.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_2006.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... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24661.0707] [GTR parameters ] . ( 1 sec) [ -24139.7416] [Alpha ][ 0.500960] . ( 1 sec) [ -23989.2197] [ 3730] [depth= 11] . ( 2 sec) [ -23926.9054] [ 3708] [depth= 10] . ( 2 sec) [ -23879.3112] [ 3695] [depth= 4] . ( 2 sec) [ -23869.7462] [ 3693] [depth= 2] . ( 2 sec) [ -23854.3650] [ 3688] [depth= 3] . ( 2 sec) [ -23790.7284] [ 3675] [depth= 6] . ( 2 sec) [ -23594.8356] [ 3661] [depth= 4] . ( 2 sec) [ -23205.9777] [ 3659] [depth= 13] . ( 2 sec) [ -22869.6042] [ 3627] [depth= 3] . ( 2 sec) [ -22854.7753] [ 3618] [depth= 1] . ( 3 sec) [ -22698.0549] [ 3585] [depth= 10] . ( 3 sec) [ -22395.4580] [ 3575] [depth= 7] . ( 3 sec) [ -22384.8675] [ 3565] [depth= 7] . ( 3 sec) [ -22265.0571] [ 3543] [depth= 7] . ( 3 sec) [ -22258.1428] [ 3541] [depth= 2] . ( 3 sec) [ -22190.4923] [ 3526] [depth= 4] . ( 3 sec) [ -22169.2848] [ 3515] [depth= 3] . ( 3 sec) [ -22150.5556] [ 3512] [depth= 1] . ( 4 sec) [ -21989.1390] [ 3484] [depth= 8] . ( 4 sec) [ -21949.6916] [ 3470] [depth= 1] . ( 4 sec) [ -21464.6752] [ 3455] [depth= 9] . ( 4 sec) [ -21022.8685] [ 3454] [depth= 3] . ( 4 sec) [ -20846.9767] [ 3393] [depth= 11] . ( 4 sec) [ -20777.4778] [ 3394] [depth= 3] . ( 5 sec) [ -20696.7755] [ 3378] [depth= 2] . ( 5 sec) [ -20660.0583] [ 3360] [depth= 6] . ( 5 sec) [ -20653.0137] [ 3363] [depth= 1] . ( 5 sec) [ -20496.6612] [ 3343] [depth= 9] . ( 5 sec) [ -20122.1150] [ 3318] [depth= 10] . ( 5 sec) [ -19981.6435] [ 3262] [depth= 9] . ( 5 sec) [ -19797.2646] [ 3239] [depth= 1] . ( 6 sec) [ -19726.6007] [ 3198] [depth= 10] . ( 6 sec) [ -19663.9064] [ 3184] [depth= 6] . ( 6 sec) [ -19554.7746] [ 3164] [depth= 13] . ( 6 sec) [ -19482.8457] [ 3150] [depth= 11] . ( 6 sec) [ -19118.6815] [ 3144] [depth= 6] . ( 6 sec) [ -18911.3087] [ 3047] [depth= 5] . ( 6 sec) [ -18788.1218] [ 3032] [depth= 10] . ( 7 sec) [ -18732.1820] [ 3014] [depth= 1] . ( 7 sec) [ -18628.1888] [ 2959] [depth= 11] . ( 7 sec) [ -18563.8959] [ 2949] [depth= 11] . ( 7 sec) [ -18428.6189] [ 2911] [depth= 2] . ( 7 sec) [ -18419.0783] [ 2905] [depth= 3] . ( 7 sec) [ -18396.4848] [ 2903] [depth= 2] . ( 7 sec) [ -18391.2286] [ 2901] [depth= 2] . ( 7 sec) [ -18359.7616] [ 2916] [depth= 1] . ( 8 sec) [ -18338.2469] [ 2901] [depth= 1] . ( 8 sec) [ -18334.9916] [ 2900] [depth= 1] . ( 8 sec) [ -18282.4344] [ 2900] [depth= 1] . ( 8 sec) [ -18263.3892] [ 2903] [depth= 3] . ( 8 sec) [ -18174.5467] [ 2895] [depth= 4] . ( 8 sec) [ -18048.8853] [ 2868] [depth= 2] . ( 8 sec) [ -18024.9471] [ 2864] [depth= 2] . ( 9 sec) [ -17958.1602] [ 2841] [depth= 6] . ( 9 sec) [ -17941.1813] [ 2862] [depth= 1] . ( 9 sec) [ -17750.9488] [ 2805] [depth= 4] . ( 9 sec) [ -17720.4596] [ 2805] [depth= 1] . ( 9 sec) [ -17644.0543] [ 2775] [depth= 15] . ( 9 sec) [ -17634.0997] [ 2773] [depth= 1] . ( 10 sec) [ -17607.6660] [ 2764] [depth= 1] . ( 10 sec) [ -17536.4557] [ 2750] [depth= 2] . ( 10 sec) [ -17303.3839] [ 2753] [depth= 7] . ( 10 sec) [ -17303.2592] [ 2753] [depth= 1] . ( 10 sec) [ -17283.3292] [ 2752] [depth= 2] . ( 10 sec) [ -17280.9089] [ 2749] [depth= 3] . ( 10 sec) [ -17266.5853] [ 2747] [depth= 3] . ( 11 sec) [ -17263.8540] [ 2745] [depth= 1] . ( 11 sec) [ -17258.8522] [ 2744] [depth= 1] . ( 11 sec) [ -17084.8460] [ 2708] [depth= 7] . ( 11 sec) [ -17069.8861] [ 2706] [depth= 1] . ( 11 sec) [ -17025.7405] [ 2693] [depth= 8] . ( 11 sec) [ -16033.9130] [ 2629] [depth= 9] . ( 11 sec) [ -16032.8396] [ 2632] [depth= 1] . ( 11 sec) [ -16010.8493] [ 2621] [depth= 1] . ( 12 sec) [ -15999.6705] [ 2620] [depth= 3] . ( 12 sec) [ -15911.7341] [ 2604] [depth= 11] . ( 12 sec) [ -15868.0882] [ 2596] [depth= 5] . ( 12 sec) [ -15776.4746] [ 2568] [depth= 8] . ( 13 sec) [ -15720.0250] [ 2563] [depth= 3] . ( 13 sec) [ -15653.4248] [ 2565] [depth= 4] . ( 13 sec) [ -15639.9329] [ 2560] [depth= 2] . ( 13 sec) [ -15629.7383] [ 2558] [depth= 2] . ( 13 sec) [ -15629.2637] [ 2558] [depth= 1] . ( 13 sec) [ -15618.2296] [ 2555] [depth= 6] . ( 13 sec) [ -15577.5558] [ 2545] [depth= 1] . ( 14 sec) [ -15555.3804] [ 2540] [depth= 5] . ( 14 sec) [ -15524.8839] [ 2522] [depth= 5] . ( 14 sec) [ -15349.4241] [ 2509] [depth= 3] . ( 14 sec) [ -15348.5598] [ 2507] [depth= 1] . ( 14 sec) [ -15323.4449] [ 2494] [depth= 2] . ( 14 sec) [ -15321.9464] [ 2496] [depth= 1] . ( 15 sec) [ -15291.4615] [ 2488] [depth= 3] . ( 15 sec) [ -15287.0103] [ 2492] [depth= 8] . ( 15 sec) [ -15284.3296] [ 2491] [depth= 1] . ( 15 sec) [ -15280.1463] [ 2491] [depth= 1] . ( 15 sec) [ -15272.9750] [ 2487] [depth= 3] . ( 15 sec) [ -15248.6629] [ 2484] [depth= 1] . ( 16 sec) [ -15245.7351] [ 2484] [depth= 1] . ( 16 sec) [ -15222.1843] [ 2474] [depth= 3] . ( 16 sec) [ -15205.5702] [ 2475] [depth= 2] . ( 16 sec) [ -15141.9942] [ 2453] [depth= 1] . ( 17 sec) [ -15047.0988] [Branch lengths ] . ( 22 sec) [ -14516.4346] [GTR parameters ] . ( 22 sec) [ -14386.0009] [Alpha ][ 0.250961] . ( 22 sec) [ -14352.9990] [ 2453] [depth= 3] . ( 23 sec) [ -14336.5969] [ 2448] [depth= 1] . ( 23 sec) [ -14330.1098] [ 2442] [depth= 2] . ( 23 sec) [ -14313.3634] [ 2444] [depth= 5] . ( 23 sec) [ -14294.7420] [ 2429] [depth= 1] . ( 23 sec) [ -14291.2976] [ 2429] [depth= 2] . ( 24 sec) [ -14287.0795] [ 2429] [depth= 1] . ( 24 sec) [ -14257.8910] [ 2418] [depth= 2] . ( 24 sec) [ -14251.9210] [ 2417] [depth= 1] . ( 24 sec) [ -14240.6933] [ 2405] [depth= 2] . ( 24 sec) [ -14239.2418] [ 2405] [depth= 1] . ( 24 sec) [ -14238.4480] [ 2405] [depth= 1] . ( 25 sec) [ -14238.0780] [ 2404] [depth= 1] . ( 25 sec) [ -14236.7516] [ 2400] [depth= 1] . ( 26 sec) [ -14154.2695] [ 2368] [depth= 3] . ( 26 sec) [ -14123.7373] [ 2356] [depth= 1] . ( 26 sec) [ -14114.0291] [ 2353] [depth= 2] . ( 27 sec) [ -14056.1339] [ 2323] [depth= 1] . ( 27 sec) [ -14041.0898] [ 2322] [depth= 1] . ( 27 sec) [ -14037.1652] [ 2321] [depth= 2] . ( 27 sec) [ -14036.3522] [ 2320] [depth= 1] . ( 27 sec) [ -14036.1996] [ 2318] [depth= 1] . ( 28 sec) [ -14035.8439] [ 2318] [depth= 1] . ( 29 sec) [ -14031.7267] [ 2322] [depth= 1] . ( 29 sec) [ -14029.3908] [ 2317] [depth= 1] . ( 29 sec) [ -14028.5305] [ 2318] [depth= 1] . ( 30 sec) [ -14026.0953] [ 2318] [depth= 1] . ( 31 sec) [ -14024.8392] [ 2319] [depth= 4] . ( 31 sec) [ -14024.4343] [ 2317] [depth= 1] . ( 32 sec) [ -14020.0132] [ 2315] [depth= 1] . ( 33 sec) [ -14019.8548] [ 2315] [depth= 1] . ( 34 sec) [ -14019.7075] [ 2314] [depth= 1] . ( 34 sec) [ -14019.6311] [ 2318] [depth= 1] . ( 34 sec) [ -14017.9707] [ 2314] [depth= 2] . ( 35 sec) [ -14017.0571] [ 2316] [depth= 1] . ( 35 sec) [ -14016.1097] [ 2320] [depth= 2] . ( 38 sec) [ -14015.7142] [ 2318] [depth= 1] . ( 38 sec) [ -14013.6710] [ 2314] [depth= 1] . ( 40 sec) [ -13990.9127] [Branch lengths ] . ( 45 sec) [ -13990.1158] [GTR parameters ] . ( 45 sec) [ -13990.0889] [Alpha ][ 0.248310] . ( 46 sec) [ -13988.2438] [ 2315] [depth= 1] . ( 50 sec) [ -13987.9096] [ 2315] [depth= 2] . ( 51 sec) [ -13987.7167] [ 2312] [depth= 1] . ( 59 sec) [ -13987.5135] [ 2316] [depth= 1] . ( 64 sec) [ -13986.5110] [Branch lengths ] . ( 68 sec) [ -13986.4983] [GTR parameters ] . ( 68 sec) [ -13986.4915] [Alpha ][ 0.249578] . ( 75 sec) [ -13986.4310] [ 2312] [depth= 1] . ( 86 sec) [ -13986.0551] [Branch lengths ] . ( 88 sec) [ -13986.0549] [GTR parameters ] . ( 88 sec) [ -13986.0527] [Alpha ][ 0.250281] . ( 167 sec) [ -13986.0310] [Branch lengths ] . ( 167 sec) [ -13986.0310] [Topology ] . ( 169 sec) [ -13986.0288] [Topology ] . ( 171 sec) [ -13986.0282] [Topology ] . ( 172 sec) [ -13986.0280] [GTR parameters ] . ( 173 sec) [ -13986.0278] [Alpha ][ 0.250531] . ( 173 sec) [ -13986.0278] [Topology ] . ( 175 sec) [ -13986.0274] [Topology ] . ( 178 sec) [ -13986.0273] [GTR parameters ] . ( 178 sec) [ -13986.0273] [Alpha ][ 0.250531] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13986.027309. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23946.5343] [GTR parameters ] . ( 2 sec) [ -23436.3906] [Alpha ][ 0.500960] . ( 2 sec) [ -23102.0038] [ 3675] [depth= 6] . ( 2 sec) [ -22914.4290] [ 3651] [depth= 8] . ( 2 sec) [ -22684.3795] [ 3653] [depth= 1] . ( 2 sec) [ -22671.1036] [ 3649] [depth= 1] . ( 2 sec) [ -22594.7748] [ 3596] [depth= 2] . ( 2 sec) [ -22564.2263] [ 3591] [depth= 2] . ( 2 sec) [ -22315.1467] [ 3584] [depth= 3] . ( 2 sec) [ -22170.5415] [ 3584] [depth= 2] . ( 3 sec) [ -22105.6132] [ 3557] [depth= 6] . ( 3 sec) [ -22104.2392] [ 3558] [depth= 1] . ( 3 sec) [ -22022.9837] [ 3545] [depth= 2] . ( 3 sec) [ -21869.2856] [ 3509] [depth= 13] . ( 3 sec) [ -21833.4524] [ 3489] [depth= 6] . ( 3 sec) [ -21770.2444] [ 3491] [depth= 1] . ( 3 sec) [ -21150.3018] [ 3458] [depth= 15] . ( 3 sec) [ -20768.0478] [ 3385] [depth= 10] . ( 3 sec) [ -20682.1165] [ 3356] [depth= 15] . ( 4 sec) [ -20670.0096] [ 3353] [depth= 14] . ( 4 sec) [ -20496.0201] [ 3347] [depth= 15] . ( 4 sec) [ -20393.7790] [ 3341] [depth= 2] . ( 4 sec) [ -20356.5670] [ 3330] [depth= 5] . ( 4 sec) [ -20197.7867] [ 3313] [depth= 17] . ( 4 sec) [ -20103.4632] [ 3296] [depth= 11] . ( 4 sec) [ -19972.7745] [ 3285] [depth= 5] . ( 4 sec) [ -19766.0728] [ 3250] [depth= 13] . ( 5 sec) [ -19706.2161] [ 3248] [depth= 13] . ( 5 sec) [ -19643.3513] [ 3246] [depth= 3] . ( 5 sec) [ -19637.6602] [ 3249] [depth= 1] . ( 5 sec) [ -19578.9745] [ 3238] [depth= 14] . ( 5 sec) [ -19491.7645] [ 3207] [depth= 2] . ( 5 sec) [ -19336.1830] [ 3159] [depth= 10] . ( 6 sec) [ -19029.9440] [ 3113] [depth= 5] . ( 6 sec) [ -19018.1191] [ 3113] [depth= 2] . ( 6 sec) [ -19014.6804] [ 3113] [depth= 1] . ( 6 sec) [ -19004.4036] [ 3111] [depth= 1] . ( 6 sec) [ -18823.3186] [ 3094] [depth= 11] . ( 6 sec) [ -18815.0076] [ 3090] [depth= 2] . ( 6 sec) [ -18721.9410] [ 3068] [depth= 3] . ( 6 sec) [ -18392.0299] [ 2985] [depth= 1] . ( 7 sec) [ -18284.9528] [ 2941] [depth= 4] . ( 7 sec) [ -18180.4287] [ 2919] [depth= 13] . ( 7 sec) [ -17940.8003] [ 2858] [depth= 12] . ( 7 sec) [ -17703.8801] [ 2833] [depth= 1] . ( 7 sec) [ -17305.9533] [ 2797] [depth= 10] . ( 7 sec) [ -17264.0450] [ 2790] [depth= 7] . ( 7 sec) [ -17220.3780] [ 2780] [depth= 1] . ( 7 sec) [ -17192.1433] [ 2775] [depth= 14] . ( 7 sec) [ -17170.9055] [ 2775] [depth= 1] . ( 8 sec) [ -17169.0837] [ 2776] [depth= 15] . ( 8 sec) [ -17128.2294] [ 2767] [depth= 13] . ( 8 sec) [ -17084.2795] [ 2752] [depth= 2] . ( 8 sec) [ -17050.5977] [ 2740] [depth= 1] . ( 8 sec) [ -17049.5092] [ 2739] [depth= 2] . ( 8 sec) [ -16626.5325] [ 2705] [depth= 8] . ( 8 sec) [ -16553.3556] [ 2686] [depth= 5] . ( 9 sec) [ -16527.7770] [ 2688] [depth= 2] . ( 9 sec) [ -16516.2600] [ 2680] [depth= 8] . ( 9 sec) [ -16490.8043] [ 2675] [depth= 2] . ( 9 sec) [ -16408.0836] [ 2658] [depth= 5] . ( 9 sec) [ -16288.8467] [ 2648] [depth= 5] . ( 9 sec) [ -16274.6147] [ 2648] [depth= 1] . ( 9 sec) [ -16262.8440] [ 2643] [depth= 1] . ( 9 sec) [ -16078.8716] [ 2640] [depth= 15] . ( 10 sec) [ -16076.0525] [ 2645] [depth= 2] . ( 10 sec) [ -16056.3361] [ 2636] [depth= 14] . ( 10 sec) [ -16009.8948] [ 2620] [depth= 7] . ( 11 sec) [ -15961.0516] [ 2607] [depth= 1] . ( 11 sec) [ -15841.6640] [ 2594] [depth= 9] . ( 11 sec) [ -15819.6162] [ 2601] [depth= 3] . ( 11 sec) [ -15817.4985] [ 2585] [depth= 10] . ( 11 sec) [ -15785.2133] [ 2569] [depth= 5] . ( 11 sec) [ -15747.8329] [ 2557] [depth= 1] . ( 12 sec) [ -15744.2163] [ 2554] [depth= 1] . ( 12 sec) [ -15734.6172] [ 2554] [depth= 4] . ( 12 sec) [ -15718.8760] [ 2559] [depth= 9] . ( 12 sec) [ -15654.0523] [ 2544] [depth= 6] . ( 12 sec) [ -15641.8079] [ 2547] [depth= 1] . ( 12 sec) [ -15635.6959] [ 2544] [depth= 1] . ( 12 sec) [ -15534.7835] [ 2510] [depth= 1] . ( 12 sec) [ -15454.1555] [ 2495] [depth= 5] . ( 13 sec) [ -15451.9374] [ 2496] [depth= 4] . ( 13 sec) [ -15338.6198] [ 2453] [depth= 9] . ( 13 sec) [ -15253.1016] [ 2436] [depth= 4] . ( 13 sec) [ -15235.1151] [ 2431] [depth= 4] . ( 13 sec) [ -15219.0257] [ 2426] [depth= 1] . ( 13 sec) [ -15193.4934] [ 2422] [depth= 2] . ( 13 sec) [ -15138.5153] [ 2411] [depth= 1] . ( 14 sec) [ -15138.2316] [ 2402] [depth= 9] . ( 14 sec) [ -15125.4382] [ 2402] [depth= 1] . ( 14 sec) [ -15121.0566] [ 2395] [depth= 9] . ( 15 sec) [ -15110.9493] [ 2395] [depth= 12] . ( 15 sec) [ -14987.7852] [ 2372] [depth= 2] . ( 15 sec) [ -14982.7981] [ 2375] [depth= 1] . ( 15 sec) [ -14982.5373] [ 2375] [depth= 1] . ( 15 sec) [ -14976.5585] [ 2375] [depth= 1] . ( 16 sec) [ -14968.7879] [ 2373] [depth= 1] . ( 16 sec) [ -14966.0015] [ 2375] [depth= 1] . ( 17 sec) [ -14866.4806] [Branch lengths ] . ( 21 sec) [ -14375.2857] [GTR parameters ] . ( 21 sec) [ -14256.8658] [Alpha ][ 0.250961] . ( 21 sec) [ -14256.0373] [ 2373] [depth= 1] . ( 21 sec) [ -14171.3448] [ 2345] [depth= 2] . ( 21 sec) [ -14159.3878] [ 2347] [depth= 3] . ( 22 sec) [ -14131.2528] [ 2335] [depth= 6] . ( 22 sec) [ -14130.9480] [ 2339] [depth= 1] . ( 23 sec) [ -14127.1511] [ 2331] [depth= 1] . ( 24 sec) [ -14126.5607] [ 2332] [depth= 2] . ( 24 sec) [ -14125.0244] [ 2334] [depth= 2] . ( 24 sec) [ -14120.1103] [ 2330] [depth= 2] . ( 24 sec) [ -14114.0747] [ 2330] [depth= 1] . ( 25 sec) [ -14086.1624] [ 2331] [depth= 1] . ( 25 sec) [ -14082.4976] [ 2331] [depth= 1] . ( 25 sec) [ -14078.2557] [ 2330] [depth= 1] . ( 26 sec) [ -14077.9173] [ 2330] [depth= 1] . ( 27 sec) [ -14076.5669] [ 2330] [depth= 2] . ( 28 sec) [ -14041.1039] [ 2319] [depth= 3] . ( 28 sec) [ -14039.8942] [ 2315] [depth= 1] . ( 28 sec) [ -14033.5306] [ 2313] [depth= 1] . ( 28 sec) [ -14032.0423] [ 2313] [depth= 1] . ( 29 sec) [ -14032.0056] [ 2312] [depth= 1] . ( 30 sec) [ -14030.8900] [ 2313] [depth= 1] . ( 30 sec) [ -14030.1573] [ 2310] [depth= 3] . ( 30 sec) [ -14027.9516] [ 2312] [depth= 1] . ( 30 sec) [ -14022.3699] [ 2310] [depth= 1] . ( 31 sec) [ -14022.1515] [ 2314] [depth= 2] . ( 31 sec) [ -14019.2823] [ 2310] [depth= 1] . ( 32 sec) [ -14018.7968] [ 2312] [depth= 1] . ( 33 sec) [ -14017.6173] [ 2310] [depth= 1] . ( 34 sec) [ -14016.9905] [ 2311] [depth= 1] . ( 35 sec) [ -14015.7244] [ 2312] [depth= 1] . ( 36 sec) [ -14014.4335] [ 2310] [depth= 1] . ( 36 sec) [ -14014.2956] [ 2312] [depth= 1] . ( 37 sec) [ -13997.9260] [Branch lengths ] . ( 42 sec) [ -13996.7398] [GTR parameters ] . ( 42 sec) [ -13996.6991] [Alpha ][ 0.247955] . ( 43 sec) [ -13990.6417] [ 2313] [depth= 3] . ( 45 sec) [ -13990.4879] [ 2311] [depth= 1] . ( 51 sec) [ -13990.4216] [ 2313] [depth= 1] . ( 61 sec) [ -13990.4115] [ 2311] [depth= 1] . ( 62 sec) [ -13988.6297] [Branch lengths ] . ( 67 sec) [ -13988.6006] [GTR parameters ] . ( 67 sec) [ -13988.5925] [Alpha ][ 0.249346] . ( 88 sec) [ -13988.4439] [Branch lengths ] . ( 100 sec) [ -13987.1471] [ 2319] [depth= 8] . ( 116 sec) [ -13986.3708] [ 2318] [depth= 1] . ( 121 sec) [ -13986.3313] [ 2317] [depth= 1] . ( 136 sec) [ -13986.1457] [ 2317] [depth= 1] . ( 166 sec) [ -13984.4406] [Branch lengths ] . ( 170 sec) [ -13984.4122] [GTR parameters ] . ( 170 sec) [ -13984.4114] [Alpha ][ 0.248840] . ( 249 sec) [ -13984.3606] [Branch lengths ] . ( 249 sec) [ -13984.3606] [Topology ] . ( 251 sec) [ -13984.3600] [Topology ] . ( 251 sec) [ -13984.3599] [GTR parameters ] . ( 251 sec) [ -13984.3599] [Alpha ][ 0.248840] . Checking for NNIs, optimizing five branches... . ( 266 sec) [ -13984.1465] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13984.146514. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -25424.0440] [GTR parameters ] . ( 3 sec) [ -24811.0751] [Alpha ][ 0.500960] . ( 3 sec) [ -24560.8873] [ 3785] [depth= 10] . ( 3 sec) [ -24119.3244] [ 3764] [depth= 11] . ( 3 sec) [ -24100.2541] [ 3771] [depth= 1] . ( 3 sec) [ -24061.9716] [ 3756] [depth= 4] . ( 4 sec) [ -24012.5847] [ 3749] [depth= 2] . ( 4 sec) [ -23924.4177] [ 3735] [depth= 11] . ( 4 sec) [ -23907.8283] [ 3733] [depth= 1] . ( 4 sec) [ -23677.7450] [ 3730] [depth= 6] . ( 4 sec) [ -23642.1992] [ 3721] [depth= 3] . ( 4 sec) [ -23638.6388] [ 3720] [depth= 1] . ( 4 sec) [ -23365.5813] [ 3716] [depth= 2] . ( 4 sec) [ -23037.0191] [ 3716] [depth= 5] . ( 4 sec) [ -22725.6012] [ 3690] [depth= 10] . ( 5 sec) [ -22628.3425] [ 3669] [depth= 7] . ( 5 sec) [ -22524.9786] [ 3638] [depth= 20] . ( 5 sec) [ -22504.2621] [ 3621] [depth= 9] . ( 5 sec) [ -22372.8285] [ 3618] [depth= 4] . ( 5 sec) [ -22288.1571] [ 3612] [depth= 6] . ( 5 sec) [ -21840.3425] [ 3559] [depth= 13] . ( 5 sec) [ -21596.1785] [ 3546] [depth= 1] . ( 5 sec) [ -21572.5030] [ 3542] [depth= 10] . ( 6 sec) [ -21300.9554] [ 3518] [depth= 1] . ( 6 sec) [ -21257.5990] [ 3486] [depth= 11] . ( 6 sec) [ -21227.1612] [ 3485] [depth= 5] . ( 6 sec) [ -20999.9633] [ 3459] [depth= 7] . ( 6 sec) [ -20906.2337] [ 3467] [depth= 1] . ( 6 sec) [ -20739.9159] [ 3457] [depth= 8] . ( 6 sec) [ -20335.8551] [ 3412] [depth= 1] . ( 6 sec) [ -20068.4731] [ 3360] [depth= 15] . ( 6 sec) [ -20045.4140] [ 3351] [depth= 1] . ( 7 sec) [ -20025.7677] [ 3346] [depth= 6] . ( 7 sec) [ -19558.7141] [ 3286] [depth= 4] . ( 7 sec) [ -19551.4733] [ 3293] [depth= 1] . ( 7 sec) [ -19492.2845] [ 3274] [depth= 13] . ( 7 sec) [ -19384.4542] [ 3271] [depth= 18] . ( 7 sec) [ -19351.9608] [ 3246] [depth= 1] . ( 7 sec) [ -18792.6109] [ 3170] [depth= 4] . ( 7 sec) [ -18747.5305] [ 3150] [depth= 2] . ( 8 sec) [ -18696.6059] [ 3146] [depth= 1] . ( 8 sec) [ -18620.9708] [ 3121] [depth= 5] . ( 8 sec) [ -18579.2365] [ 3118] [depth= 11] . ( 8 sec) [ -18398.8381] [ 3097] [depth= 18] . ( 8 sec) [ -18133.3244] [ 3075] [depth= 15] . ( 8 sec) [ -18019.6702] [ 3047] [depth= 12] . ( 8 sec) [ -18010.6839] [ 3052] [depth= 1] . ( 8 sec) [ -17800.7129] [ 3046] [depth= 1] . ( 9 sec) [ -17735.8049] [ 3030] [depth= 4] . ( 9 sec) [ -17607.9191] [ 2998] [depth= 1] . ( 9 sec) [ -17397.9726] [ 2989] [depth= 14] . ( 9 sec) [ -17359.0378] [ 2984] [depth= 3] . ( 9 sec) [ -17334.4322] [ 2981] [depth= 5] . ( 9 sec) [ -17297.6945] [ 2980] [depth= 1] . ( 9 sec) [ -17120.6709] [ 2987] [depth= 1] . ( 9 sec) [ -17045.7400] [ 2972] [depth= 6] . ( 10 sec) [ -17028.8947] [ 2968] [depth= 1] . ( 10 sec) [ -17005.0076] [ 2962] [depth= 6] . ( 10 sec) [ -16853.2208] [ 2941] [depth= 3] . ( 10 sec) [ -16711.5323] [ 2879] [depth= 3] . ( 10 sec) [ -16704.9033] [ 2877] [depth= 1] . ( 10 sec) [ -16668.9213] [ 2862] [depth= 2] . ( 10 sec) [ -16654.3510] [ 2860] [depth= 1] . ( 10 sec) [ -16561.1220] [ 2854] [depth= 2] . ( 11 sec) [ -16556.1795] [ 2854] [depth= 1] . ( 11 sec) [ -16465.3249] [ 2839] [depth= 1] . ( 11 sec) [ -16311.9500] [ 2784] [depth= 10] . ( 11 sec) [ -16278.4025] [ 2778] [depth= 1] . ( 11 sec) [ -16153.2970] [ 2778] [depth= 11] . ( 11 sec) [ -16138.3734] [ 2772] [depth= 1] . ( 11 sec) [ -16123.9104] [ 2766] [depth= 2] . ( 12 sec) [ -16117.7391] [ 2763] [depth= 1] . ( 12 sec) [ -16087.0188] [ 2762] [depth= 3] . ( 12 sec) [ -16085.8280] [ 2763] [depth= 2] . ( 12 sec) [ -16067.4224] [ 2756] [depth= 3] . ( 12 sec) [ -16062.1228] [ 2756] [depth= 1] . ( 12 sec) [ -16036.6512] [ 2744] [depth= 4] . ( 13 sec) [ -16005.4546] [ 2737] [depth= 1] . ( 13 sec) [ -15976.2192] [ 2732] [depth= 1] . ( 13 sec) [ -15915.3260] [ 2714] [depth= 11] . ( 13 sec) [ -15859.4365] [ 2686] [depth= 9] . ( 13 sec) [ -15854.2562] [ 2694] [depth= 1] . ( 14 sec) [ -15846.2600] [ 2690] [depth= 6] . ( 14 sec) [ -15615.7702] [ 2628] [depth= 5] . ( 14 sec) [ -15607.1009] [ 2626] [depth= 4] . ( 14 sec) [ -15590.0278] [ 2631] [depth= 1] . ( 14 sec) [ -15587.4893] [ 2628] [depth= 1] . ( 14 sec) [ -15460.5741] [ 2594] [depth= 4] . ( 14 sec) [ -15448.4708] [ 2593] [depth= 1] . ( 14 sec) [ -15431.2542] [ 2588] [depth= 1] . ( 14 sec) [ -15427.3146] [ 2587] [depth= 1] . ( 15 sec) [ -15356.4552] [ 2586] [depth= 5] . ( 15 sec) [ -15298.2469] [ 2527] [depth= 5] . ( 15 sec) [ -15292.8063] [ 2527] [depth= 1] . ( 15 sec) [ -15284.2580] [ 2523] [depth= 8] . ( 15 sec) [ -15116.7800] [ 2489] [depth= 1] . ( 16 sec) [ -15096.8859] [ 2478] [depth= 2] . ( 16 sec) [ -15092.8584] [ 2474] [depth= 4] . ( 16 sec) [ -15071.1371] [ 2468] [depth= 3] . ( 16 sec) [ -15069.2560] [ 2466] [depth= 1] . ( 16 sec) [ -14926.4760] [ 2427] [depth= 5] . ( 16 sec) [ -14896.5037] [ 2421] [depth= 5] . ( 16 sec) [ -14879.4323] [ 2422] [depth= 7] . ( 16 sec) [ -14845.0509] [ 2413] [depth= 7] . ( 17 sec) [ -14816.6182] [ 2409] [depth= 2] . ( 17 sec) [ -14811.0498] [ 2405] [depth= 7] . ( 17 sec) [ -14746.6539] [ 2399] [depth= 1] . ( 17 sec) [ -14741.4608] [ 2398] [depth= 1] . ( 17 sec) [ -14734.0710] [ 2398] [depth= 2] . ( 18 sec) [ -14724.3585] [ 2400] [depth= 1] . ( 18 sec) [ -14722.4276] [ 2401] [depth= 1] . ( 19 sec) [ -14588.0613] [Branch lengths ] . ( 24 sec) [ -14360.6579] [GTR parameters ] . ( 24 sec) [ -14239.2456] [Alpha ][ 0.250961] . ( 24 sec) [ -14234.6506] [ 2403] [depth= 2] . ( 25 sec) [ -14194.5597] [ 2391] [depth= 5] . ( 25 sec) [ -14184.5364] [ 2377] [depth= 3] . ( 25 sec) [ -14182.9415] [ 2377] [depth= 1] . ( 25 sec) [ -14180.0440] [ 2370] [depth= 5] . ( 26 sec) [ -14172.2465] [ 2371] [depth= 2] . ( 26 sec) [ -14171.6626] [ 2372] [depth= 1] . ( 26 sec) [ -14162.0305] [ 2361] [depth= 1] . ( 26 sec) [ -14151.1089] [ 2364] [depth= 1] . ( 26 sec) [ -14147.0971] [ 2363] [depth= 1] . ( 27 sec) [ -14137.8980] [ 2356] [depth= 2] . ( 27 sec) [ -14131.5532] [ 2350] [depth= 2] . ( 27 sec) [ -14130.4427] [ 2349] [depth= 1] . ( 28 sec) [ -14129.8141] [ 2350] [depth= 1] . ( 29 sec) [ -14129.5223] [ 2348] [depth= 2] . ( 29 sec) [ -14122.7124] [ 2348] [depth= 1] . ( 29 sec) [ -14121.4994] [ 2350] [depth= 1] . ( 29 sec) [ -14117.5018] [ 2349] [depth= 7] . ( 30 sec) [ -14117.1444] [ 2349] [depth= 1] . ( 30 sec) [ -14116.5480] [ 2351] [depth= 1] . ( 31 sec) [ -14116.3585] [ 2349] [depth= 1] . ( 31 sec) [ -14115.9693] [ 2353] [depth= 1] . ( 32 sec) [ -14038.8734] [ 2319] [depth= 1] . ( 32 sec) [ -14029.2940] [ 2321] [depth= 1] . ( 33 sec) [ -14029.2387] [ 2322] [depth= 1] . ( 33 sec) [ -14028.9067] [ 2327] [depth= 1] . ( 33 sec) [ -14028.3902] [ 2328] [depth= 1] . ( 36 sec) [ -14026.6280] [ 2332] [depth= 1] . ( 36 sec) [ -14024.0654] [ 2331] [depth= 1] . ( 37 sec) [ -14023.3861] [ 2333] [depth= 1] . ( 40 sec) [ -14023.3406] [ 2329] [depth= 1] . ( 43 sec) [ -13997.1497] [Branch lengths ] . ( 46 sec) [ -13996.2639] [GTR parameters ] . ( 47 sec) [ -13996.2586] [Alpha ][ 0.249780] . ( 47 sec) [ -13996.1773] [ 2327] [depth= 1] . ( 51 sec) [ -13995.7194] [ 2325] [depth= 1] . ( 55 sec) [ -13995.5906] [ 2323] [depth= 1] . ( 59 sec) [ -13995.3552] [ 2327] [depth= 5] . ( 67 sec) [ -13993.9472] [ 2326] [depth= 1] . ( 69 sec) [ -13991.8155] [Branch lengths ] . ( 72 sec) [ -13991.8022] [GTR parameters ] . ( 72 sec) [ -13991.8022] [Alpha ][ 0.249780] . ( 95 sec) [ -13991.6932] [Branch lengths ] . ( 175 sec) [ -13991.6872] [Branch lengths ] . ( 175 sec) [ -13991.6872] [Topology ] . ( 177 sec) [ -13991.6867] [Topology ] . ( 177 sec) [ -13991.6866] [GTR parameters ] . ( 178 sec) [ -13991.6855] [Alpha ][ 0.249206] . ( 178 sec) [ -13991.6855] [Topology ] . ( 180 sec) [ -13991.6852] [Topology ] . ( 181 sec) [ -13991.6846] [GTR parameters ] . ( 182 sec) [ -13991.6846] [Alpha ][ 0.249206] . Checking for NNIs, optimizing five branches... . ( 197 sec) [ -13991.2008] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13991.200834. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24003.1252] [GTR parameters ] . ( 1 sec) [ -23483.5501] [Alpha ][ 0.500960] . ( 1 sec) [ -23220.2491] [ 3707] [depth= 7] . ( 1 sec) [ -23141.2857] [ 3695] [depth= 5] . ( 2 sec) [ -23017.3406] [ 3675] [depth= 4] . ( 2 sec) [ -22995.7121] [ 3662] [depth= 1] . ( 2 sec) [ -22831.3081] [ 3644] [depth= 9] . ( 2 sec) [ -22637.0932] [ 3633] [depth= 7] . ( 2 sec) [ -22568.3730] [ 3608] [depth= 1] . ( 2 sec) [ -22436.3684] [ 3594] [depth= 8] . ( 2 sec) [ -22429.3312] [ 3593] [depth= 1] . ( 2 sec) [ -22412.7041] [ 3589] [depth= 3] . ( 3 sec) [ -22386.5465] [ 3579] [depth= 2] . ( 3 sec) [ -22275.0520] [ 3577] [depth= 7] . ( 3 sec) [ -22207.3734] [ 3572] [depth= 4] . ( 3 sec) [ -22199.0028] [ 3574] [depth= 1] . ( 3 sec) [ -22112.5036] [ 3565] [depth= 5] . ( 3 sec) [ -21925.3672] [ 3557] [depth= 1] . ( 3 sec) [ -21771.3824] [ 3526] [depth= 6] . ( 3 sec) [ -21753.0559] [ 3555] [depth= 1] . ( 3 sec) [ -21672.8405] [ 3547] [depth= 4] . ( 4 sec) [ -21621.6780] [ 3506] [depth= 8] . ( 4 sec) [ -21527.7962] [ 3488] [depth= 3] . ( 4 sec) [ -21447.1646] [ 3477] [depth= 5] . ( 4 sec) [ -21433.6823] [ 3483] [depth= 1] . ( 4 sec) [ -21348.3275] [ 3481] [depth= 8] . ( 4 sec) [ -21265.0308] [ 3446] [depth= 1] . ( 4 sec) [ -21219.9062] [ 3427] [depth= 6] . ( 4 sec) [ -21186.9693] [ 3430] [depth= 1] . ( 5 sec) [ -20798.2795] [ 3401] [depth= 5] . ( 5 sec) [ -20120.1997] [ 3296] [depth= 1] . ( 5 sec) [ -20030.5166] [ 3289] [depth= 8] . ( 5 sec) [ -19980.0221] [ 3281] [depth= 12] . ( 5 sec) [ -19702.0085] [ 3243] [depth= 14] . ( 5 sec) [ -19643.9902] [ 3246] [depth= 2] . ( 5 sec) [ -19182.3663] [ 3137] [depth= 8] . ( 5 sec) [ -19030.2527] [ 3122] [depth= 7] . ( 6 sec) [ -18976.0399] [ 3119] [depth= 1] . ( 6 sec) [ -18891.0583] [ 3084] [depth= 13] . ( 6 sec) [ -18818.6321] [ 3069] [depth= 2] . ( 6 sec) [ -18784.4431] [ 3061] [depth= 1] . ( 6 sec) [ -18676.8539] [ 3045] [depth= 10] . ( 6 sec) [ -18649.9869] [ 3035] [depth= 1] . ( 6 sec) [ -18327.4640] [ 2944] [depth= 7] . ( 7 sec) [ -18200.3664] [ 2926] [depth= 8] . ( 7 sec) [ -18196.2954] [ 2925] [depth= 1] . ( 7 sec) [ -18193.2257] [ 2927] [depth= 2] . ( 7 sec) [ -18151.4794] [ 2910] [depth= 2] . ( 7 sec) [ -18048.7622] [ 2877] [depth= 14] . ( 7 sec) [ -18001.1376] [ 2867] [depth= 1] . ( 7 sec) [ -17639.4618] [ 2853] [depth= 14] . ( 7 sec) [ -17624.5915] [ 2850] [depth= 2] . ( 8 sec) [ -17620.8758] [ 2849] [depth= 1] . ( 8 sec) [ -17585.3506] [ 2842] [depth= 7] . ( 8 sec) [ -17488.0185] [ 2819] [depth= 1] . ( 8 sec) [ -17483.6865] [ 2820] [depth= 1] . ( 8 sec) [ -17274.8029] [ 2815] [depth= 10] . ( 8 sec) [ -17081.6182] [ 2814] [depth= 8] . ( 8 sec) [ -17079.2567] [ 2811] [depth= 3] . ( 9 sec) [ -17020.0216] [ 2786] [depth= 1] . ( 9 sec) [ -16905.8852] [ 2775] [depth= 7] . ( 9 sec) [ -16897.8579] [ 2772] [depth= 1] . ( 9 sec) [ -16824.4598] [ 2751] [depth= 1] . ( 9 sec) [ -16720.4771] [ 2745] [depth= 8] . ( 9 sec) [ -16673.9348] [ 2744] [depth= 1] . ( 9 sec) [ -16646.5684] [ 2764] [depth= 1] . ( 10 sec) [ -16394.4116] [ 2711] [depth= 16] . ( 10 sec) [ -16363.1572] [ 2690] [depth= 1] . ( 10 sec) [ -16357.9927] [ 2686] [depth= 4] . ( 10 sec) [ -16262.6924] [ 2678] [depth= 7] . ( 10 sec) [ -16253.0042] [ 2672] [depth= 5] . ( 10 sec) [ -16236.5198] [ 2670] [depth= 1] . ( 10 sec) [ -16202.6588] [ 2657] [depth= 4] . ( 10 sec) [ -16176.0884] [ 2651] [depth= 2] . ( 10 sec) [ -16156.4293] [ 2644] [depth= 1] . ( 11 sec) [ -16139.3690] [ 2641] [depth= 3] . ( 11 sec) [ -16118.4526] [ 2639] [depth= 5] . ( 11 sec) [ -16117.8703] [ 2641] [depth= 1] . ( 11 sec) [ -16030.4489] [ 2615] [depth= 16] . ( 11 sec) [ -16029.2910] [ 2614] [depth= 1] . ( 11 sec) [ -15977.5490] [ 2602] [depth= 1] . ( 12 sec) [ -15948.8081] [ 2599] [depth= 1] . ( 12 sec) [ -15921.5730] [ 2595] [depth= 1] . ( 12 sec) [ -15897.8063] [ 2595] [depth= 1] . ( 12 sec) [ -15884.7006] [ 2593] [depth= 1] . ( 12 sec) [ -15881.5063] [ 2595] [depth= 1] . ( 12 sec) [ -15799.3684] [ 2588] [depth= 10] . ( 12 sec) [ -15761.8052] [ 2575] [depth= 4] . ( 13 sec) [ -15743.3312] [ 2568] [depth= 1] . ( 13 sec) [ -15730.9550] [ 2563] [depth= 1] . ( 13 sec) [ -15725.4849] [ 2560] [depth= 3] . ( 13 sec) [ -15707.6301] [ 2550] [depth= 4] . ( 13 sec) [ -15696.7843] [ 2547] [depth= 2] . ( 13 sec) [ -15574.3348] [ 2534] [depth= 4] . ( 14 sec) [ -15572.8999] [ 2534] [depth= 1] . ( 14 sec) [ -15571.9832] [ 2540] [depth= 14] . ( 14 sec) [ -15571.2021] [ 2541] [depth= 1] . ( 14 sec) [ -15566.9323] [ 2536] [depth= 11] . ( 14 sec) [ -15558.2104] [ 2529] [depth= 1] . ( 14 sec) [ -15540.3643] [ 2524] [depth= 1] . ( 15 sec) [ -15485.1333] [ 2512] [depth= 7] . ( 15 sec) [ -15484.9915] [ 2512] [depth= 1] . ( 15 sec) [ -15363.7950] [ 2507] [depth= 2] . ( 15 sec) [ -15361.7842] [ 2506] [depth= 1] . ( 15 sec) [ -15348.4163] [ 2499] [depth= 4] . ( 15 sec) [ -15205.3175] [ 2455] [depth= 1] . ( 15 sec) [ -15188.3541] [ 2433] [depth= 6] . ( 15 sec) [ -15185.7074] [ 2431] [depth= 2] . ( 16 sec) [ -15174.6622] [ 2424] [depth= 7] . ( 16 sec) [ -15166.7763] [ 2423] [depth= 2] . ( 17 sec) [ -15164.4975] [ 2423] [depth= 1] . ( 17 sec) [ -15148.1795] [ 2421] [depth= 1] . ( 17 sec) [ -15046.6963] [ 2394] [depth= 1] . ( 18 sec) [ -14912.8815] [Branch lengths ] . ( 22 sec) [ -14398.4005] [GTR parameters ] . ( 23 sec) [ -14276.2241] [Alpha ][ 0.250961] . ( 23 sec) [ -14275.4694] [ 2393] [depth= 1] . ( 23 sec) [ -14265.5215] [ 2391] [depth= 1] . ( 23 sec) [ -14264.7112] [ 2391] [depth= 2] . ( 23 sec) [ -14257.5344] [ 2388] [depth= 3] . ( 24 sec) [ -14222.2245] [ 2377] [depth= 1] . ( 24 sec) [ -14222.0659] [ 2377] [depth= 1] . ( 24 sec) [ -14212.2375] [ 2376] [depth= 1] . ( 24 sec) [ -14212.1471] [ 2374] [depth= 2] . ( 24 sec) [ -14209.4103] [ 2371] [depth= 1] . ( 25 sec) [ -14203.0466] [ 2369] [depth= 1] . ( 25 sec) [ -14201.6540] [ 2368] [depth= 1] . ( 25 sec) [ -14200.7760] [ 2368] [depth= 1] . ( 25 sec) [ -14194.5579] [ 2368] [depth= 2] . ( 26 sec) [ -14191.0617] [ 2366] [depth= 1] . ( 26 sec) [ -14185.6583] [ 2367] [depth= 1] . ( 26 sec) [ -14182.1938] [ 2367] [depth= 1] . ( 26 sec) [ -14107.2002] [ 2339] [depth= 4] . ( 27 sec) [ -14105.8883] [ 2340] [depth= 1] . ( 27 sec) [ -14091.8755] [ 2336] [depth= 1] . ( 27 sec) [ -14091.8177] [ 2334] [depth= 1] . ( 28 sec) [ -14084.0983] [ 2332] [depth= 1] . ( 28 sec) [ -14074.4564] [ 2326] [depth= 7] . ( 28 sec) [ -14074.2761] [ 2330] [depth= 1] . ( 28 sec) [ -14067.9906] [ 2328] [depth= 1] . ( 28 sec) [ -14067.3966] [ 2329] [depth= 2] . ( 29 sec) [ -14064.0554] [ 2326] [depth= 2] . ( 29 sec) [ -14060.9936] [ 2325] [depth= 3] . ( 29 sec) [ -14050.8025] [ 2323] [depth= 2] . ( 30 sec) [ -14036.8800] [ 2320] [depth= 2] . ( 30 sec) [ -14036.5134] [ 2323] [depth= 4] . ( 31 sec) [ -14036.3114] [ 2325] [depth= 1] . ( 31 sec) [ -14031.5717] [ 2323] [depth= 2] . ( 32 sec) [ -14026.8246] [ 2320] [depth= 1] . ( 32 sec) [ -14022.2736] [ 2318] [depth= 1] . ( 32 sec) [ -14022.1111] [ 2321] [depth= 2] . ( 32 sec) [ -14020.1673] [ 2320] [depth= 1] . ( 33 sec) [ -14019.1702] [ 2317] [depth= 1] . ( 33 sec) [ -14013.5151] [ 2313] [depth= 2] . ( 33 sec) [ -14013.3731] [ 2310] [depth= 1] . ( 35 sec) [ -14013.3099] [ 2313] [depth= 1] . ( 36 sec) [ -14009.0919] [ 2310] [depth= 1] . ( 38 sec) [ -13995.2610] [Branch lengths ] . ( 43 sec) [ -13994.1975] [GTR parameters ] . ( 43 sec) [ -13994.1887] [Alpha ][ 0.249443] . ( 52 sec) [ -13993.8709] [ 2313] [depth= 1] . ( 58 sec) [ -13990.1634] [ 2316] [depth= 3] . ( 60 sec) [ -13989.5556] [Branch lengths ] . ( 65 sec) [ -13989.5403] [GTR parameters ] . ( 65 sec) [ -13989.5403] [Alpha ][ 0.249443] . ( 69 sec) [ -13988.8893] [ 2319] [depth= 3] . ( 73 sec) [ -13988.6897] [ 2314] [depth= 1] . ( 77 sec) [ -13988.5797] [ 2313] [depth= 1] . ( 79 sec) [ -13987.7864] [ 2314] [depth= 1] . ( 85 sec) [ -13985.0159] [Branch lengths ] . ( 90 sec) [ -13985.0090] [GTR parameters ] . ( 90 sec) [ -13985.0087] [Alpha ][ 0.249103] . ( 110 sec) [ -13984.8463] [Branch lengths ] . ( 180 sec) [ -13984.8153] [ 2314] [depth= 1] . ( 187 sec) [ -13984.7864] [Branch lengths ] . ( 191 sec) [ -13984.7852] [GTR parameters ] . ( 191 sec) [ -13984.7850] [Alpha ][ 0.249352] . ( 192 sec) [ -13984.7850] [Topology ] . ( 193 sec) [ -13984.7841] [Topology ] . ( 195 sec) [ -13984.7841] [GTR parameters ] . ( 195 sec) [ -13984.7841] [Alpha ][ 0.249352] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13984.784074. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23979.7106] [GTR parameters ] . ( 1 sec) [ -23457.1523] [Alpha ][ 0.500960] . ( 1 sec) [ -23227.0054] [ 3760] [depth= 7] . ( 1 sec) [ -23067.2976] [ 3752] [depth= 3] . ( 1 sec) [ -22815.1556] [ 3731] [depth= 7] . ( 1 sec) [ -22573.3396] [ 3660] [depth= 1] . ( 2 sec) [ -22539.9538] [ 3654] [depth= 8] . ( 2 sec) [ -22488.7639] [ 3651] [depth= 1] . ( 2 sec) [ -22445.6375] [ 3648] [depth= 4] . ( 2 sec) [ -22350.4098] [ 3630] [depth= 8] . ( 2 sec) [ -22321.6335] [ 3627] [depth= 1] . ( 2 sec) [ -22274.3548] [ 3626] [depth= 1] . ( 2 sec) [ -22253.1601] [ 3627] [depth= 2] . ( 2 sec) [ -22231.1338] [ 3618] [depth= 11] . ( 2 sec) [ -22086.8783] [ 3616] [depth= 1] . ( 3 sec) [ -21896.5414] [ 3594] [depth= 2] . ( 3 sec) [ -21302.3495] [ 3590] [depth= 8] . ( 3 sec) [ -20973.5968] [ 3533] [depth= 20] . ( 3 sec) [ -20779.4333] [ 3459] [depth= 12] . ( 3 sec) [ -20724.1823] [ 3437] [depth= 11] . ( 3 sec) [ -20689.4516] [ 3428] [depth= 6] . ( 3 sec) [ -20607.7519] [ 3412] [depth= 7] . ( 4 sec) [ -20596.1676] [ 3411] [depth= 2] . ( 4 sec) [ -20244.5886] [ 3350] [depth= 10] . ( 4 sec) [ -20207.4950] [ 3348] [depth= 1] . ( 4 sec) [ -20026.8110] [ 3297] [depth= 11] . ( 4 sec) [ -19776.7811] [ 3269] [depth= 6] . ( 4 sec) [ -19772.9878] [ 3270] [depth= 1] . ( 4 sec) [ -19739.7137] [ 3266] [depth= 1] . ( 4 sec) [ -19611.7984] [ 3259] [depth= 2] . ( 4 sec) [ -19601.4860] [ 3252] [depth= 2] . ( 5 sec) [ -19600.3598] [ 3250] [depth= 3] . ( 5 sec) [ -19547.9136] [ 3231] [depth= 14] . ( 5 sec) [ -19453.4623] [ 3230] [depth= 6] . ( 5 sec) [ -19249.5884] [ 3213] [depth= 11] . ( 5 sec) [ -19103.3573] [ 3229] [depth= 1] . ( 5 sec) [ -19052.3289] [ 3218] [depth= 9] . ( 5 sec) [ -18855.9841] [ 3164] [depth= 4] . ( 5 sec) [ -18594.1987] [ 3118] [depth= 1] . ( 5 sec) [ -18513.2005] [ 3099] [depth= 8] . ( 6 sec) [ -18501.2333] [ 3089] [depth= 5] . ( 6 sec) [ -18321.2807] [ 3044] [depth= 10] . ( 6 sec) [ -18318.3113] [ 3044] [depth= 2] . ( 6 sec) [ -18312.1168] [ 3043] [depth= 10] . ( 6 sec) [ -18150.5479] [ 3014] [depth= 1] . ( 6 sec) [ -18117.5170] [ 2993] [depth= 11] . ( 6 sec) [ -18045.1320] [ 2978] [depth= 11] . ( 6 sec) [ -18042.9233] [ 2981] [depth= 1] . ( 7 sec) [ -17972.2571] [ 2954] [depth= 10] . ( 7 sec) [ -17846.3860] [ 2925] [depth= 8] . ( 7 sec) [ -17833.2628] [ 2925] [depth= 1] . ( 7 sec) [ -17584.4187] [ 2896] [depth= 10] . ( 7 sec) [ -17569.7532] [ 2893] [depth= 8] . ( 7 sec) [ -17491.5083] [ 2891] [depth= 5] . ( 7 sec) [ -17489.2154] [ 2888] [depth= 1] . ( 7 sec) [ -17480.3878] [ 2887] [depth= 1] . ( 8 sec) [ -17479.1464] [ 2890] [depth= 1] . ( 8 sec) [ -17473.1089] [ 2888] [depth= 1] . ( 8 sec) [ -17468.8101] [ 2890] [depth= 1] . ( 8 sec) [ -17456.2540] [ 2884] [depth= 3] . ( 8 sec) [ -17360.6052] [ 2876] [depth= 14] . ( 8 sec) [ -17343.3544] [ 2876] [depth= 1] . ( 8 sec) [ -17308.1705] [ 2858] [depth= 14] . ( 8 sec) [ -17302.0408] [ 2884] [depth= 1] . ( 9 sec) [ -17058.2258] [ 2768] [depth= 12] . ( 9 sec) [ -16911.6511] [ 2746] [depth= 2] . ( 9 sec) [ -16879.9254] [ 2739] [depth= 6] . ( 9 sec) [ -16776.3261] [ 2706] [depth= 3] . ( 9 sec) [ -16635.8307] [ 2657] [depth= 10] . ( 9 sec) [ -16609.6969] [ 2650] [depth= 4] . ( 9 sec) [ -16529.4955] [ 2626] [depth= 11] . ( 9 sec) [ -16484.1374] [ 2599] [depth= 4] . ( 9 sec) [ -16459.1681] [ 2597] [depth= 3] . ( 10 sec) [ -16454.9438] [ 2599] [depth= 2] . ( 10 sec) [ -16386.4731] [ 2591] [depth= 3] . ( 10 sec) [ -16238.3349] [ 2589] [depth= 1] . ( 10 sec) [ -16184.9075] [ 2574] [depth= 9] . ( 10 sec) [ -16108.2487] [ 2566] [depth= 1] . ( 10 sec) [ -16005.0388] [ 2564] [depth= 6] . ( 10 sec) [ -15969.0571] [ 2556] [depth= 6] . ( 11 sec) [ -15844.4089] [ 2528] [depth= 7] . ( 11 sec) [ -15779.6047] [ 2511] [depth= 1] . ( 11 sec) [ -15686.2393] [ 2492] [depth= 1] . ( 11 sec) [ -15675.7558] [ 2497] [depth= 2] . ( 11 sec) [ -15520.9328] [ 2493] [depth= 1] . ( 11 sec) [ -15502.9395] [ 2481] [depth= 3] . ( 11 sec) [ -15464.4038] [ 2478] [depth= 3] . ( 12 sec) [ -15421.4282] [ 2467] [depth= 3] . ( 12 sec) [ -15377.4002] [ 2452] [depth= 9] . ( 12 sec) [ -15253.1663] [ 2448] [depth= 3] . ( 12 sec) [ -15250.7595] [ 2453] [depth= 5] . ( 12 sec) [ -15250.4248] [ 2451] [depth= 1] . ( 12 sec) [ -15249.8048] [ 2448] [depth= 3] . ( 12 sec) [ -15243.2167] [ 2445] [depth= 1] . ( 13 sec) [ -15238.0080] [ 2444] [depth= 1] . ( 13 sec) [ -15232.2314] [ 2442] [depth= 1] . ( 13 sec) [ -15142.6532] [ 2417] [depth= 3] . ( 13 sec) [ -15134.3871] [ 2417] [depth= 1] . ( 13 sec) [ -15069.9119] [ 2407] [depth= 7] . ( 13 sec) [ -15058.0178] [ 2399] [depth= 1] . ( 13 sec) [ -15052.4660] [ 2405] [depth= 5] . ( 13 sec) [ -15048.2447] [ 2408] [depth= 5] . ( 14 sec) [ -15034.1749] [ 2401] [depth= 4] . ( 14 sec) [ -15032.8396] [ 2398] [depth= 1] . ( 14 sec) [ -15032.4455] [ 2401] [depth= 1] . ( 14 sec) [ -14993.7623] [ 2399] [depth= 5] . ( 14 sec) [ -14985.0319] [ 2394] [depth= 1] . ( 14 sec) [ -14963.2594] [ 2389] [depth= 4] . ( 14 sec) [ -14962.7924] [ 2389] [depth= 1] . ( 15 sec) [ -14949.5256] [ 2393] [depth= 3] . ( 15 sec) [ -14936.3766] [ 2391] [depth= 2] . ( 16 sec) [ -14863.0924] [ 2367] [depth= 6] . ( 16 sec) [ -14859.2523] [ 2367] [depth= 2] . ( 16 sec) [ -14855.9124] [ 2367] [depth= 1] . ( 17 sec) [ -14760.9781] [Branch lengths ] . ( 22 sec) [ -14237.4487] [GTR parameters ] . ( 22 sec) [ -14117.2088] [Alpha ][ 0.250961] . ( 23 sec) [ -14102.7019] [ 2355] [depth= 3] . ( 23 sec) [ -14099.7191] [ 2352] [depth= 4] . ( 24 sec) [ -14098.9893] [ 2356] [depth= 1] . ( 24 sec) [ -14097.9090] [ 2356] [depth= 1] . ( 24 sec) [ -14097.4784] [ 2351] [depth= 2] . ( 25 sec) [ -14096.8652] [ 2348] [depth= 1] . ( 25 sec) [ -14095.2594] [ 2353] [depth= 2] . ( 25 sec) [ -14065.3607] [ 2347] [depth= 1] . ( 25 sec) [ -14060.9773] [ 2345] [depth= 1] . ( 25 sec) [ -14060.7064] [ 2345] [depth= 1] . ( 26 sec) [ -14048.8201] [ 2342] [depth= 3] . ( 26 sec) [ -14045.8407] [ 2341] [depth= 1] . ( 26 sec) [ -14044.1068] [ 2341] [depth= 1] . ( 27 sec) [ -14043.4030] [ 2341] [depth= 5] . ( 27 sec) [ -14040.9943] [ 2342] [depth= 1] . ( 27 sec) [ -14039.9492] [ 2337] [depth= 2] . ( 28 sec) [ -14039.0213] [ 2335] [depth= 1] . ( 29 sec) [ -14030.1209] [ 2339] [depth= 1] . ( 29 sec) [ -14029.8436] [ 2336] [depth= 1] . ( 30 sec) [ -14026.8207] [ 2337] [depth= 1] . ( 31 sec) [ -14025.1762] [ 2336] [depth= 1] . ( 32 sec) [ -14024.4936] [ 2334] [depth= 1] . ( 32 sec) [ -14013.7304] [ 2321] [depth= 8] . ( 32 sec) [ -14013.6627] [ 2322] [depth= 1] . ( 34 sec) [ -14013.5151] [ 2324] [depth= 1] . ( 34 sec) [ -14008.6656] [ 2321] [depth= 7] . ( 36 sec) [ -14005.5576] [ 2318] [depth= 1] . ( 37 sec) [ -14004.2405] [ 2321] [depth= 1] . ( 38 sec) [ -14003.9640] [ 2321] [depth= 1] . ( 38 sec) [ -14002.2777] [ 2321] [depth= 1] . ( 39 sec) [ -13999.5165] [ 2319] [depth= 3] . ( 40 sec) [ -13987.8802] [Branch lengths ] . ( 44 sec) [ -13987.0132] [GTR parameters ] . ( 44 sec) [ -13986.9839] [Alpha ][ 0.248197] . ( 56 sec) [ -13986.9408] [ 2319] [depth= 1] . ( 66 sec) [ -13986.1108] [Branch lengths ] . ( 69 sec) [ -13986.1030] [GTR parameters ] . ( 69 sec) [ -13986.0998] [Alpha ][ 0.249059] . ( 78 sec) [ -13985.3332] [ 2317] [depth= 1] . ( 79 sec) [ -13985.2149] [ 2311] [depth= 1] . ( 88 sec) [ -13984.9289] [ 2312] [depth= 1] . ( 147 sec) [ -13983.8412] [Branch lengths ] . ( 151 sec) [ -13983.8315] [GTR parameters ] . ( 151 sec) [ -13983.8299] [Alpha ][ 0.249662] . ( 230 sec) [ -13983.7498] [Branch lengths ] . ( 230 sec) [ -13983.7498] [Topology ] . ( 232 sec) [ -13983.7449] [Topology ] . ( 234 sec) [ -13983.7435] [Topology ] . ( 236 sec) [ -13983.7429] [Topology ] . ( 237 sec) [ -13983.7426] [GTR parameters ] . ( 237 sec) [ -13983.7423] [Alpha ][ 0.249912] . ( 237 sec) [ -13983.7423] [Topology ] . ( 239 sec) [ -13983.7419] [Topology ] . ( 240 sec) [ -13983.7419] [GTR parameters ] . ( 240 sec) [ -13983.7419] [Alpha ][ 0.249912] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13983.741921. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -15011.6040] [GTR parameters ] . ( 2 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 2 sec) [ -14780.7799] [Topology ] . ( 3 sec) [ -14624.4043] [Topology ] . ( 5 sec) [ -14602.8474] [Topology ] . ( 7 sec) [ -14597.0947] [Topology ] . ( 9 sec) [ -14595.2996] [Topology ] . ( 11 sec) [ -14594.6333] [Topology ] . ( 13 sec) [ -14594.3799] [Topology ] . ( 15 sec) [ -14594.2815] [Topology ] . ( 17 sec) [ -14594.2428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -14114.5883] [GTR parameters ] . ( 37 sec) [ -14006.0829] [Alpha ][ 0.250961] . ( 37 sec) [ -14006.0829] [Topology ] . ( 39 sec) [ -14001.9646] [Topology ] . ( 41 sec) [ -14000.6200] [Topology ] . ( 43 sec) [ -14000.2713] [Topology ] . ( 45 sec) [ -14000.1289] [Topology ] . ( 47 sec) [ -14000.0645] [Topology ] . ( 49 sec) [ -14000.0344] [Topology ] . ( 51 sec) [ -14000.0201] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -13998.9233] [GTR parameters ] . ( 71 sec) [ -13998.9208] [Alpha ][ 0.250133] . ( 71 sec) [ -13998.9208] [Topology ] . ( 73 sec) [ -13998.8831] [Topology ] . ( 75 sec) [ -13998.8674] [Topology ] . ( 77 sec) [ -13998.8600] [Topology ] . ( 78 sec) [ -13998.8564] [Topology ] . ( 80 sec) [ -13998.8547] [Topology ] . ( 82 sec) [ -13998.8539] [Topology ] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -13998.8521] [GTR parameters ] . ( 99 sec) [ -13998.8503] [Alpha ][ 0.250757] . ( 99 sec) [ -13998.8503] [Topology ] . ( 101 sec) [ -13998.8493] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -13998.8493] [GTR parameters ] . ( 117 sec) [ -13998.8493] [Alpha ][ 0.250757] . ( 117 sec) [ -13998.8493] [Topology ] . ( 119 sec) [ -13998.8488] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 150 sec) [ -15011.6040] [GTR parameters ] . ( 151 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 151 sec) [ -14763.5982] [ 2324] [depth= 1] . ( 152 sec) [ -14761.9657] [ 2324] [depth= 1] . ( 152 sec) [ -14761.4417] [ 2324] [depth= 1] . ( 152 sec) [ -14758.9385] [ 2324] [depth= 1] . ( 153 sec) [ -14754.4887] [ 2324] [depth= 1] . ( 154 sec) [ -14748.4513] [ 2324] [depth= 1] . ( 154 sec) [ -14747.6244] [ 2326] [depth= 1] . ( 154 sec) [ -14747.5440] [ 2328] [depth= 1] . ( 154 sec) [ -14746.2770] [ 2326] [depth= 1] . ( 155 sec) [ -14745.4215] [ 2324] [depth= 1] . ( 155 sec) [ -14739.8437] [ 2319] [depth= 1] . ( 156 sec) [ -14735.4461] [ 2319] [depth= 2] . ( 156 sec) [ -14733.8271] [ 2315] [depth= 2] . ( 156 sec) [ -14733.4227] [ 2319] [depth= 1] . ( 157 sec) [ -14733.2549] [ 2320] [depth= 1] . ( 157 sec) [ -14731.6522] [ 2320] [depth= 1] . ( 158 sec) [ -14727.5651] [ 2319] [depth= 1] . ( 158 sec) [ -14718.8341] [ 2318] [depth= 2] . ( 158 sec) [ -14717.4738] [ 2320] [depth= 1] . ( 160 sec) [ -14705.6155] [ 2324] [depth= 2] . ( 160 sec) [ -14696.6055] [ 2318] [depth= 2] . ( 160 sec) [ -14692.9109] [ 2318] [depth= 1] . ( 160 sec) [ -14692.2380] [ 2318] [depth= 1] . ( 161 sec) [ -14691.2322] [ 2320] [depth= 1] . ( 161 sec) [ -14683.0303] [ 2318] [depth= 1] . ( 163 sec) [ -14681.9770] [ 2319] [depth= 1] . ( 163 sec) [ -14680.2524] [ 2319] [depth= 2] . ( 164 sec) [ -14679.7118] [ 2320] [depth= 1] . ( 164 sec) [ -14679.3119] [ 2324] [depth= 4] . ( 164 sec) [ -14676.9398] [ 2323] [depth= 1] . ( 164 sec) [ -14676.6320] [ 2326] [depth= 1] . ( 164 sec) [ -14676.5942] [ 2331] [depth= 5] . ( 165 sec) [ -14675.0120] [ 2325] [depth= 2] . ( 165 sec) [ -14671.4546] [ 2325] [depth= 1] . ( 166 sec) [ -14668.0383] [ 2325] [depth= 1] . ( 166 sec) [ -14665.0324] [ 2325] [depth= 1] . ( 168 sec) [ -14620.0875] [Branch lengths ] . ( 172 sec) [ -14145.3710] [GTR parameters ] . ( 172 sec) [ -14030.6974] [Alpha ][ 0.250961] . ( 173 sec) [ -14030.5817] [ 2324] [depth= 1] . ( 174 sec) [ -14030.5434] [ 2327] [depth= 1] . ( 175 sec) [ -14028.9277] [ 2327] [depth= 2] . ( 176 sec) [ -14026.9323] [ 2327] [depth= 1] . ( 177 sec) [ -14025.9535] [ 2325] [depth= 1] . ( 178 sec) [ -14024.4685] [ 2322] [depth= 1] . ( 180 sec) [ -14019.0906] [ 2315] [depth= 4] . ( 181 sec) [ -14018.2908] [ 2313] [depth= 1] . ( 183 sec) [ -14018.0722] [ 2314] [depth= 1] . ( 187 sec) [ -14016.4404] [ 2316] [depth= 1] . ( 187 sec) [ -14011.6093] [ 2314] [depth= 2] . ( 187 sec) [ -14010.9861] [ 2316] [depth= 1] . ( 188 sec) [ -14010.6796] [ 2318] [depth= 1] . ( 188 sec) [ -14007.6593] [ 2313] [depth= 2] . ( 189 sec) [ -14007.6479] [ 2313] [depth= 2] . ( 190 sec) [ -14006.4128] [ 2316] [depth= 1] . ( 191 sec) [ -14005.9963] [ 2313] [depth= 1] . ( 192 sec) [ -13997.3082] [Branch lengths ] . ( 197 sec) [ -13996.3161] [GTR parameters ] . ( 197 sec) [ -13996.2355] [Alpha ][ 0.246642] . ( 205 sec) [ -13995.8097] [ 2311] [depth= 1] . ( 217 sec) [ -13993.9109] [Branch lengths ] . ( 222 sec) [ -13993.8880] [GTR parameters ] . ( 222 sec) [ -13993.8731] [Alpha ][ 0.248524] . ( 242 sec) [ -13993.6177] [Branch lengths ] . ( 320 sec) [ -13993.5906] [Branch lengths ] . ( 320 sec) [ -13993.5906] [Topology ] . ( 322 sec) [ -13993.5883] [Topology ] . ( 324 sec) [ -13993.5876] [Topology ] . ( 327 sec) [ -13993.5844] [GTR parameters ] . ( 327 sec) [ -13993.5791] [Alpha ][ 0.249640] . ( 327 sec) [ -13993.5791] [Topology ] . ( 329 sec) [ -13993.5779] [Topology ] . ( 331 sec) [ -13993.5774] [Topology ] . ( 334 sec) [ -13993.5771] [GTR parameters ] . ( 334 sec) [ -13993.5771] [Alpha ][ 0.249640] . ( 334 sec) [ -13993.5771] [Topology ] . ( 336 sec) [ -13993.5768] [Topology ] . ( 336 sec) [ -13993.5768] [GTR parameters ] . ( 336 sec) [ -13993.5768] [Alpha ][ 0.249640] . Checking for NNIs, optimizing five branches... . ( 351 sec) [ -13993.2261] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -13998.848836 . Log likelihood obtained after SPR moves : -13993.226072 . Log likelihood of the current tree: -13993.226072. . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Best log likelihood : -13983.741921 . Time used 0h6m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1514.87user 0.00system 25:25.91elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps