41 sec) [ -6840.3497] [Alpha ][ 0.910570] . ( 41 sec) [ -6840.3497] [Topology ] . ( 42 sec) [ -6840.3492] [Topology ] . ( 42 sec) [ -6840.3492] [GTR parameters ] . ( 42 sec) [ -6840.3492] [Alpha ][ 0.910570] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6840.349156. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23736.8902] [GTR parameters ] . ( 1 sec) [ -23355.0680] [Alpha ][ 0.500960] . ( 1 sec) [ -23018.0941] [ 3461] [depth= 7] . ( 1 sec) [ -22684.2465] [ 3399] [depth= 6] . ( 1 sec) [ -22652.1788] [ 3388] [depth= 4] . ( 1 sec) [ -22574.1829] [ 3387] [depth= 1] . ( 1 sec) [ -22489.3772] [ 3352] [depth= 2] . ( 1 sec) [ -22462.7541] [ 3350] [depth= 2] . ( 1 sec) [ -22317.5504] [ 3341] [depth= 6] . ( 1 sec) [ -22206.7115] [ 3335] [depth= 5] . ( 1 sec) [ -21933.9007] [ 3232] [depth= 6] . ( 1 sec) [ -21632.8306] [ 3218] [depth= 5] . ( 1 sec) [ -21544.9605] [ 3216] [depth= 1] . ( 1 sec) [ -21473.9716] [ 3134] [depth= 1] . ( 1 sec) [ -21174.5377] [ 3046] [depth= 10] . ( 1 sec) [ -20954.7455] [ 3051] [depth= 4] . ( 1 sec) [ -17604.0429] [ 3058] [depth= 1] . ( 2 sec) [ -17568.1851] [ 3034] [depth= 8] . ( 2 sec) [ -17525.8935] [ 3026] [depth= 6] . ( 2 sec) [ -17406.6738] [ 2979] [depth= 1] . ( 2 sec) [ -17268.9668] [ 2972] [depth= 7] . ( 2 sec) [ -16853.9091] [ 2936] [depth= 10] . ( 2 sec) [ -16834.2369] [ 2954] [depth= 1] . ( 2 sec) [ -16562.1561] [ 2858] [depth= 4] . ( 2 sec) [ -16302.7102] [ 2771] [depth= 10] . ( 2 sec) [ -16104.6953] [ 2755] [depth= 3] . ( 2 sec) [ -15941.3850] [ 2754] [depth= 1] . ( 2 sec) [ -15821.9558] [ 2718] [depth= 10] . ( 2 sec) [ -15637.5287] [ 2676] [depth= 1] . ( 2 sec) [ -15450.5167] [ 2612] [depth= 10] . ( 2 sec) [ -15446.2582] [ 2610] [depth= 1] . ( 2 sec) [ -14889.0055] [ 2628] [depth= 1] . ( 2 sec) [ -14532.9491] [ 2595] [depth= 2] . ( 2 sec) [ -14456.6419] [ 2584] [depth= 1] . ( 2 sec) [ -14443.9589] [ 2585] [depth= 5] . ( 2 sec) [ -14348.6010] [ 2576] [depth= 3] . ( 2 sec) [ -14256.7639] [ 2539] [depth= 2] . ( 2 sec) [ -13918.5357] [ 2458] [depth= 3] . ( 2 sec) [ -13657.5514] [ 2388] [depth= 3] . ( 2 sec) [ -13540.0962] [ 2319] [depth= 2] . ( 2 sec) [ -13501.4369] [ 2315] [depth= 4] . ( 2 sec) [ -13129.6172] [ 2246] [depth= 6] . ( 2 sec) [ -13128.0193] [ 2246] [depth= 1] . ( 3 sec) [ -13126.9961] [ 2246] [depth= 1] . ( 3 sec) [ -12984.4286] [ 2218] [depth= 12] . ( 3 sec) [ -10717.9714] [ 2203] [depth= 2] . ( 3 sec) [ -10320.5040] [ 2165] [depth= 1] . ( 3 sec) [ -9720.6436] [ 2072] [depth= 4] . ( 3 sec) [ -9679.0087] [ 2067] [depth= 13] . ( 3 sec) [ -9423.2101] [ 2055] [depth= 1] . ( 3 sec) [ -9338.0862] [ 2042] [depth= 4] . ( 3 sec) [ -9150.4407] [ 2048] [depth= 6] . ( 3 sec) [ -9117.4558] [ 2044] [depth= 2] . ( 3 sec) [ -9046.7376] [ 2029] [depth= 4] . ( 3 sec) [ -8932.3054] [ 1996] [depth= 5] . ( 3 sec) [ -8801.3254] [ 1970] [depth= 8] . ( 3 sec) [ -8656.8628] [ 1957] [depth= 1] . ( 3 sec) [ -8645.8963] [ 1960] [depth= 1] . ( 3 sec) [ -8631.2155] [ 1959] [depth= 10] . ( 3 sec) [ -8292.3604] [ 1812] [depth= 7] . ( 3 sec) [ -8292.2521] [ 1816] [depth= 1] . ( 3 sec) [ -8268.0761] [ 1818] [depth= 1] . ( 3 sec) [ -8106.8683] [ 1805] [depth= 1] . ( 3 sec) [ -7936.1673] [ 1740] [depth= 6] . ( 3 sec) [ -7926.3759] [ 1732] [depth= 1] . ( 4 sec) [ -7921.9349] [ 1737] [depth= 2] . ( 4 sec) [ -7919.3939] [ 1719] [depth= 7] . ( 4 sec) [ -7917.7366] [ 1716] [depth= 1] . ( 4 sec) [ -7916.1855] [ 1713] [depth= 1] . ( 4 sec) [ -7882.5001] [ 1712] [depth= 1] . ( 4 sec) [ -7744.5635] [ 1645] [depth= 4] . ( 4 sec) [ -7744.4114] [ 1647] [depth= 1] . ( 4 sec) [ -7655.1193] [ 1632] [depth= 2] . ( 4 sec) [ -7632.8144] [ 1626] [depth= 3] . ( 4 sec) [ -7625.5329] [ 1632] [depth= 1] . ( 4 sec) [ -7621.9518] [ 1625] [depth= 7] . ( 4 sec) [ -7429.9279] [ 1559] [depth= 2] . ( 4 sec) [ -7367.7783] [ 1559] [depth= 1] . ( 4 sec) [ -7342.3006] [ 1563] [depth= 1] . ( 4 sec) [ -7333.8357] [ 1553] [depth= 2] . ( 4 sec) [ -7333.7220] [ 1549] [depth= 1] . ( 4 sec) [ -7250.3936] [ 1487] [depth= 11] . ( 4 sec) [ -7174.8145] [ 1447] [depth= 1] . ( 4 sec) [ -7173.0461] [ 1445] [depth= 1] . ( 5 sec) [ -7026.8208] [Branch lengths ] . ( 5 sec) [ -7021.9736] [GTR parameters ] . ( 5 sec) [ -7000.4564] [Alpha ][ 0.845233] . ( 5 sec) [ -6944.7910] [ 1424] [depth= 2] . ( 5 sec) [ -6944.4505] [ 1425] [depth= 1] . ( 6 sec) [ -6915.6403] [ 1405] [depth= 1] . ( 6 sec) [ -6893.6455] [ 1392] [depth= 1] . ( 6 sec) [ -6882.8031] [ 1381] [depth= 2] . ( 6 sec) [ -6882.3133] [ 1383] [depth= 2] . ( 6 sec) [ -6882.3003] [ 1387] [depth= 1] . ( 6 sec) [ -6874.5725] [ 1385] [depth= 1] . ( 6 sec) [ -6865.7099] [ 1382] [depth= 2] . ( 6 sec) [ -6864.1470] [ 1379] [depth= 1] . ( 6 sec) [ -6863.3332] [ 1380] [depth= 1] . ( 6 sec) [ -6859.8985] [ 1376] [depth= 1] . ( 7 sec) [ -6859.8585] [ 1376] [depth= 1] . ( 7 sec) [ -6859.5414] [ 1377] [depth= 1] . ( 7 sec) [ -6855.7553] [ 1373] [depth= 1] . ( 7 sec) [ -6854.4244] [ 1378] [depth= 5] . ( 7 sec) [ -6852.6206] [ 1375] [depth= 1] . ( 7 sec) [ -6852.5318] [ 1374] [depth= 1] . ( 8 sec) [ -6851.9396] [ 1379] [depth= 1] . ( 8 sec) [ -6851.7234] [ 1374] [depth= 1] . ( 9 sec) [ -6842.4762] [Branch lengths ] . ( 9 sec) [ -6842.2362] [GTR parameters ] . ( 9 sec) [ -6841.8569] [Alpha ][ 0.910529] . ( 10 sec) [ -6840.9585] [ 1378] [depth= 1] . ( 13 sec) [ -6840.4220] [Branch lengths ] . ( 13 sec) [ -6840.4150] [GTR parameters ] . ( 14 sec) [ -6840.4150] [Alpha ][ 0.910529] . ( 18 sec) [ -6840.3537] [Branch lengths ] . ( 38 sec) [ -6840.3492] [Branch lengths ] . ( 38 sec) [ -6840.3492] [Topology ] . ( 38 sec) [ -6840.3490] [Topology ] . ( 39 sec) [ -6840.3489] [GTR parameters ] . ( 39 sec) [ -6840.3489] [Alpha ][ 0.910529] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6840.348875. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6901.023459 . ( 1 sec) [ -6897.4830] [GTR parameters ] . ( 1 sec) [ -6896.2294] [Alpha ][ 0.867784] . ( 1 sec) [ -6896.2294] [Topology ] . ( 2 sec) [ -6854.9826] [Topology ] . ( 2 sec) [ -6848.5129] [Topology ] . ( 3 sec) [ -6847.5405] [Topology ] . ( 4 sec) [ -6847.1551] [Topology ] . ( 4 sec) [ -6846.9790] [Topology ] . ( 5 sec) [ -6846.8982] [Topology ] . ( 6 sec) [ -6846.8629] [Topology ] . ( 7 sec) [ -6846.8473] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.847277 . ( 12 sec) [ -6846.7912] [GTR parameters ] . ( 12 sec) [ -6846.6948] [Alpha ][ 0.900748] . ( 12 sec) [ -6846.6948] [Topology ] . ( 13 sec) [ -6846.6778] [Topology ] . ( 13 sec) [ -6846.6709] [Topology ] . ( 14 sec) [ -6846.6678] [Topology ] . ( 15 sec) [ -6846.6664] [Topology ] . ( 15 sec) [ -6846.6657] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.665678 . ( 21 sec) [ -6846.6656] [GTR parameters ] . ( 21 sec) [ -6846.6648] [Alpha ][ 0.903758] . ( 21 sec) [ -6846.6648] [Topology ] . ( 21 sec) [ -6846.6644] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.664389 . ( 26 sec) [ -6846.6644] [GTR parameters ] . ( 27 sec) [ -6846.6644] [Alpha ][ 0.903758] . ( 27 sec) [ -6846.6644] [Topology ] . ( 27 sec) [ -6846.6642] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 38 sec) [ -6897.4830] [GTR parameters ] . ( 38 sec) [ -6896.2294] [Alpha ][ 0.867784] . ( 38 sec) [ -6895.8096] [ 1375] [depth= 1] . ( 38 sec) [ -6895.2942] [ 1373] [depth= 1] . ( 38 sec) [ -6893.1697] [ 1373] [depth= 1] . ( 38 sec) [ -6891.8901] [ 1373] [depth= 1] . ( 38 sec) [ -6879.6208] [ 1372] [depth= 2] . ( 39 sec) [ -6878.5843] [ 1371] [depth= 1] . ( 39 sec) [ -6876.3357] [ 1372] [depth= 1] . ( 39 sec) [ -6876.0006] [ 1375] [depth= 1] . ( 39 sec) [ -6875.0245] [ 1376] [depth= 1] . ( 39 sec) [ -6874.4301] [ 1376] [depth= 1] . ( 39 sec) [ -6874.3400] [ 1376] [depth= 1] . ( 40 sec) [ -6874.1483] [ 1379] [depth= 1] . ( 40 sec) [ -6865.8024] [ 1383] [depth= 4] . ( 40 sec) [ -6862.2962] [ 1381] [depth= 2] . ( 40 sec) [ -6860.6229] [ 1382] [depth= 1] . ( 40 sec) [ -6860.1004] [ 1382] [depth= 1] . ( 40 sec) [ -6856.8223] [ 1386] [depth= 1] . ( 40 sec) [ -6856.4520] [ 1382] [depth= 1] . ( 41 sec) [ -6846.0383] [Branch lengths ] . ( 41 sec) [ -6845.9586] [GTR parameters ] . ( 41 sec) [ -6845.8781] [Alpha ][ 0.898235] . ( 42 sec) [ -6843.0671] [ 1379] [depth= 1] . ( 42 sec) [ -6842.4326] [ 1383] [depth= 1] . ( 43 sec) [ -6842.2954] [ 1378] [depth= 1] . ( 44 sec) [ -6842.1386] [ 1378] [depth= 1] . ( 45 sec) [ -6840.5218] [Branch lengths ] . ( 46 sec) [ -6840.5076] [GTR parameters ] . ( 46 sec) [ -6840.5014] [Alpha ][ 0.906999] . ( 50 sec) [ -6840.3669] [Branch lengths ] . ( 70 sec) [ -6840.3516] [Branch lengths ] . ( 70 sec) [ -6840.3516] [Topology ] . ( 71 sec) [ -6840.3505] [Topology ] . ( 71 sec) [ -6840.3502] [Topology ] . ( 71 sec) [ -6840.3500] [GTR parameters ] . ( 72 sec) [ -6840.3489] [Alpha ][ 0.910664] . ( 72 sec) [ -6840.3489] [Topology ] . ( 72 sec) [ -6840.3487] [Topology ] . ( 72 sec) [ -6840.3486] [GTR parameters ] . ( 72 sec) [ -6840.3486] [Alpha ][ 0.910664] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6846.664201 . Log likelihood obtained after SPR moves : -6840.348627 . Log likelihood of the current tree: -6840.348627. . Printing the most likely tree in file 'data73.phy_phyml_tree.txt'... . Best log likelihood : -6840.348627 . Time used 0h1m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo