.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data33.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... . 449 patterns found. (out of a total of 500 sites) . 47 sites without polymorphism (9.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23019.5278] [GTR parameters ] . ( 1 sec) [ -22624.8027] [Alpha ][ 0.500960] . ( 1 sec) [ -22432.8340] [ 5101] [depth= 7] . ( 1 sec) [ -22424.0480] [ 5108] [depth= 1] . ( 1 sec) [ -22113.0793] [ 5027] [depth= 5] . ( 1 sec) [ -22022.4098] [ 5007] [depth= 1] . ( 2 sec) [ -21842.5190] [ 4986] [depth= 1] . ( 2 sec) [ -21718.9334] [ 4925] [depth= 1] . ( 2 sec) [ -21457.1432] [ 4883] [depth= 7] . ( 2 sec) [ -21229.7923] [ 4824] [depth= 5] . ( 2 sec) [ -21182.4480] [ 4819] [depth= 3] . ( 2 sec) [ -21107.4651] [ 4804] [depth= 1] . ( 2 sec) [ -20929.1956] [ 4697] [depth= 13] . ( 2 sec) [ -20705.1839] [ 4654] [depth= 11] . ( 2 sec) [ -20621.7914] [ 4634] [depth= 13] . ( 2 sec) [ -20508.5551] [ 4622] [depth= 2] . ( 2 sec) [ -19821.5407] [ 4567] [depth= 6] . ( 2 sec) [ -19673.3290] [ 4562] [depth= 3] . ( 2 sec) [ -19372.3998] [ 4535] [depth= 4] . ( 2 sec) [ -19234.5368] [ 4481] [depth= 4] . ( 2 sec) [ -18909.7354] [ 4430] [depth= 6] . ( 2 sec) [ -18132.0627] [ 4367] [depth= 11] . ( 2 sec) [ -18031.9241] [ 4369] [depth= 2] . ( 3 sec) [ -17690.8975] [ 4242] [depth= 12] . ( 3 sec) [ -17573.7187] [ 4181] [depth= 1] . ( 3 sec) [ -17532.7337] [ 4153] [depth= 1] . ( 3 sec) [ -17507.3862] [ 4154] [depth= 9] . ( 3 sec) [ -17056.1907] [ 4029] [depth= 1] . ( 3 sec) [ -17010.9693] [ 4062] [depth= 8] . ( 3 sec) [ -16842.8252] [ 3988] [depth= 4] . ( 3 sec) [ -16566.2730] [ 3956] [depth= 13] . ( 3 sec) [ -16163.6842] [ 3855] [depth= 2] . ( 3 sec) [ -16159.9573] [ 3838] [depth= 5] . ( 3 sec) [ -15848.6044] [ 3803] [depth= 4] . ( 3 sec) [ -15374.5562] [ 3720] [depth= 3] . ( 4 sec) [ -14700.4232] [ 3646] [depth= 7] . ( 4 sec) [ -14586.7382] [ 3644] [depth= 1] . ( 4 sec) [ -14297.9861] [ 3575] [depth= 2] . ( 4 sec) [ -14170.4650] [ 3541] [depth= 1] . ( 4 sec) [ -14054.0632] [ 3563] [depth= 1] . ( 4 sec) [ -13934.1599] [ 3556] [depth= 1] . ( 4 sec) [ -13914.2509] [ 3557] [depth= 1] . ( 4 sec) [ -13862.0228] [ 3560] [depth= 8] . ( 4 sec) [ -13713.5689] [ 3438] [depth= 9] . ( 4 sec) [ -13171.6692] [ 3385] [depth= 1] . ( 4 sec) [ -12862.5111] [ 3310] [depth= 13] . ( 5 sec) [ -12845.7573] [ 3307] [depth= 1] . ( 5 sec) [ -12816.7351] [ 3356] [depth= 1] . ( 5 sec) [ -12576.0261] [ 3208] [depth= 13] . ( 5 sec) [ -12547.1126] [ 3209] [depth= 1] . ( 5 sec) [ -12312.7785] [ 3121] [depth= 9] . ( 5 sec) [ -12180.7446] [ 3085] [depth= 2] . ( 5 sec) [ -12162.0380] [ 3079] [depth= 1] . ( 5 sec) [ -12105.4308] [ 3069] [depth= 3] . ( 5 sec) [ -12075.2806] [ 3059] [depth= 1] . ( 5 sec) [ -12066.0662] [ 3057] [depth= 1] . ( 6 sec) [ -12055.1198] [ 3055] [depth= 1] . ( 6 sec) [ -12021.1800] [ 3044] [depth= 1] . ( 6 sec) [ -11633.1809] [ 2903] [depth= 10] . ( 6 sec) [ -11632.2756] [ 2905] [depth= 1] . ( 6 sec) [ -11521.1553] [ 2831] [depth= 6] . ( 6 sec) [ -11487.0686] [ 2846] [depth= 2] . ( 6 sec) [ -11278.3076] [ 2706] [depth= 10] . ( 6 sec) [ -11234.5923] [ 2702] [depth= 1] . ( 6 sec) [ -11190.7298] [ 2681] [depth= 1] . ( 7 sec) [ -11158.3842] [ 2669] [depth= 1] . ( 7 sec) [ -10995.5147] [ 2607] [depth= 3] . ( 7 sec) [ -10993.4555] [ 2609] [depth= 1] . ( 7 sec) [ -10971.5199] [ 2601] [depth= 3] . ( 7 sec) [ -10928.7334] [ 2582] [depth= 3] . ( 7 sec) [ -10898.3280] [ 2580] [depth= 1] . ( 7 sec) [ -10810.2691] [ 2513] [depth= 6] . ( 7 sec) [ -10772.6536] [ 2506] [depth= 1] . ( 7 sec) [ -10669.8721] [ 2503] [depth= 4] . ( 7 sec) [ -10645.0897] [ 2459] [depth= 8] . ( 7 sec) [ -10642.8751] [ 2453] [depth= 1] . ( 7 sec) [ -10545.6838] [ 2399] [depth= 5] . ( 7 sec) [ -10542.7877] [ 2398] [depth= 1] . ( 7 sec) [ -10526.0654] [ 2391] [depth= 1] . ( 8 sec) [ -10509.9863] [ 2380] [depth= 2] . ( 8 sec) [ -10509.0705] [ 2383] [depth= 1] . ( 8 sec) [ -10236.8382] [Branch lengths ] . ( 9 sec) [ -10233.4829] [GTR parameters ] . ( 9 sec) [ -10179.6857] [Alpha ][ 1.000369] . ( 9 sec) [ -10178.2016] [ 2381] [depth= 1] . ( 9 sec) [ -10165.9160] [ 2365] [depth= 1] . ( 9 sec) [ -10164.9207] [ 2362] [depth= 1] . ( 9 sec) [ -10160.8802] [ 2361] [depth= 1] . ( 9 sec) [ -10160.4269] [ 2362] [depth= 1] . ( 9 sec) [ -10147.0343] [ 2342] [depth= 2] . ( 10 sec) [ -10133.8902] [ 2346] [depth= 1] . ( 10 sec) [ -10127.6258] [ 2339] [depth= 1] . ( 10 sec) [ -10119.6446] [ 2336] [depth= 1] . ( 10 sec) [ -10112.4229] [ 2344] [depth= 1] . ( 11 sec) [ -10112.2568] [ 2347] [depth= 1] . ( 11 sec) [ -10106.7934] [ 2338] [depth= 3] . ( 12 sec) [ -10106.6977] [ 2334] [depth= 1] . ( 12 sec) [ -10086.1507] [Branch lengths ] . ( 12 sec) [ -10086.0336] [GTR parameters ] . ( 13 sec) [ -10084.8497] [Alpha ][ 1.118342] . ( 13 sec) [ -10084.7822] [ 2322] [depth= 1] . ( 13 sec) [ -10084.4080] [ 2326] [depth= 1] . ( 16 sec) [ -10082.6280] [Branch lengths ] . ( 16 sec) [ -10082.6263] [GTR parameters ] . ( 16 sec) [ -10082.6129] [Alpha ][ 1.132065] . ( 19 sec) [ -10082.1931] [Branch lengths ] . ( 38 sec) [ -10082.1092] [ 2335] [depth= 1] . ( 42 sec) [ -10081.8499] [Branch lengths ] . ( 43 sec) [ -10081.8386] [GTR parameters ] . ( 43 sec) [ -10081.8385] [Alpha ][ 1.130756] . ( 43 sec) [ -10081.8385] [Topology ] . ( 44 sec) [ -10081.7998] [Topology ] . ( 44 sec) [ -10081.7802] [Topology ] . ( 45 sec) [ -10081.7661] [Topology ] . ( 46 sec) [ -10081.7559] [Topology ] . ( 47 sec) [ -10081.7480] [Topology ] . ( 48 sec) [ -10081.7416] [Topology ] . ( 48 sec) [ -10081.7414] [GTR parameters ] . ( 48 sec) [ -10081.7414] [Alpha ][ 1.131887] . ( 48 sec) [ -10081.7414] [Topology ] . ( 49 sec) [ -10081.7360] [Topology ] . ( 50 sec) [ -10081.7316] [Topology ] . ( 51 sec) [ -10081.7278] [Topology ] . ( 51 sec) [ -10081.7246] [Topology ] . ( 52 sec) [ -10081.7219] [Topology ] . ( 53 sec) [ -10081.7197] [Topology ] . ( 53 sec) [ -10081.7196] [GTR parameters ] . ( 53 sec) [ -10081.7196] [Alpha ][ 1.131887] . ( 53 sec) [ -10081.7196] [Topology ] . ( 54 sec) [ -10081.7177] [Topology ] . ( 55 sec) [ -10081.7161] [Topology ] . ( 56 sec) [ -10081.7147] [Topology ] . ( 57 sec) [ -10081.7136] [Topology ] . ( 58 sec) [ -10081.7127] [Topology ] . ( 58 sec) [ -10081.7127] [GTR parameters ] . ( 58 sec) [ -10081.7127] [Alpha ][ 1.131887] . ( 58 sec) [ -10081.7127] [Topology ] . ( 59 sec) [ -10081.7119] [Topology ] . ( 59 sec) [ -10081.7119] [GTR parameters ] . ( 59 sec) [ -10081.7119] [Alpha ][ 1.131887] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10081.711881. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -25011.9278] [GTR parameters ] . ( 1 sec) [ -24545.6327] [Alpha ][ 0.500960] . ( 1 sec) [ -24409.1280] [ 5179] [depth= 9] . ( 1 sec) [ -24270.7430] [ 5128] [depth= 2] . ( 1 sec) [ -24104.0492] [ 5105] [depth= 4] . ( 1 sec) [ -24094.1497] [ 5109] [depth= 1] . ( 1 sec) [ -24076.6853] [ 5086] [depth= 1] . ( 2 sec) [ -24043.5444] [ 5035] [depth= 2] . ( 2 sec) [ -23866.6425] [ 4994] [depth= 2] . ( 2 sec) [ -23693.1956] [ 4973] [depth= 5] . ( 2 sec) [ -23607.2097] [ 4965] [depth= 4] . ( 2 sec) [ -23243.2498] [ 4829] [depth= 5] . ( 2 sec) [ -23210.6412] [ 4824] [depth= 1] . ( 2 sec) [ -22906.2547] [ 4775] [depth= 8] . ( 2 sec) [ -22258.6105] [ 4605] [depth= 11] . ( 2 sec) [ -21902.3354] [ 4553] [depth= 3] . ( 2 sec) [ -21833.7670] [ 4517] [depth= 7] . ( 2 sec) [ -21042.6727] [ 4513] [depth= 1] . ( 2 sec) [ -20915.4645] [ 4425] [depth= 10] . ( 2 sec) [ -20844.6949] [ 4425] [depth= 3] . ( 2 sec) [ -20256.7790] [ 4318] [depth= 9] . ( 3 sec) [ -20247.6277] [ 4309] [depth= 2] . ( 3 sec) [ -19813.0965] [ 4225] [depth= 5] . ( 3 sec) [ -19790.9109] [ 4207] [depth= 3] . ( 3 sec) [ -19786.7486] [ 4204] [depth= 1] . ( 3 sec) [ -19597.9758] [ 4150] [depth= 9] . ( 3 sec) [ -18825.7223] [ 4158] [depth= 1] . ( 3 sec) [ -17942.7782] [ 4123] [depth= 7] . ( 3 sec) [ -17881.6910] [ 4086] [depth= 5] . ( 3 sec) [ -17544.7290] [ 3985] [depth= 9] . ( 3 sec) [ -16636.8406] [ 3822] [depth= 13] . ( 3 sec) [ -16626.2342] [ 3827] [depth= 2] . ( 4 sec) [ -16373.4321] [ 3708] [depth= 10] . ( 4 sec) [ -15999.2558] [ 3577] [depth= 1] . ( 4 sec) [ -15727.8182] [ 3507] [depth= 10] . ( 4 sec) [ -15706.1023] [ 3504] [depth= 1] . ( 4 sec) [ -15649.6870] [ 3408] [depth= 9] . ( 4 sec) [ -15464.5580] [ 3414] [depth= 1] . ( 4 sec) [ -14346.5266] [ 3382] [depth= 2] . ( 4 sec) [ -14300.7039] [ 3313] [depth= 9] . ( 4 sec) [ -14217.1724] [ 3334] [depth= 7] . ( 4 sec) [ -14073.5989] [ 3288] [depth= 1] . ( 4 sec) [ -13994.9119] [ 3250] [depth= 1] . ( 5 sec) [ -13857.8918] [ 3191] [depth= 4] . ( 5 sec) [ -13788.0405] [ 3171] [depth= 1] . ( 5 sec) [ -13719.1543] [ 3143] [depth= 2] . ( 5 sec) [ -13635.0282] [ 3136] [depth= 1] . ( 5 sec) [ -13379.1106] [ 3100] [depth= 2] . ( 5 sec) [ -13273.4110] [ 3086] [depth= 1] . ( 5 sec) [ -12614.6264] [ 3079] [depth= 1] . ( 5 sec) [ -12547.2698] [ 3054] [depth= 1] . ( 5 sec) [ -12502.4725] [ 3052] [depth= 5] . ( 5 sec) [ -12314.0563] [ 2966] [depth= 1] . ( 5 sec) [ -12203.8205] [ 2899] [depth= 8] . ( 5 sec) [ -12200.4529] [ 2897] [depth= 2] . ( 6 sec) [ -12150.8311] [ 2849] [depth= 3] . ( 6 sec) [ -12139.7204] [ 2853] [depth= 1] . ( 6 sec) [ -12041.0425] [ 2799] [depth= 4] . ( 6 sec) [ -12016.5794] [ 2833] [depth= 1] . ( 6 sec) [ -12014.9140] [ 2829] [depth= 1] . ( 6 sec) [ -12006.4534] [ 2794] [depth= 1] . ( 7 sec) [ -11993.6234] [ 2812] [depth= 1] . ( 7 sec) [ -11981.3534] [ 2829] [depth= 1] . ( 7 sec) [ -11921.5224] [ 2832] [depth= 1] . ( 7 sec) [ -11871.0101] [ 2836] [depth= 1] . ( 7 sec) [ -11850.0068] [ 2819] [depth= 1] . ( 8 sec) [ -11790.9887] [ 2805] [depth= 1] . ( 8 sec) [ -11547.3642] [ 2716] [depth= 9] . ( 8 sec) [ -11518.5949] [ 2683] [depth= 5] . ( 8 sec) [ -11475.7821] [ 2686] [depth= 1] . ( 8 sec) [ -11445.1215] [ 2685] [depth= 3] . ( 9 sec) [ -11369.8746] [ 2687] [depth= 3] . ( 9 sec) [ -11349.6430] [ 2691] [depth= 3] . ( 9 sec) [ -11255.5328] [ 2666] [depth= 5] . ( 9 sec) [ -11114.7875] [ 2613] [depth= 1] . ( 9 sec) [ -11086.2306] [ 2612] [depth= 1] . ( 9 sec) [ -11075.4839] [ 2611] [depth= 2] . ( 10 sec) [ -10671.6038] [Branch lengths ] . ( 11 sec) [ -10668.9551] [GTR parameters ] . ( 11 sec) [ -10621.8404] [Alpha ][ 0.990566] . ( 11 sec) [ -10609.3892] [ 2601] [depth= 1] . ( 11 sec) [ -10595.2543] [ 2600] [depth= 5] . ( 11 sec) [ -10583.2545] [ 2593] [depth= 1] . ( 11 sec) [ -10574.0834] [ 2598] [depth= 4] . ( 12 sec) [ -10545.9178] [ 2556] [depth= 5] . ( 12 sec) [ -10396.9496] [ 2501] [depth= 3] . ( 12 sec) [ -10384.7359] [ 2494] [depth= 1] . ( 12 sec) [ -10383.6546] [ 2486] [depth= 1] . ( 12 sec) [ -10380.1789] [ 2475] [depth= 1] . ( 13 sec) [ -10361.7167] [ 2476] [depth= 2] . ( 13 sec) [ -10361.3576] [ 2478] [depth= 1] . ( 13 sec) [ -10358.3319] [ 2476] [depth= 1] . ( 13 sec) [ -10329.6240] [ 2456] [depth= 2] . ( 13 sec) [ -10296.9239] [ 2441] [depth= 6] . ( 14 sec) [ -10240.2373] [ 2419] [depth= 1] . ( 14 sec) [ -10238.9420] [ 2419] [depth= 1] . ( 14 sec) [ -10232.7697] [ 2412] [depth= 1] . ( 14 sec) [ -10228.4221] [ 2412] [depth= 1] . ( 14 sec) [ -10228.3901] [ 2411] [depth= 1] . ( 15 sec) [ -10215.2839] [ 2427] [depth= 2] . ( 15 sec) [ -10214.0236] [ 2431] [depth= 1] . ( 15 sec) [ -10213.2745] [ 2429] [depth= 1] . ( 15 sec) [ -10199.9695] [ 2426] [depth= 2] . ( 16 sec) [ -10196.1489] [ 2408] [depth= 1] . ( 16 sec) [ -10195.8384] [ 2411] [depth= 1] . ( 16 sec) [ -10149.1190] [ 2363] [depth= 1] . ( 16 sec) [ -10149.0370] [ 2363] [depth= 1] . ( 17 sec) [ -10139.1751] [ 2342] [depth= 1] . ( 17 sec) [ -10139.0478] [ 2344] [depth= 1] . ( 17 sec) [ -10090.6229] [Branch lengths ] . ( 17 sec) [ -10090.4730] [GTR parameters ] . ( 17 sec) [ -10089.1218] [Alpha ][ 1.116445] . ( 18 sec) [ -10089.1102] [ 2333] [depth= 1] . ( 18 sec) [ -10089.0212] [ 2329] [depth= 1] . ( 18 sec) [ -10088.4455] [ 2330] [depth= 1] . ( 18 sec) [ -10086.7332] [ 2328] [depth= 1] . ( 18 sec) [ -10086.4400] [ 2332] [depth= 1] . ( 19 sec) [ -10086.2735] [ 2332] [depth= 1] . ( 19 sec) [ -10086.1852] [ 2332] [depth= 1] . ( 20 sec) [ -10086.0609] [ 2331] [depth= 1] . ( 20 sec) [ -10085.9604] [ 2332] [depth= 1] . ( 21 sec) [ -10083.6700] [Branch lengths ] . ( 21 sec) [ -10083.6573] [GTR parameters ] . ( 21 sec) [ -10083.6407] [Alpha ][ 1.131714] . ( 25 sec) [ -10083.3768] [Branch lengths ] . ( 27 sec) [ -10083.3195] [ 2332] [depth= 1] . ( 42 sec) [ -10083.2733] [ 2341] [depth= 1] . ( 45 sec) [ -10083.1170] [Branch lengths ] . ( 45 sec) [ -10083.1059] [GTR parameters ] . ( 45 sec) [ -10083.1058] [Alpha ][ 1.130582] . ( 45 sec) [ -10083.1058] [Topology ] . ( 46 sec) [ -10083.0887] [Topology ] . ( 47 sec) [ -10083.0755] [Topology ] . ( 48 sec) [ -10083.0648] [Topology ] . ( 48 sec) [ -10083.0558] [Topology ] . ( 49 sec) [ -10083.0479] [Topology ] . ( 50 sec) [ -10083.0412] [Topology ] . ( 50 sec) [ -10083.0411] [GTR parameters ] . ( 50 sec) [ -10083.0411] [Alpha ][ 1.130582] . ( 50 sec) [ -10083.0411] [Topology ] . ( 51 sec) [ -10083.0352] [Topology ] . ( 52 sec) [ -10083.0302] [Topology ] . ( 53 sec) [ -10083.0259] [Topology ] . ( 54 sec) [ -10083.0223] [Topology ] . ( 55 sec) [ -10083.0192] [Topology ] . ( 56 sec) [ -10083.0166] [Topology ] . ( 56 sec) [ -10083.0166] [GTR parameters ] . ( 56 sec) [ -10083.0166] [Alpha ][ 1.130582] . ( 56 sec) [ -10083.0166] [Topology ] . ( 57 sec) [ -10083.0144] [Topology ] . ( 57 sec) [ -10083.0125] [Topology ] . ( 58 sec) [ -10083.0110] [Topology ] . ( 59 sec) [ -10083.0098] [Topology ] . ( 60 sec) [ -10083.0087] [Topology ] . ( 61 sec) [ -10083.0079] [Topology ] . ( 61 sec) [ -10083.0079] [GTR parameters ] . ( 61 sec) [ -10083.0079] [Alpha ][ 1.130582] . ( 61 sec) [ -10083.0079] [Topology ] . ( 62 sec) [ -10083.0071] [Topology ] . ( 62 sec) [ -10083.0071] [GTR parameters ] . ( 62 sec) [ -10083.0071] [Alpha ][ 1.130582] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -10081.7137] [Topology ] . Checking for NNIs, optimizing five branches... . ( 77 sec) [ -10081.7135] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10081.713459. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -28363.4159] [GTR parameters ] . ( 0 sec) [ -27911.5597] [Alpha ][ 0.500960] . ( 1 sec) [ -27485.4616] [ 5296] [depth= 4] . ( 1 sec) [ -26783.0709] [ 5197] [depth= 6] . ( 1 sec) [ -26608.2151] [ 5180] [depth= 4] . ( 1 sec) [ -26415.0149] [ 5166] [depth= 1] . ( 1 sec) [ -26077.4755] [ 5042] [depth= 5] . ( 1 sec) [ -23377.2679] [ 5026] [depth= 6] . ( 1 sec) [ -23043.6710] [ 4998] [depth= 11] . ( 1 sec) [ -22592.0905] [ 4900] [depth= 9] . ( 1 sec) [ -22038.9415] [ 4840] [depth= 7] . ( 1 sec) [ -21527.4236] [ 4826] [depth= 5] . ( 1 sec) [ -21177.8598] [ 4741] [depth= 8] . ( 1 sec) [ -21164.4877] [ 4719] [depth= 6] . ( 1 sec) [ -20814.1719] [ 4704] [depth= 3] . ( 1 sec) [ -19409.1008] [ 4622] [depth= 5] . ( 1 sec) [ -18655.9027] [ 4605] [depth= 1] . ( 1 sec) [ -18369.8686] [ 4566] [depth= 9] . ( 1 sec) [ -18029.2633] [ 4401] [depth= 6] . ( 1 sec) [ -17323.0202] [ 4443] [depth= 1] . ( 1 sec) [ -16857.9083] [ 4375] [depth= 6] . ( 1 sec) [ -16644.7618] [ 4319] [depth= 1] . ( 2 sec) [ -16606.8420] [ 4260] [depth= 10] . ( 2 sec) [ -16232.7602] [ 4175] [depth= 2] . ( 2 sec) [ -15991.3243] [ 4063] [depth= 3] . ( 2 sec) [ -15547.3539] [ 3947] [depth= 2] . ( 2 sec) [ -15101.7071] [ 3802] [depth= 3] . ( 2 sec) [ -14818.9783] [ 3725] [depth= 7] . ( 2 sec) [ -14796.4732] [ 3705] [depth= 1] . ( 2 sec) [ -14659.7079] [ 3719] [depth= 1] . ( 2 sec) [ -14158.4950] [ 3606] [depth= 6] . ( 2 sec) [ -14018.8867] [ 3527] [depth= 8] . ( 2 sec) [ -13613.6046] [ 3445] [depth= 3] . ( 2 sec) [ -13506.3005] [ 3373] [depth= 1] . ( 2 sec) [ -13339.3474] [ 3299] [depth= 2] . ( 2 sec) [ -13219.2155] [ 3283] [depth= 3] . ( 2 sec) [ -13090.4269] [ 3177] [depth= 10] . ( 2 sec) [ -13062.8813] [ 3169] [depth= 7] . ( 2 sec) [ -13058.7823] [ 3170] [depth= 1] . ( 2 sec) [ -12741.2771] [ 3075] [depth= 12] . ( 3 sec) [ -12680.0035] [ 3051] [depth= 1] . ( 3 sec) [ -12588.8631] [ 3044] [depth= 2] . ( 3 sec) [ -12448.4163] [ 3005] [depth= 1] . ( 3 sec) [ -12254.4201] [ 2999] [depth= 3] . ( 3 sec) [ -12110.8413] [ 2948] [depth= 3] . ( 3 sec) [ -12069.9764] [ 2940] [depth= 1] . ( 3 sec) [ -11806.7488] [ 2864] [depth= 2] . ( 3 sec) [ -11770.9558] [ 2853] [depth= 1] . ( 3 sec) [ -11620.7514] [ 2816] [depth= 7] . ( 3 sec) [ -11550.1538] [ 2783] [depth= 1] . ( 3 sec) [ -11535.3191] [ 2780] [depth= 7] . ( 3 sec) [ -11477.4063] [ 2770] [depth= 2] . ( 3 sec) [ -11376.6978] [ 2758] [depth= 1] . ( 3 sec) [ -11324.2049] [ 2755] [depth= 2] . ( 3 sec) [ -11304.9318] [ 2752] [depth= 1] . ( 3 sec) [ -11213.2746] [ 2697] [depth= 4] . ( 3 sec) [ -11205.3860] [ 2736] [depth= 1] . ( 3 sec) [ -11197.7517] [ 2697] [depth= 1] . ( 3 sec) [ -11197.0973] [ 2701] [depth= 1] . ( 3 sec) [ -11166.3793] [ 2670] [depth= 1] . ( 3 sec) [ -11047.4469] [ 2621] [depth= 3] . ( 4 sec) [ -11040.4079] [ 2636] [depth= 1] . ( 4 sec) [ -11039.9050] [ 2638] [depth= 1] . ( 4 sec) [ -10981.6027] [ 2615] [depth= 4] . ( 4 sec) [ -10950.6325] [ 2599] [depth= 1] . ( 4 sec) [ -10945.8384] [ 2597] [depth= 1] . ( 4 sec) [ -10922.6374] [ 2613] [depth= 1] . ( 4 sec) [ -10901.7856] [ 2599] [depth= 1] . ( 4 sec) [ -10888.7846] [ 2583] [depth= 1] . ( 4 sec) [ -10804.7511] [ 2537] [depth= 1] . ( 4 sec) [ -10794.7929] [ 2533] [depth= 3] . ( 4 sec) [ -10777.3383] [ 2571] [depth= 1] . ( 4 sec) [ -10755.8012] [ 2555] [depth= 2] . ( 4 sec) [ -10718.8032] [ 2471] [depth= 3] . ( 4 sec) [ -10715.2402] [ 2465] [depth= 1] . ( 5 sec) [ -10711.5842] [ 2448] [depth= 1] . ( 5 sec) [ -10711.5120] [ 2452] [depth= 1] . ( 5 sec) [ -10709.2143] [ 2449] [depth= 1] . ( 5 sec) [ -10361.7100] [Branch lengths ] . ( 6 sec) [ -10359.7947] [GTR parameters ] . ( 6 sec) [ -10313.1299] [Alpha ][ 0.992595] . ( 6 sec) [ -10310.1012] [ 2424] [depth= 2] . ( 6 sec) [ -10308.2848] [ 2424] [depth= 3] . ( 6 sec) [ -10305.5589] [ 2424] [depth= 1] . ( 6 sec) [ -10304.7390] [ 2426] [depth= 1] . ( 7 sec) [ -10300.1343] [ 2429] [depth= 1] . ( 7 sec) [ -10300.1187] [ 2427] [depth= 1] . ( 7 sec) [ -10300.0946] [ 2424] [depth= 1] . ( 7 sec) [ -10292.3029] [ 2417] [depth= 2] . ( 7 sec) [ -10222.3496] [ 2368] [depth= 3] . ( 7 sec) [ -10137.8268] [ 2330] [depth= 2] . ( 8 sec) [ -10130.5042] [ 2322] [depth= 1] . ( 8 sec) [ -10124.9298] [ 2324] [depth= 1] . ( 8 sec) [ -10118.1316] [ 2329] [depth= 1] . ( 8 sec) [ -10117.9956] [ 2329] [depth= 1] . ( 8 sec) [ -10109.7024] [ 2337] [depth= 1] . ( 8 sec) [ -10108.4705] [ 2336] [depth= 1] . ( 9 sec) [ -10107.8196] [ 2337] [depth= 1] . ( 9 sec) [ -10107.7507] [ 2341] [depth= 1] . ( 10 sec) [ -10101.2980] [ 2331] [depth= 1] . ( 10 sec) [ -10086.5467] [Branch lengths ] . ( 10 sec) [ -10086.3757] [GTR parameters ] . ( 11 sec) [ -10084.9380] [Alpha ][ 1.123499] . ( 11 sec) [ -10084.9270] [ 2327] [depth= 1] . ( 14 sec) [ -10084.1510] [Branch lengths ] . ( 14 sec) [ -10084.1504] [GTR parameters ] . ( 14 sec) [ -10084.1459] [Alpha ][ 1.131465] . ( 16 sec) [ -10084.1228] [ 2336] [depth= 1] . ( 22 sec) [ -10083.6852] [ 2327] [depth= 1] . ( 34 sec) [ -10083.4247] [Branch lengths ] . ( 35 sec) [ -10083.4082] [GTR parameters ] . ( 35 sec) [ -10083.4078] [Alpha ][ 1.133633] . ( 35 sec) [ -10083.4078] [Topology ] . ( 37 sec) [ -10083.3252] [Topology ] . ( 38 sec) [ -10083.2827] [Topology ] . ( 38 sec) [ -10083.2547] [Topology ] . ( 39 sec) [ -10083.2355] [Topology ] . ( 40 sec) [ -10083.2217] [Topology ] . ( 41 sec) [ -10083.2120] [Topology ] . ( 41 sec) [ -10083.2114] [GTR parameters ] . ( 41 sec) [ -10083.2113] [Alpha ][ 1.134766] . ( 42 sec) [ -10083.2113] [Topology ] . ( 42 sec) [ -10083.2041] [Topology ] . ( 43 sec) [ -10083.1990] [Topology ] . ( 44 sec) [ -10083.1953] [Topology ] . ( 45 sec) [ -10083.1927] [Topology ] . ( 46 sec) [ -10083.1908] [Topology ] . ( 46 sec) [ -10083.1895] [Topology ] . ( 47 sec) [ -10083.1892] [GTR parameters ] . ( 47 sec) [ -10083.1892] [Alpha ][ 1.134766] . ( 47 sec) [ -10083.1892] [Topology ] . ( 48 sec) [ -10083.1882] [Topology ] . ( 49 sec) [ -10083.1875] [Topology ] . ( 49 sec) [ -10083.1875] [GTR parameters ] . ( 49 sec) [ -10083.1875] [Alpha ][ 1.134766] . ( 49 sec) [ -10083.1875] [Topology ] . ( 50 sec) [ -10083.1870] [Topology ] . ( 50 sec) [ -10083.1870] [GTR parameters ] . ( 50 sec) [ -10083.1870] [Alpha ][ 1.134766] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -10081.9143] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -10081.7942] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10081.794208. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -25094.6451] [GTR parameters ] . ( 0 sec) [ -24641.7643] [Alpha ][ 0.500960] . ( 0 sec) [ -24595.4246] [ 5146] [depth= 10] . ( 0 sec) [ -24370.0328] [ 5102] [depth= 9] . ( 0 sec) [ -24178.1915] [ 5040] [depth= 2] . ( 0 sec) [ -24046.2184] [ 4982] [depth= 1] . ( 0 sec) [ -23905.8183] [ 4914] [depth= 4] . ( 0 sec) [ -23207.8132] [ 4900] [depth= 2] . ( 1 sec) [ -23129.4165] [ 4875] [depth= 4] . ( 1 sec) [ -23076.6080] [ 4836] [depth= 1] . ( 1 sec) [ -22686.1309] [ 4716] [depth= 8] . ( 1 sec) [ -22424.4333] [ 4627] [depth= 1] . ( 1 sec) [ -22333.0050] [ 4606] [depth= 4] . ( 1 sec) [ -21185.2385] [ 4508] [depth= 8] . ( 1 sec) [ -20912.4804] [ 4501] [depth= 6] . ( 1 sec) [ -20802.9442] [ 4471] [depth= 2] . ( 1 sec) [ -20750.6216] [ 4335] [depth= 11] . ( 1 sec) [ -20581.2914] [ 4331] [depth= 1] . ( 1 sec) [ -20525.9218] [ 4309] [depth= 1] . ( 1 sec) [ -20443.8730] [ 4330] [depth= 3] . ( 1 sec) [ -19643.6525] [ 4451] [depth= 1] . ( 1 sec) [ -19456.4129] [ 4417] [depth= 6] . ( 1 sec) [ -19163.2739] [ 4388] [depth= 3] . ( 1 sec) [ -18812.1804] [ 4311] [depth= 9] . ( 1 sec) [ -18678.8767] [ 4288] [depth= 1] . ( 1 sec) [ -18541.0136] [ 4284] [depth= 1] . ( 1 sec) [ -18385.4969] [ 4232] [depth= 1] . ( 1 sec) [ -18122.3431] [ 4148] [depth= 2] . ( 1 sec) [ -18038.5828] [ 4151] [depth= 2] . ( 1 sec) [ -17666.3662] [ 4002] [depth= 1] . ( 2 sec) [ -16818.7595] [ 3936] [depth= 12] . ( 2 sec) [ -16596.9447] [ 3886] [depth= 7] . ( 2 sec) [ -16224.6031] [ 3871] [depth= 2] . ( 2 sec) [ -15882.9287] [ 3804] [depth= 15] . ( 2 sec) [ -15520.4182] [ 3683] [depth= 16] . ( 2 sec) [ -15278.1891] [ 3673] [depth= 5] . ( 2 sec) [ -15221.9528] [ 3661] [depth= 1] . ( 2 sec) [ -15209.4051] [ 3661] [depth= 5] . ( 2 sec) [ -15204.9432] [ 3662] [depth= 1] . ( 2 sec) [ -15124.8429] [ 3654] [depth= 2] . ( 2 sec) [ -14830.5684] [ 3563] [depth= 5] . ( 2 sec) [ -14722.3361] [ 3552] [depth= 3] . ( 2 sec) [ -14696.5043] [ 3582] [depth= 3] . ( 2 sec) [ -14679.3114] [ 3583] [depth= 1] . ( 2 sec) [ -14577.2954] [ 3550] [depth= 1] . ( 2 sec) [ -14360.2418] [ 3564] [depth= 1] . ( 2 sec) [ -14187.1044] [ 3560] [depth= 2] . ( 2 sec) [ -14170.9079] [ 3561] [depth= 3] . ( 2 sec) [ -13903.8438] [ 3510] [depth= 2] . ( 2 sec) [ -13714.3997] [ 3449] [depth= 4] . ( 3 sec) [ -13683.2785] [ 3427] [depth= 1] . ( 3 sec) [ -13536.9398] [ 3396] [depth= 3] . ( 3 sec) [ -13481.9251] [ 3397] [depth= 9] . ( 3 sec) [ -13425.6567] [ 3388] [depth= 1] . ( 3 sec) [ -13420.2850] [ 3381] [depth= 1] . ( 3 sec) [ -13393.7290] [ 3348] [depth= 3] . ( 3 sec) [ -13215.7716] [ 3301] [depth= 1] . ( 3 sec) [ -13009.8359] [ 3215] [depth= 8] . ( 3 sec) [ -12966.1310] [ 3201] [depth= 1] . ( 3 sec) [ -12887.2874] [ 3160] [depth= 1] . ( 3 sec) [ -12886.8629] [ 3165] [depth= 1] . ( 3 sec) [ -12864.7039] [ 3150] [depth= 1] . ( 3 sec) [ -12830.5717] [ 3111] [depth= 3] . ( 3 sec) [ -12789.4383] [ 3095] [depth= 1] . ( 3 sec) [ -12780.2536] [ 3088] [depth= 1] . ( 3 sec) [ -12778.5840] [ 3081] [depth= 1] . ( 3 sec) [ -12679.3232] [ 3082] [depth= 2] . ( 3 sec) [ -12645.3835] [ 3066] [depth= 2] . ( 3 sec) [ -12486.8363] [ 3049] [depth= 3] . ( 3 sec) [ -12359.6446] [ 3042] [depth= 1] . ( 4 sec) [ -12035.2047] [ 2985] [depth= 1] . ( 4 sec) [ -11823.2991] [ 2899] [depth= 1] . ( 4 sec) [ -11692.1602] [ 2886] [depth= 2] . ( 4 sec) [ -11688.5522] [ 2887] [depth= 1] . ( 4 sec) [ -11684.1652] [ 2873] [depth= 1] . ( 4 sec) [ -11310.5568] [ 2733] [depth= 3] . ( 4 sec) [ -11171.4500] [ 2709] [depth= 2] . ( 4 sec) [ -11115.1335] [ 2712] [depth= 3] . ( 4 sec) [ -11017.3590] [ 2676] [depth= 1] . ( 4 sec) [ -11017.1639] [ 2681] [depth= 1] . ( 4 sec) [ -10956.8108] [ 2648] [depth= 3] . ( 4 sec) [ -10953.9687] [ 2648] [depth= 1] . ( 4 sec) [ -10922.1555] [ 2601] [depth= 6] . ( 4 sec) [ -10919.1633] [ 2601] [depth= 3] . ( 4 sec) [ -10914.6397] [ 2617] [depth= 1] . ( 4 sec) [ -10912.1068] [ 2601] [depth= 1] . ( 4 sec) [ -10911.9057] [ 2604] [depth= 1] . ( 5 sec) [ -10552.1769] [Branch lengths ] . ( 5 sec) [ -10550.2671] [GTR parameters ] . ( 5 sec) [ -10509.9069] [Alpha ][ 0.928253] . ( 6 sec) [ -10507.4905] [ 2587] [depth= 4] . ( 6 sec) [ -10503.4519] [ 2584] [depth= 1] . ( 6 sec) [ -10499.1141] [ 2569] [depth= 1] . ( 6 sec) [ -10495.6756] [ 2579] [depth= 1] . ( 6 sec) [ -10495.5465] [ 2555] [depth= 1] . ( 6 sec) [ -10492.7543] [ 2551] [depth= 1] . ( 6 sec) [ -10483.9531] [ 2507] [depth= 1] . ( 6 sec) [ -10358.4255] [ 2456] [depth= 3] . ( 6 sec) [ -10358.1149] [ 2458] [depth= 1] . ( 6 sec) [ -10336.9502] [ 2434] [depth= 6] . ( 6 sec) [ -10336.6284] [ 2439] [depth= 1] . ( 6 sec) [ -10303.3460] [ 2449] [depth= 2] . ( 7 sec) [ -10296.6852] [ 2448] [depth= 2] . ( 7 sec) [ -10296.4819] [ 2400] [depth= 1] . ( 7 sec) [ -10291.1034] [ 2397] [depth= 1] . ( 7 sec) [ -10221.8616] [ 2359] [depth= 2] . ( 7 sec) [ -10212.5546] [ 2335] [depth= 2] . ( 7 sec) [ -10208.8764] [ 2342] [depth= 2] . ( 7 sec) [ -10208.8474] [ 2341] [depth= 1] . ( 7 sec) [ -10208.2528] [ 2347] [depth= 1] . ( 8 sec) [ -10206.9708] [ 2345] [depth= 1] . ( 8 sec) [ -10190.8246] [ 2342] [depth= 1] . ( 8 sec) [ -10190.4142] [ 2343] [depth= 1] . ( 8 sec) [ -10190.2753] [ 2344] [depth= 1] . ( 8 sec) [ -10139.9566] [ 2343] [depth= 1] . ( 8 sec) [ -10131.7013] [ 2338] [depth= 1] . ( 8 sec) [ -10131.2481] [ 2338] [depth= 1] . ( 8 sec) [ -10130.2006] [ 2342] [depth= 1] . ( 8 sec) [ -10122.8278] [ 2347] [depth= 1] . ( 8 sec) [ -10122.2864] [ 2345] [depth= 1] . ( 9 sec) [ -10093.7429] [Branch lengths ] . ( 9 sec) [ -10093.5465] [GTR parameters ] . ( 9 sec) [ -10090.4754] [Alpha ][ 1.112460] . ( 10 sec) [ -10090.4615] [ 2344] [depth= 1] . ( 10 sec) [ -10090.1171] [ 2337] [depth= 3] . ( 13 sec) [ -10088.6768] [Branch lengths ] . ( 13 sec) [ -10088.6614] [GTR parameters ] . ( 13 sec) [ -10088.6517] [Alpha ][ 1.124057] . ( 13 sec) [ -10087.8884] [ 2327] [depth= 1] . ( 14 sec) [ -10087.6872] [ 2335] [depth= 1] . ( 16 sec) [ -10086.8213] [Branch lengths ] . ( 16 sec) [ -10086.8018] [GTR parameters ] . ( 16 sec) [ -10086.8014] [Alpha ][ 1.121549] . ( 20 sec) [ -10085.8214] [Branch lengths ] . ( 40 sec) [ -10085.4136] [Branch lengths ] . ( 40 sec) [ -10085.4136] [Topology ] . ( 41 sec) [ -10085.3245] [Topology ] . ( 42 sec) [ -10084.9523] [Topology ] . ( 42 sec) [ -10083.4344] [Topology ] . ( 43 sec) [ -10082.2254] [Topology ] . ( 44 sec) [ -10081.9459] [Topology ] . ( 45 sec) [ -10081.8846] [Topology ] . ( 45 sec) [ -10081.8836] [GTR parameters ] . ( 45 sec) [ -10081.8786] [Alpha ][ 1.129860] . ( 45 sec) [ -10081.8786] [Topology ] . ( 46 sec) [ -10081.8620] [Topology ] . ( 47 sec) [ -10081.8557] [Topology ] . ( 48 sec) [ -10081.8521] [Topology ] . ( 48 sec) [ -10081.8495] [Topology ] . ( 49 sec) [ -10081.8475] [Topology ] . ( 50 sec) [ -10081.8459] [Topology ] . ( 50 sec) [ -10081.8458] [GTR parameters ] . ( 50 sec) [ -10081.8458] [Alpha ][ 1.129860] . ( 50 sec) [ -10081.8458] [Topology ] . ( 51 sec) [ -10081.8444] [Topology ] . ( 52 sec) [ -10081.8433] [Topology ] . ( 53 sec) [ -10081.8423] [Topology ] . ( 53 sec) [ -10081.8423] [GTR parameters ] . ( 53 sec) [ -10081.8423] [Alpha ][ 1.129860] . ( 53 sec) [ -10081.8423] [Topology ] . ( 54 sec) [ -10081.8416] [Topology ] . ( 54 sec) [ -10081.8416] [GTR parameters ] . ( 54 sec) [ -10081.8416] [Alpha ][ 1.129860] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -10081.7215] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10081.721515. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -28758.9902] [GTR parameters ] . ( 1 sec) [ -28314.0104] [Alpha ][ 0.500960] . ( 1 sec) [ -28197.8512] [ 5278] [depth= 5] . ( 1 sec) [ -27966.0995] [ 5222] [depth= 6] . ( 1 sec) [ -27851.5184] [ 5188] [depth= 3] . ( 1 sec) [ -27800.2635] [ 5191] [depth= 4] . ( 1 sec) [ -27563.9376] [ 5147] [depth= 3] . ( 1 sec) [ -27430.3330] [ 5131] [depth= 2] . ( 1 sec) [ -26999.0312] [ 5083] [depth= 17] . ( 1 sec) [ -26000.3443] [ 4884] [depth= 21] . ( 1 sec) [ -25844.5683] [ 4836] [depth= 9] . ( 1 sec) [ -25266.1321] [ 4858] [depth= 4] . ( 1 sec) [ -24997.7532] [ 4863] [depth= 8] . ( 1 sec) [ -24558.2151] [ 4802] [depth= 16] . ( 1 sec) [ -24548.7224] [ 4802] [depth= 1] . ( 1 sec) [ -23873.7341] [ 4752] [depth= 2] . ( 1 sec) [ -23437.9471] [ 4591] [depth= 3] . ( 1 sec) [ -23200.3544] [ 4532] [depth= 5] . ( 1 sec) [ -23124.5848] [ 4482] [depth= 10] . ( 1 sec) [ -19263.1946] [ 4479] [depth= 1] . ( 1 sec) [ -18994.1451] [ 4467] [depth= 1] . ( 1 sec) [ -18554.6986] [ 4454] [depth= 5] . ( 1 sec) [ -17961.6524] [ 4351] [depth= 5] . ( 2 sec) [ -17595.5015] [ 4262] [depth= 9] . ( 2 sec) [ -17411.8758] [ 4239] [depth= 3] . ( 2 sec) [ -16640.6787] [ 4204] [depth= 7] . ( 2 sec) [ -16357.3143] [ 4164] [depth= 8] . ( 2 sec) [ -16296.9791] [ 4107] [depth= 9] . ( 2 sec) [ -16231.8489] [ 4110] [depth= 4] . ( 2 sec) [ -16211.2377] [ 4112] [depth= 10] . ( 2 sec) [ -16169.8369] [ 4045] [depth= 1] . ( 2 sec) [ -15942.7375] [ 3932] [depth= 3] . ( 2 sec) [ -15934.3416] [ 3905] [depth= 6] . ( 2 sec) [ -15521.1144] [ 3809] [depth= 5] . ( 2 sec) [ -14971.8246] [ 3647] [depth= 10] . ( 2 sec) [ -14703.6338] [ 3569] [depth= 7] . ( 2 sec) [ -14586.0171] [ 3528] [depth= 1] . ( 2 sec) [ -14469.9062] [ 3480] [depth= 4] . ( 2 sec) [ -14456.6243] [ 3481] [depth= 11] . ( 2 sec) [ -14422.6480] [ 3474] [depth= 1] . ( 2 sec) [ -14334.9946] [ 3443] [depth= 3] . ( 2 sec) [ -14272.8401] [ 3401] [depth= 1] . ( 3 sec) [ -14072.0151] [ 3370] [depth= 9] . ( 3 sec) [ -14069.6590] [ 3370] [depth= 1] . ( 3 sec) [ -13839.4624] [ 3322] [depth= 8] . ( 3 sec) [ -13572.9253] [ 3262] [depth= 3] . ( 3 sec) [ -13519.4697] [ 3252] [depth= 1] . ( 3 sec) [ -13052.5923] [ 3209] [depth= 2] . ( 3 sec) [ -12936.0071] [ 3140] [depth= 1] . ( 3 sec) [ -12753.5410] [ 3041] [depth= 3] . ( 3 sec) [ -12573.9296] [ 2964] [depth= 8] . ( 3 sec) [ -12353.5128] [ 2915] [depth= 1] . ( 3 sec) [ -12343.3362] [ 2972] [depth= 1] . ( 3 sec) [ -12195.8904] [ 2868] [depth= 2] . ( 3 sec) [ -12084.9373] [ 2848] [depth= 7] . ( 3 sec) [ -11970.3213] [ 2799] [depth= 4] . ( 3 sec) [ -11802.8946] [ 2733] [depth= 2] . ( 3 sec) [ -11520.5309] [ 2655] [depth= 6] . ( 3 sec) [ -11507.0028] [ 2653] [depth= 1] . ( 4 sec) [ -11502.6658] [ 2671] [depth= 1] . ( 4 sec) [ -11488.0991] [ 2630] [depth= 1] . ( 4 sec) [ -11377.1510] [ 2614] [depth= 4] . ( 4 sec) [ -11344.1650] [ 2588] [depth= 1] . ( 4 sec) [ -11340.8722] [ 2586] [depth= 1] . ( 4 sec) [ -11325.6768] [ 2582] [depth= 1] . ( 4 sec) [ -11303.9841] [ 2581] [depth= 2] . ( 4 sec) [ -11243.0584] [ 2542] [depth= 2] . ( 4 sec) [ -11229.3957] [ 2557] [depth= 1] . ( 4 sec) [ -11216.0799] [ 2556] [depth= 1] . ( 4 sec) [ -11190.6678] [ 2521] [depth= 7] . ( 4 sec) [ -11180.7682] [ 2515] [depth= 2] . ( 4 sec) [ -11137.1639] [ 2501] [depth= 1] . ( 4 sec) [ -11091.8652] [ 2506] [depth= 3] . ( 4 sec) [ -11056.6261] [ 2498] [depth= 1] . ( 4 sec) [ -11055.0952] [ 2502] [depth= 1] . ( 4 sec) [ -11039.1605] [ 2480] [depth= 2] . ( 4 sec) [ -11036.0194] [ 2478] [depth= 1] . ( 4 sec) [ -10925.3886] [ 2480] [depth= 2] . ( 5 sec) [ -10457.9797] [Branch lengths ] . ( 6 sec) [ -10455.9087] [GTR parameters ] . ( 6 sec) [ -10406.6012] [Alpha ][ 0.998934] . ( 6 sec) [ -10395.8716] [ 2464] [depth= 4] . ( 6 sec) [ -10393.7238] [ 2454] [depth= 3] . ( 6 sec) [ -10392.4862] [ 2455] [depth= 2] . ( 6 sec) [ -10366.4942] [ 2441] [depth= 1] . ( 6 sec) [ -10358.1549] [ 2436] [depth= 1] . ( 6 sec) [ -10324.4418] [ 2423] [depth= 1] . ( 6 sec) [ -10297.6761] [ 2395] [depth= 2] . ( 6 sec) [ -10288.2202] [ 2389] [depth= 1] . ( 6 sec) [ -10284.6367] [ 2385] [depth= 1] . ( 7 sec) [ -10279.3509] [ 2390] [depth= 4] . ( 7 sec) [ -10275.5140] [ 2390] [depth= 2] . ( 7 sec) [ -10272.1832] [ 2375] [depth= 1] . ( 7 sec) [ -10224.2702] [ 2344] [depth= 2] . ( 7 sec) [ -10216.1584] [ 2364] [depth= 1] . ( 7 sec) [ -10202.0753] [ 2358] [depth= 1] . ( 7 sec) [ -10201.5079] [ 2363] [depth= 1] . ( 7 sec) [ -10170.1834] [ 2344] [depth= 1] . ( 7 sec) [ -10153.3623] [ 2331] [depth= 1] . ( 8 sec) [ -10152.5945] [ 2336] [depth= 1] . ( 8 sec) [ -10152.2856] [ 2336] [depth= 1] . ( 8 sec) [ -10141.4456] [ 2332] [depth= 1] . ( 8 sec) [ -10141.1624] [ 2331] [depth= 1] . ( 9 sec) [ -10137.8426] [ 2345] [depth= 1] . ( 9 sec) [ -10095.9166] [Branch lengths ] . ( 9 sec) [ -10095.7923] [GTR parameters ] . ( 9 sec) [ -10094.7048] [Alpha ][ 1.109374] . ( 10 sec) [ -10094.3930] [ 2346] [depth= 1] . ( 10 sec) [ -10091.8847] [ 2332] [depth= 1] . ( 12 sec) [ -10091.1447] [ 2332] [depth= 1] . ( 12 sec) [ -10091.0967] [ 2332] [depth= 1] . ( 13 sec) [ -10085.8889] [Branch lengths ] . ( 13 sec) [ -10085.8766] [GTR parameters ] . ( 13 sec) [ -10085.8508] [Alpha ][ 1.128118] . ( 15 sec) [ -10085.8298] [ 2332] [depth= 1] . ( 16 sec) [ -10085.0547] [Branch lengths ] . ( 16 sec) [ -10085.0544] [GTR parameters ] . ( 16 sec) [ -10085.0544] [Alpha ][ 1.129246] . ( 20 sec) [ -10084.7000] [ 2341] [depth= 1] . ( 29 sec) [ -10084.6771] [ 2346] [depth= 1] . ( 32 sec) [ -10084.6122] [ 2346] [depth= 1] . ( 36 sec) [ -10083.2912] [Branch lengths ] . ( 36 sec) [ -10083.2883] [GTR parameters ] . ( 36 sec) [ -10083.2883] [Alpha ][ 1.128117] . ( 48 sec) [ -10083.2039] [ 2341] [depth= 1] . ( 56 sec) [ -10083.0896] [Branch lengths ] . ( 56 sec) [ -10083.0881] [GTR parameters ] . ( 57 sec) [ -10083.0876] [Alpha ][ 1.130855] . ( 57 sec) [ -10083.0876] [Topology ] . ( 57 sec) [ -10083.0704] [Topology ] . ( 58 sec) [ -10083.0594] [Topology ] . ( 59 sec) [ -10083.0507] [Topology ] . ( 60 sec) [ -10083.0434] [Topology ] . ( 61 sec) [ -10083.0372] [Topology ] . ( 62 sec) [ -10083.0319] [Topology ] . ( 62 sec) [ -10083.0318] [GTR parameters ] . ( 62 sec) [ -10083.0318] [Alpha ][ 1.130855] . ( 62 sec) [ -10083.0318] [Topology ] . ( 63 sec) [ -10083.0273] [Topology ] . ( 63 sec) [ -10083.0234] [Topology ] . ( 64 sec) [ -10083.0202] [Topology ] . ( 65 sec) [ -10083.0174] [Topology ] . ( 66 sec) [ -10083.0151] [Topology ] . ( 67 sec) [ -10083.0132] [Topology ] . ( 67 sec) [ -10083.0131] [GTR parameters ] . ( 67 sec) [ -10083.0131] [Alpha ][ 1.130855] . ( 67 sec) [ -10083.0131] [Topology ] . ( 68 sec) [ -10083.0115] [Topology ] . ( 69 sec) [ -10083.0102] [Topology ] . ( 70 sec) [ -10083.0091] [Topology ] . ( 70 sec) [ -10083.0082] [Topology ] . ( 71 sec) [ -10083.0081] [GTR parameters ] . ( 71 sec) [ -10083.0081] [Alpha ][ 1.130855] . ( 71 sec) [ -10083.0081] [Topology ] . ( 71 sec) [ -10083.0074] [Topology ] . ( 72 sec) [ -10083.0074] [GTR parameters ] . ( 72 sec) [ -10083.0074] [Alpha ][ 1.130855] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -10081.7138] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10081.713835. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10151.781372 . ( 0 sec) [ -10150.4304] [GTR parameters ] . ( 0 sec) [ -10149.1164] [Alpha ][ 1.135049] . ( 0 sec) [ -10149.1164] [Topology ] . ( 1 sec) [ -10097.5748] [Topology ] . ( 2 sec) [ -10087.6357] [Topology ] . ( 3 sec) [ -10084.4119] [Topology ] . ( 4 sec) [ -10083.0900] [Topology ] . ( 4 sec) [ -10082.4992] [Topology ] . ( 5 sec) [ -10082.2214] [Topology ] . ( 6 sec) [ -10082.0866] [Topology ] . ( 7 sec) [ -10082.0197] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -10081.9079] [Topology ] . Before opt ts/t=1.000000 LK=-10081.907934 . ( 15 sec) [ -10081.8414] [GTR parameters ] . ( 15 sec) [ -10081.8402] [Alpha ][ 1.130698] . ( 15 sec) [ -10081.8402] [Topology ] . ( 16 sec) [ -10081.7853] [Topology ] . ( 16 sec) [ -10081.7664] [Topology ] . ( 17 sec) [ -10081.7508] [Topology ] . ( 18 sec) [ -10081.7394] [Topology ] . ( 19 sec) [ -10081.7319] [Topology ] . ( 20 sec) [ -10081.7267] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10081.726687 . ( 27 sec) [ -10081.7266] [GTR parameters ] . ( 27 sec) [ -10081.7266] [Alpha ][ 1.131828] . ( 27 sec) [ -10081.7266] [Topology ] . ( 28 sec) [ -10081.7228] [Topology ] . ( 29 sec) [ -10081.7199] [Topology ] . ( 30 sec) [ -10081.7177] [Topology ] . ( 31 sec) [ -10081.7159] [Topology ] . ( 32 sec) [ -10081.7145] [Topology ] . ( 32 sec) [ -10081.7133] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10081.713323 . ( 40 sec) [ -10081.7133] [GTR parameters ] . ( 40 sec) [ -10081.7133] [Alpha ][ 1.131828] . ( 40 sec) [ -10081.7133] [Topology ] . ( 41 sec) [ -10081.7124] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 56 sec) [ -10150.4304] [GTR parameters ] . ( 56 sec) [ -10149.1164] [Alpha ][ 1.135049] . ( 56 sec) [ -10147.4557] [ 2331] [depth= 1] . ( 56 sec) [ -10147.2494] [ 2330] [depth= 1] . ( 57 sec) [ -10147.0769] [ 2331] [depth= 1] . ( 57 sec) [ -10146.8627] [ 2330] [depth= 1] . ( 57 sec) [ -10133.0958] [ 2339] [depth= 1] . ( 57 sec) [ -10132.9135] [ 2330] [depth= 1] . ( 58 sec) [ -10131.9798] [ 2339] [depth= 1] . ( 58 sec) [ -10128.7436] [ 2330] [depth= 1] . ( 58 sec) [ -10127.5067] [ 2333] [depth= 1] . ( 58 sec) [ -10127.3508] [ 2330] [depth= 1] . ( 59 sec) [ -10088.5205] [Branch lengths ] . ( 59 sec) [ -10088.4932] [GTR parameters ] . ( 59 sec) [ -10088.4922] [Alpha ][ 1.131203] . ( 59 sec) [ -10088.4612] [ 2319] [depth= 1] . ( 59 sec) [ -10088.3981] [ 2330] [depth= 1] . ( 60 sec) [ -10087.5956] [ 2339] [depth= 1] . ( 62 sec) [ -10084.5132] [Branch lengths ] . ( 63 sec) [ -10084.4925] [GTR parameters ] . ( 63 sec) [ -10084.4911] [Alpha ][ 1.126565] . ( 63 sec) [ -10083.9318] [ 2328] [depth= 1] . ( 66 sec) [ -10082.1710] [Branch lengths ] . ( 66 sec) [ -10082.1696] [GTR parameters ] . ( 66 sec) [ -10082.1647] [Alpha ][ 1.134865] . ( 69 sec) [ -10081.7698] [Branch lengths ] . ( 89 sec) [ -10081.7335] [Branch lengths ] . ( 89 sec) [ -10081.7335] [Topology ] . ( 90 sec) [ -10081.7279] [Topology ] . ( 91 sec) [ -10081.7245] [Topology ] . ( 92 sec) [ -10081.7218] [Topology ] . ( 92 sec) [ -10081.7196] [Topology ] . ( 93 sec) [ -10081.7178] [Topology ] . ( 94 sec) [ -10081.7163] [Topology ] . ( 94 sec) [ -10081.7161] [GTR parameters ] . ( 94 sec) [ -10081.7154] [Alpha ][ 1.131481] . ( 94 sec) [ -10081.7154] [Topology ] . ( 95 sec) [ -10081.7141] [Topology ] . ( 96 sec) [ -10081.7130] [Topology ] . ( 97 sec) [ -10081.7121] [Topology ] . ( 97 sec) [ -10081.7121] [GTR parameters ] . ( 97 sec) [ -10081.7121] [Alpha ][ 1.131481] . ( 97 sec) [ -10081.7121] [Topology ] . ( 98 sec) [ -10081.7114] [Topology ] . ( 98 sec) [ -10081.7114] [GTR parameters ] . ( 98 sec) [ -10081.7114] [Alpha ][ 1.131481] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10081.712370 . Log likelihood obtained after SPR moves : -10081.711411 . Log likelihood of the current tree: -10081.711411. . Printing the most likely tree in file 'data33.phy_phyml_tree.txt'... . Best log likelihood : -10081.711411 . Time used 0h1m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo