.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_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... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -55000.5603] [GTR parameters ] . ( 1 sec) [ -53440.2653] [Alpha ][ 0.500960] . ( 2 sec) [ -53020.3585] [11308] [depth= 12] . ( 2 sec) [ -52714.2237] [11238] [depth= 11] . ( 2 sec) [ -52369.7594] [11211] [depth= 6] . ( 2 sec) [ -52269.5101] [11167] [depth= 1] . ( 2 sec) [ -52097.6602] [11129] [depth= 6] . ( 2 sec) [ -51937.3480] [11100] [depth= 2] . ( 3 sec) [ -51916.1384] [11088] [depth= 7] . ( 3 sec) [ -51814.8674] [11058] [depth= 2] . ( 3 sec) [ -51469.5221] [11045] [depth= 9] . ( 3 sec) [ -51398.7641] [11035] [depth= 1] . ( 3 sec) [ -51369.3982] [11028] [depth= 5] . ( 4 sec) [ -51309.9371] [11006] [depth= 1] . ( 4 sec) [ -51256.4560] [11002] [depth= 4] . ( 4 sec) [ -51198.9582] [10986] [depth= 5] . ( 4 sec) [ -51176.8443] [10977] [depth= 5] . ( 4 sec) [ -50862.3315] [10965] [depth= 5] . ( 4 sec) [ -50822.2859] [10960] [depth= 2] . ( 4 sec) [ -50441.2108] [10950] [depth= 5] . ( 5 sec) [ -50250.9843] [10937] [depth= 14] . ( 5 sec) [ -50020.6815] [10899] [depth= 7] . ( 5 sec) [ -49950.6108] [10900] [depth= 19] . ( 5 sec) [ -49928.9488] [10894] [depth= 1] . ( 5 sec) [ -49825.9219] [10878] [depth= 15] . ( 5 sec) [ -49528.6613] [10842] [depth= 17] . ( 5 sec) [ -49438.8536] [10776] [depth= 1] . ( 6 sec) [ -49251.4399] [10735] [depth= 2] . ( 6 sec) [ -49094.0177] [10728] [depth= 2] . ( 6 sec) [ -48944.1074] [10723] [depth= 12] . ( 6 sec) [ -48695.2215] [10683] [depth= 13] . ( 6 sec) [ -48481.0598] [10624] [depth= 16] . ( 6 sec) [ -48464.6846] [10621] [depth= 6] . ( 7 sec) [ -48445.3956] [10610] [depth= 23] . ( 7 sec) [ -48246.8321] [10589] [depth= 31] . ( 7 sec) [ -48091.0751] [10555] [depth= 1] . ( 7 sec) [ -47919.4542] [10514] [depth= 18] . ( 7 sec) [ -47585.9731] [10498] [depth= 11] . ( 7 sec) [ -47365.4622] [10414] [depth= 1] . ( 8 sec) [ -47197.3708] [10333] [depth= 5] . ( 8 sec) [ -46968.0188] [10314] [depth= 16] . ( 8 sec) [ -46867.0655] [10310] [depth= 1] . ( 8 sec) [ -46569.6077] [10273] [depth= 14] . ( 8 sec) [ -46369.1810] [10226] [depth= 3] . ( 8 sec) [ -46197.3100] [10210] [depth= 17] . ( 8 sec) [ -46189.5192] [10228] [depth= 1] . ( 9 sec) [ -45938.5796] [10199] [depth= 4] . ( 9 sec) [ -45531.9583] [10040] [depth= 21] . ( 9 sec) [ -45521.5104] [10037] [depth= 20] . ( 9 sec) [ -45183.1663] [ 9975] [depth= 26] . ( 9 sec) [ -44999.5439] [ 9950] [depth= 8] . ( 9 sec) [ -44556.5572] [ 9840] [depth= 24] . ( 10 sec) [ -44075.8220] [ 9767] [depth= 12] . ( 10 sec) [ -44056.0838] [ 9765] [depth= 1] . ( 10 sec) [ -43815.2740] [ 9682] [depth= 15] . ( 10 sec) [ -43705.7305] [ 9628] [depth= 1] . ( 10 sec) [ -43358.5508] [ 9548] [depth= 7] . ( 11 sec) [ -43352.4060] [ 9548] [depth= 1] . ( 11 sec) [ -42969.4793] [ 9506] [depth= 5] . ( 11 sec) [ -42658.0378] [ 9477] [depth= 18] . ( 11 sec) [ -42235.5155] [ 9465] [depth= 2] . ( 11 sec) [ -41765.3830] [ 9383] [depth= 13] . ( 11 sec) [ -41689.4313] [ 9382] [depth= 1] . ( 11 sec) [ -41565.3100] [ 9381] [depth= 9] . ( 12 sec) [ -41379.9816] [ 9288] [depth= 8] . ( 12 sec) [ -41156.5949] [ 9238] [depth= 14] . ( 12 sec) [ -41097.0653] [ 9224] [depth= 1] . ( 12 sec) [ -40824.0477] [ 9181] [depth= 5] . ( 12 sec) [ -40766.3693] [ 9171] [depth= 1] . ( 12 sec) [ -40628.3845] [ 9116] [depth= 26] . ( 13 sec) [ -40525.9121] [ 9091] [depth= 1] . ( 13 sec) [ -40390.7423] [ 9075] [depth= 8] . ( 13 sec) [ -40294.3425] [ 9056] [depth= 18] . ( 13 sec) [ -40196.2566] [ 9021] [depth= 2] . ( 13 sec) [ -40153.9774] [ 8985] [depth= 9] . ( 14 sec) [ -39967.9091] [ 8953] [depth= 4] . ( 14 sec) [ -39795.4365] [ 8925] [depth= 8] . ( 14 sec) [ -39764.1698] [ 8910] [depth= 6] . ( 14 sec) [ -39600.9005] [ 8903] [depth= 1] . ( 14 sec) [ -39313.4471] [ 8849] [depth= 8] . ( 14 sec) [ -39113.7483] [ 8809] [depth= 18] . ( 14 sec) [ -39009.0325] [ 8679] [depth= 4] . ( 15 sec) [ -39007.9532] [ 8676] [depth= 18] . ( 15 sec) [ -38981.2792] [ 8677] [depth= 1] . ( 15 sec) [ -38534.9936] [ 8630] [depth= 15] . ( 15 sec) [ -38183.3970] [ 8509] [depth= 2] . ( 15 sec) [ -38116.3008] [ 8495] [depth= 6] . ( 15 sec) [ -38074.2859] [ 8487] [depth= 1] . ( 16 sec) [ -38050.6012] [ 8483] [depth= 2] . ( 16 sec) [ -37958.9510] [ 8476] [depth= 8] . ( 16 sec) [ -37790.2400] [ 8413] [depth= 21] . ( 16 sec) [ -37754.2544] [ 8406] [depth= 4] . ( 16 sec) [ -37754.0528] [ 8407] [depth= 6] . ( 16 sec) [ -37668.8738] [ 8374] [depth= 4] . ( 17 sec) [ -37647.2474] [ 8367] [depth= 5] . ( 17 sec) [ -37417.3987] [ 8268] [depth= 13] . ( 17 sec) [ -37411.7276] [ 8267] [depth= 3] . ( 17 sec) [ -37290.3267] [ 8192] [depth= 3] . ( 17 sec) [ -37122.4976] [ 8176] [depth= 19] . ( 18 sec) [ -36993.7102] [ 8100] [depth= 17] . ( 18 sec) [ -36895.8209] [ 8061] [depth= 1] . ( 18 sec) [ -36791.6145] [ 8009] [depth= 7] . ( 18 sec) [ -36506.2063] [ 8017] [depth= 17] . ( 18 sec) [ -36493.8106] [ 8017] [depth= 2] . ( 19 sec) [ -36443.9444] [ 8013] [depth= 2] . ( 19 sec) [ -36361.3612] [ 7983] [depth= 1] . ( 19 sec) [ -36219.7164] [ 7926] [depth= 1] . ( 19 sec) [ -36121.5744] [ 7916] [depth= 8] . ( 19 sec) [ -36049.7227] [ 7890] [depth= 5] . ( 19 sec) [ -35702.5828] [ 7889] [depth= 1] . ( 20 sec) [ -35605.5537] [ 7865] [depth= 2] . ( 20 sec) [ -35545.7532] [ 7863] [depth= 2] . ( 20 sec) [ -35378.0241] [ 7767] [depth= 14] . ( 20 sec) [ -35282.8526] [ 7742] [depth= 9] . ( 20 sec) [ -35075.3938] [ 7726] [depth= 11] . ( 20 sec) [ -35069.4160] [ 7724] [depth= 1] . ( 21 sec) [ -34909.5921] [ 7674] [depth= 10] . ( 21 sec) [ -34519.7533] [ 7602] [depth= 19] . ( 21 sec) [ -34503.6647] [ 7599] [depth= 1] . ( 21 sec) [ -34481.2809] [ 7603] [depth= 1] . ( 21 sec) [ -34458.2954] [ 7603] [depth= 1] . ( 21 sec) [ -34453.0765] [ 7599] [depth= 1] . ( 22 sec) [ -34446.6366] [ 7597] [depth= 1] . ( 22 sec) [ -34434.7825] [ 7583] [depth= 1] . ( 22 sec) [ -34415.2376] [ 7584] [depth= 1] . ( 22 sec) [ -34331.1408] [ 7560] [depth= 22] . ( 22 sec) [ -34329.4543] [ 7560] [depth= 1] . ( 23 sec) [ -34327.2788] [ 7563] [depth= 2] . ( 23 sec) [ -34312.6759] [ 7557] [depth= 1] . ( 23 sec) [ -34208.0148] [ 7535] [depth= 29] . ( 24 sec) [ -34204.6509] [ 7537] [depth= 1] . ( 24 sec) [ -34197.2335] [ 7536] [depth= 2] . ( 24 sec) [ -34194.2238] [ 7534] [depth= 3] . ( 24 sec) [ -34190.4014] [ 7534] [depth= 2] . ( 24 sec) [ -34186.4971] [ 7529] [depth= 2] . ( 24 sec) [ -34030.9065] [ 7461] [depth= 20] . ( 25 sec) [ -34029.9829] [ 7462] [depth= 3] . ( 25 sec) [ -34009.8110] [ 7458] [depth= 4] . ( 25 sec) [ -33978.6191] [ 7451] [depth= 1] . ( 25 sec) [ -33973.2718] [ 7447] [depth= 2] . ( 25 sec) [ -33949.1434] [ 7428] [depth= 4] . ( 25 sec) [ -33938.4511] [ 7427] [depth= 1] . ( 25 sec) [ -33920.8557] [ 7418] [depth= 16] . ( 26 sec) [ -33904.5161] [ 7407] [depth= 16] . ( 27 sec) [ -33807.8458] [ 7375] [depth= 16] . ( 27 sec) [ -33700.3368] [ 7365] [depth= 11] . ( 27 sec) [ -33503.4818] [ 7293] [depth= 6] . ( 27 sec) [ -33500.5547] [ 7301] [depth= 1] . ( 27 sec) [ -33427.6855] [ 7295] [depth= 7] . ( 27 sec) [ -33349.4332] [ 7271] [depth= 2] . ( 28 sec) [ -33341.5449] [ 7274] [depth= 1] . ( 28 sec) [ -33307.5944] [ 7256] [depth= 10] . ( 28 sec) [ -33047.5695] [ 7197] [depth= 3] . ( 28 sec) [ -33036.0070] [ 7194] [depth= 1] . ( 28 sec) [ -32997.3447] [ 7180] [depth= 5] . ( 28 sec) [ -32966.5946] [ 7164] [depth= 1] . ( 29 sec) [ -32899.6670] [ 7145] [depth= 8] . ( 29 sec) [ -32836.2468] [ 7135] [depth= 8] . ( 29 sec) [ -32804.3683] [ 7110] [depth= 2] . ( 29 sec) [ -32792.0320] [ 7108] [depth= 1] . ( 29 sec) [ -32787.3873] [ 7107] [depth= 1] . ( 30 sec) [ -32733.6457] [ 7101] [depth= 3] . ( 30 sec) [ -32730.3582] [ 7101] [depth= 1] . ( 30 sec) [ -32690.8933] [ 7092] [depth= 1] . ( 30 sec) [ -32688.5213] [ 7093] [depth= 2] . ( 30 sec) [ -32506.7904] [ 7089] [depth= 10] . ( 31 sec) [ -32415.2819] [ 7044] [depth= 3] . ( 31 sec) [ -32406.0234] [ 7042] [depth= 1] . ( 31 sec) [ -32252.6121] [ 7027] [depth= 10] . ( 31 sec) [ -32215.6393] [ 6973] [depth= 2] . ( 31 sec) [ -32161.2026] [ 6947] [depth= 4] . ( 31 sec) [ -32075.2004] [ 6928] [depth= 4] . ( 32 sec) [ -32002.5486] [ 6928] [depth= 2] . ( 32 sec) [ -31899.2619] [ 6880] [depth= 2] . ( 32 sec) [ -31879.5568] [ 6875] [depth= 1] . ( 32 sec) [ -31799.8375] [ 6849] [depth= 3] . ( 32 sec) [ -31796.8708] [ 6841] [depth= 2] . ( 32 sec) [ -31755.7094] [ 6836] [depth= 4] . ( 33 sec) [ -31637.3655] [ 6807] [depth= 1] . ( 33 sec) [ -31635.5368] [ 6812] [depth= 1] . ( 33 sec) [ -31584.4901] [ 6796] [depth= 1] . ( 33 sec) [ -31584.1993] [ 6794] [depth= 4] . ( 33 sec) [ -31579.2747] [ 6793] [depth= 2] . ( 34 sec) [ -31577.5369] [ 6793] [depth= 1] . ( 34 sec) [ -31537.5937] [ 6791] [depth= 7] . ( 34 sec) [ -31514.6485] [ 6782] [depth= 9] . ( 34 sec) [ -31465.3233] [ 6730] [depth= 6] . ( 34 sec) [ -31430.8122] [ 6724] [depth= 1] . ( 35 sec) [ -31430.6105] [ 6725] [depth= 1] . ( 35 sec) [ -31430.5980] [ 6725] [depth= 2] . ( 35 sec) [ -31423.6686] [ 6723] [depth= 1] . ( 35 sec) [ -31415.6919] [ 6720] [depth= 5] . ( 36 sec) [ -31399.1570] [ 6716] [depth= 3] . ( 36 sec) [ -31392.9061] [ 6713] [depth= 5] . ( 36 sec) [ -31373.2239] [ 6706] [depth= 9] . ( 36 sec) [ -31363.5207] [ 6704] [depth= 7] . ( 36 sec) [ -31322.4639] [ 6693] [depth= 1] . ( 37 sec) [ -31209.1312] [ 6659] [depth= 6] . ( 37 sec) [ -31203.8620] [ 6664] [depth= 1] . ( 37 sec) [ -31096.5365] [ 6632] [depth= 8] . ( 37 sec) [ -30966.7991] [ 6600] [depth= 16] . ( 37 sec) [ -30965.7311] [ 6600] [depth= 2] . ( 38 sec) [ -30964.0662] [ 6599] [depth= 1] . ( 38 sec) [ -30656.4457] [ 6517] [depth= 4] . ( 38 sec) [ -30631.9097] [ 6515] [depth= 2] . ( 38 sec) [ -30586.8490] [ 6513] [depth= 1] . ( 38 sec) [ -30532.9473] [ 6522] [depth= 3] . ( 38 sec) [ -30529.8288] [ 6524] [depth= 1] . ( 39 sec) [ -30476.5274] [ 6516] [depth= 12] . ( 39 sec) [ -30470.0001] [ 6518] [depth= 1] . ( 39 sec) [ -30461.7296] [ 6509] [depth= 3] . ( 39 sec) [ -30457.0658] [ 6505] [depth= 1] . ( 40 sec) [ -30174.7849] [ 6471] [depth= 9] . ( 40 sec) [ -30154.0047] [ 6455] [depth= 1] . ( 40 sec) [ -30144.3355] [ 6438] [depth= 1] . ( 40 sec) [ -30117.1978] [ 6417] [depth= 1] . ( 40 sec) [ -30109.3821] [ 6412] [depth= 2] . ( 41 sec) [ -30109.2323] [ 6413] [depth= 4] . ( 41 sec) [ -30088.4836] [ 6404] [depth= 1] . ( 41 sec) [ -30085.0709] [ 6404] [depth= 1] . ( 41 sec) [ -30079.8018] [ 6427] [depth= 1] . ( 42 sec) [ -29859.2385] [ 6376] [depth= 1] . ( 42 sec) [ -29773.7300] [ 6306] [depth= 14] . ( 42 sec) [ -29742.2310] [ 6291] [depth= 2] . ( 42 sec) [ -29684.3005] [ 6283] [depth= 1] . ( 42 sec) [ -29682.8433] [ 6283] [depth= 2] . ( 43 sec) [ -29663.8687] [ 6272] [depth= 7] . ( 43 sec) [ -29642.0101] [ 6263] [depth= 1] . ( 44 sec) [ -29378.9960] [Branch lengths ] . ( 52 sec) [ -28144.7448] [GTR parameters ] . ( 52 sec) [ -28089.8998] [Alpha ][ 0.360420] . ( 52 sec) [ -28087.1818] [ 6262] [depth= 1] . ( 53 sec) [ -28082.3357] [ 6263] [depth= 1] . ( 53 sec) [ -28079.5560] [ 6252] [depth= 2] . ( 53 sec) [ -28076.5469] [ 6249] [depth= 1] . ( 53 sec) [ -28026.6670] [ 6247] [depth= 8] . ( 54 sec) [ -28011.9422] [ 6237] [depth= 2] . ( 54 sec) [ -27955.8449] [ 6200] [depth= 11] . ( 54 sec) [ -27949.9095] [ 6195] [depth= 1] . ( 54 sec) [ -27945.1784] [ 6190] [depth= 4] . ( 54 sec) [ -27917.3615] [ 6173] [depth= 1] . ( 54 sec) [ -27910.1215] [ 6170] [depth= 1] . ( 55 sec) [ -27907.3872] [ 6167] [depth= 1] . ( 56 sec) [ -27904.3508] [ 6165] [depth= 2] . ( 57 sec) [ -27894.1420] [ 6159] [depth= 3] . ( 57 sec) [ -27873.1817] [ 6151] [depth= 1] . ( 57 sec) [ -27805.5728] [ 6120] [depth= 7] . ( 58 sec) [ -27804.5061] [ 6117] [depth= 1] . ( 58 sec) [ -27803.0941] [ 6116] [depth= 1] . ( 58 sec) [ -27779.3272] [ 6109] [depth= 6] . ( 58 sec) [ -27682.2449] [ 6080] [depth= 5] . ( 58 sec) [ -27681.6102] [ 6086] [depth= 1] . ( 59 sec) [ -27678.4739] [ 6083] [depth= 3] . ( 59 sec) [ -27678.2661] [ 6084] [depth= 1] . ( 60 sec) [ -27545.3333] [ 6026] [depth= 10] . ( 60 sec) [ -27544.4801] [ 6019] [depth= 1] . ( 60 sec) [ -27541.5067] [ 6018] [depth= 1] . ( 61 sec) [ -27540.3905] [ 6015] [depth= 1] . ( 61 sec) [ -27535.9091] [ 6012] [depth= 1] . ( 61 sec) [ -27535.8903] [ 6012] [depth= 1] . ( 62 sec) [ -27507.7049] [ 5991] [depth= 3] . ( 62 sec) [ -27486.0292] [ 5983] [depth= 2] . ( 62 sec) [ -27479.9134] [ 5981] [depth= 1] . ( 62 sec) [ -27475.5962] [ 5981] [depth= 1] . ( 64 sec) [ -27475.5405] [ 5986] [depth= 2] . ( 64 sec) [ -27474.3379] [ 5978] [depth= 2] . ( 65 sec) [ -27466.9232] [ 5981] [depth= 1] . ( 65 sec) [ -27464.7659] [ 5978] [depth= 1] . ( 67 sec) [ -27464.0775] [ 5975] [depth= 1] . ( 67 sec) [ -27459.4828] [ 5969] [depth= 2] . ( 69 sec) [ -27388.2756] [ 5923] [depth= 2] . ( 69 sec) [ -27377.7619] [ 5917] [depth= 1] . ( 70 sec) [ -27377.5260] [ 5916] [depth= 1] . ( 70 sec) [ -27376.7104] [ 5916] [depth= 1] . ( 72 sec) [ -27376.2899] [ 5920] [depth= 1] . ( 72 sec) [ -27373.6368] [ 5919] [depth= 1] . ( 72 sec) [ -27373.2125] [ 5919] [depth= 1] . ( 73 sec) [ -27363.3823] [ 5908] [depth= 1] . ( 74 sec) [ -27363.2630] [ 5908] [depth= 1] . ( 75 sec) [ -27363.2324] [ 5908] [depth= 1] . ( 76 sec) [ -27254.1428] [ 5841] [depth= 13] . ( 77 sec) [ -27240.7244] [ 5832] [depth= 1] . ( 77 sec) [ -27238.8910] [ 5835] [depth= 1] . ( 79 sec) [ -27238.8393] [ 5836] [depth= 1] . ( 80 sec) [ -27236.8763] [ 5836] [depth= 1] . ( 80 sec) [ -27236.5045] [ 5839] [depth= 1] . ( 80 sec) [ -27227.1424] [ 5838] [depth= 1] . ( 80 sec) [ -27223.9352] [ 5837] [depth= 2] . ( 82 sec) [ -27223.7674] [ 5838] [depth= 1] . ( 82 sec) [ -27222.3121] [ 5837] [depth= 1] . ( 82 sec) [ -27222.0534] [ 5836] [depth= 1] . ( 82 sec) [ -27209.5242] [ 5835] [depth= 2] . ( 83 sec) [ -27209.2200] [ 5835] [depth= 1] . ( 84 sec) [ -27208.0173] [ 5834] [depth= 1] . ( 84 sec) [ -27149.4943] [ 5810] [depth= 1] . ( 87 sec) [ -27143.0221] [ 5809] [depth= 6] . ( 87 sec) [ -27142.9201] [ 5809] [depth= 1] . ( 89 sec) [ -27117.0650] [ 5800] [depth= 3] . ( 91 sec) [ -27113.0614] [ 5797] [depth= 2] . ( 93 sec) [ -27100.7732] [ 5791] [depth= 1] . ( 93 sec) [ -27096.9423] [ 5788] [depth= 1] . ( 93 sec) [ -27094.6584] [ 5789] [depth= 1] . ( 93 sec) [ -27091.3745] [ 5792] [depth= 1] . ( 95 sec) [ -27029.3995] [Branch lengths ] . ( 99 sec) [ -27027.8367] [GTR parameters ] . ( 100 sec) [ -27027.0994] [Alpha ][ 0.346009] . ( 101 sec) [ -27025.8734] [ 5791] [depth= 1] . ( 101 sec) [ -27015.8811] [ 5789] [depth= 2] . ( 102 sec) [ -27011.9004] [ 5791] [depth= 1] . ( 108 sec) [ -27010.9759] [ 5794] [depth= 1] . ( 109 sec) [ -27010.9594] [ 5794] [depth= 1] . ( 115 sec) [ -27005.3619] [ 5797] [depth= 1] . ( 121 sec) [ -27005.1974] [ 5794] [depth= 1] . ( 129 sec) [ -27004.5283] [ 5797] [depth= 1] . ( 131 sec) [ -27004.5015] [ 5797] [depth= 1] . ( 131 sec) [ -26990.7020] [ 5794] [depth= 2] . ( 133 sec) [ -26985.3786] [ 5793] [depth= 1] . ( 133 sec) [ -26985.0884] [ 5789] [depth= 4] . ( 146 sec) [ -26965.3619] [Branch lengths ] . ( 150 sec) [ -26965.0738] [GTR parameters ] . ( 150 sec) [ -26963.8197] [Alpha ][ 0.327716] . ( 170 sec) [ -26963.7268] [ 5791] [depth= 1] . ( 172 sec) [ -26960.3944] [ 5796] [depth= 3] . ( 182 sec) [ -26959.6482] [ 5796] [depth= 1] . ( 195 sec) [ -26956.2691] [Branch lengths ] . ( 199 sec) [ -26956.1136] [GTR parameters ] . ( 199 sec) [ -26955.5494] [Alpha ][ 0.315911] . ( 215 sec) [ -26949.5531] [ 5795] [depth= 8] . ( 244 sec) [ -26947.9386] [Branch lengths ] . ( 248 sec) [ -26947.9242] [GTR parameters ] . ( 248 sec) [ -26947.6613] [Alpha ][ 0.308112] . ( 292 sec) [ -26947.2970] [Branch lengths ] . ( 431 sec) [ -26947.2556] [Branch lengths ] . ( 431 sec) [ -26947.2556] [Topology ] . ( 434 sec) [ -26946.8366] [Topology ] . ( 437 sec) [ -26946.5465] [Topology ] . ( 440 sec) [ -26946.5152] [Topology ] . ( 444 sec) [ -26946.5067] [Topology ] . ( 447 sec) [ -26946.5039] [Topology ] . ( 450 sec) [ -26946.5029] [Topology ] . ( 453 sec) [ -26946.5025] [Topology ] . ( 457 sec) [ -26946.4865] [GTR parameters ] . ( 457 sec) [ -26946.2417] [Alpha ][ 0.300696] . ( 457 sec) [ -26946.2417] [Topology ] . ( 461 sec) [ -26946.1568] [Topology ] . ( 464 sec) [ -26946.1327] [Topology ] . ( 467 sec) [ -26946.1248] [Topology ] . ( 470 sec) [ -26946.1220] [Topology ] . ( 474 sec) [ -26946.1210] [Topology ] . ( 477 sec) [ -26946.1160] [GTR parameters ] . ( 477 sec) [ -26946.0509] [Alpha ][ 0.296761] . ( 477 sec) [ -26946.0509] [Topology ] . ( 480 sec) [ -26946.0229] [Topology ] . ( 484 sec) [ -26946.0149] [Topology ] . ( 487 sec) [ -26946.0123] [Topology ] . ( 490 sec) [ -26946.0114] [Topology ] . ( 493 sec) [ -26946.0101] [GTR parameters ] . ( 494 sec) [ -26945.9939] [Alpha ][ 0.294808] . ( 494 sec) [ -26945.9939] [Topology ] . ( 497 sec) [ -26945.9852] [Topology ] . ( 500 sec) [ -26945.9827] [Topology ] . ( 503 sec) [ -26945.9818] [Topology ] . ( 505 sec) [ -26945.9813] [GTR parameters ] . ( 506 sec) [ -26945.9769] [Alpha ][ 0.293787] . ( 506 sec) [ -26945.9769] [Topology ] . ( 509 sec) [ -26945.9738] [Topology ] . ( 512 sec) [ -26945.9729] [Topology ] . ( 513 sec) [ -26945.9729] [GTR parameters ] . ( 513 sec) [ -26945.9719] [Alpha ][ 0.293300] . ( 513 sec) [ -26945.9719] [Topology ] . ( 516 sec) [ -26945.9706] [Topology ] . ( 520 sec) [ -26945.9702] [Topology ] . ( 521 sec) [ -26945.9701] [GTR parameters ] . ( 521 sec) [ -26945.9696] [Alpha ][ 0.292964] . ( 521 sec) [ -26945.9696] [Topology ] . ( 525 sec) [ -26945.9690] [Topology ] . ( 525 sec) [ -26945.9690] [GTR parameters ] . ( 526 sec) [ -26945.9690] [Alpha ][ 0.292964] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26945.968977. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -54189.0725] [GTR parameters ] . ( 2 sec) [ -52677.3061] [Alpha ][ 0.500960] . ( 2 sec) [ -52601.1838] [11201] [depth= 16] . ( 2 sec) [ -52433.8355] [11165] [depth= 3] . ( 3 sec) [ -52248.4743] [11165] [depth= 17] . ( 3 sec) [ -52179.4388] [11169] [depth= 1] . ( 3 sec) [ -52172.2498] [11165] [depth= 16] . ( 3 sec) [ -52098.4443] [11174] [depth= 1] . ( 3 sec) [ -51889.3746] [11142] [depth= 10] . ( 3 sec) [ -51622.4662] [11070] [depth= 2] . ( 3 sec) [ -51593.4492] [11055] [depth= 5] . ( 4 sec) [ -51164.6035] [11024] [depth= 10] . ( 4 sec) [ -51125.2437] [10974] [depth= 1] . ( 4 sec) [ -50973.0840] [10922] [depth= 10] . ( 4 sec) [ -50774.6588] [10896] [depth= 2] . ( 4 sec) [ -50745.9688] [10889] [depth= 9] . ( 4 sec) [ -50632.5213] [10856] [depth= 17] . ( 5 sec) [ -50499.7828] [10845] [depth= 3] . ( 5 sec) [ -50395.6069] [10837] [depth= 8] . ( 5 sec) [ -50116.3913] [10793] [depth= 5] . ( 5 sec) [ -49911.7400] [10766] [depth= 6] . ( 5 sec) [ -49860.7340] [10759] [depth= 11] . ( 5 sec) [ -49856.1685] [10759] [depth= 1] . ( 5 sec) [ -49809.6096] [10737] [depth= 2] . ( 6 sec) [ -49715.3124] [10727] [depth= 3] . ( 6 sec) [ -49550.3983] [10709] [depth= 24] . ( 6 sec) [ -49126.0515] [10604] [depth= 15] . ( 6 sec) [ -49084.1554] [10610] [depth= 20] . ( 6 sec) [ -49074.5909] [10609] [depth= 18] . ( 6 sec) [ -48832.3724] [10590] [depth= 1] . ( 6 sec) [ -48732.7948] [10571] [depth= 19] . ( 7 sec) [ -48593.5078] [10528] [depth= 18] . ( 7 sec) [ -48482.7706] [10525] [depth= 1] . ( 7 sec) [ -48146.5711] [10456] [depth= 11] . ( 7 sec) [ -48041.8149] [10441] [depth= 10] . ( 7 sec) [ -47873.7962] [10411] [depth= 5] . ( 7 sec) [ -47619.8939] [10357] [depth= 1] . ( 8 sec) [ -47481.1893] [10329] [depth= 1] . ( 8 sec) [ -47234.6281] [10229] [depth= 10] . ( 8 sec) [ -47101.6860] [10223] [depth= 13] . ( 8 sec) [ -46633.3468] [10156] [depth= 10] . ( 8 sec) [ -46578.1331] [10125] [depth= 1] . ( 8 sec) [ -46500.4235] [10110] [depth= 16] . ( 9 sec) [ -46471.8838] [10104] [depth= 10] . ( 9 sec) [ -46392.0429] [10105] [depth= 1] . ( 9 sec) [ -46380.0637] [10101] [depth= 3] . ( 9 sec) [ -46370.4295] [10100] [depth= 1] . ( 9 sec) [ -46009.9964] [ 9971] [depth= 24] . ( 9 sec) [ -45996.4840] [ 9972] [depth= 4] . ( 10 sec) [ -45763.0347] [ 9932] [depth= 8] . ( 10 sec) [ -45204.3657] [ 9799] [depth= 18] . ( 10 sec) [ -45200.0786] [ 9795] [depth= 16] . ( 10 sec) [ -45199.1820] [ 9795] [depth= 1] . ( 11 sec) [ -45157.9597] [ 9800] [depth= 19] . ( 11 sec) [ -45110.2509] [ 9791] [depth= 2] . ( 11 sec) [ -45106.5487] [ 9788] [depth= 1] . ( 11 sec) [ -45058.5322] [ 9768] [depth= 13] . ( 11 sec) [ -45034.1955] [ 9767] [depth= 1] . ( 11 sec) [ -45000.4348] [ 9765] [depth= 3] . ( 11 sec) [ -44856.6173] [ 9724] [depth= 1] . ( 12 sec) [ -44826.9079] [ 9709] [depth= 6] . ( 12 sec) [ -44813.5642] [ 9712] [depth= 11] . ( 12 sec) [ -44797.0284] [ 9707] [depth= 2] . ( 12 sec) [ -44723.5656] [ 9690] [depth= 14] . ( 12 sec) [ -44327.8500] [ 9691] [depth= 1] . ( 13 sec) [ -44042.7900] [ 9593] [depth= 14] . ( 13 sec) [ -43964.6047] [ 9578] [depth= 1] . ( 13 sec) [ -43561.4780] [ 9568] [depth= 11] . ( 13 sec) [ -43461.4697] [ 9546] [depth= 13] . ( 13 sec) [ -43440.3756] [ 9542] [depth= 1] . ( 13 sec) [ -43206.5521] [ 9468] [depth= 14] . ( 14 sec) [ -43016.5648] [ 9389] [depth= 12] . ( 14 sec) [ -42973.7691] [ 9366] [depth= 7] . ( 14 sec) [ -42973.7440] [ 9366] [depth= 1] . ( 14 sec) [ -42962.8594] [ 9363] [depth= 11] . ( 14 sec) [ -42955.1013] [ 9361] [depth= 1] . ( 14 sec) [ -42755.3111] [ 9337] [depth= 15] . ( 15 sec) [ -42742.3508] [ 9340] [depth= 1] . ( 15 sec) [ -42612.5274] [ 9299] [depth= 2] . ( 15 sec) [ -42493.5789] [ 9271] [depth= 17] . ( 15 sec) [ -42428.8072] [ 9241] [depth= 17] . ( 15 sec) [ -42418.2109] [ 9237] [depth= 6] . ( 15 sec) [ -42310.3467] [ 9245] [depth= 1] . ( 16 sec) [ -42101.3352] [ 9175] [depth= 10] . ( 16 sec) [ -42065.1303] [ 9168] [depth= 1] . ( 16 sec) [ -42047.9547] [ 9173] [depth= 1] . ( 16 sec) [ -41894.3855] [ 9116] [depth= 8] . ( 16 sec) [ -41890.1564] [ 9114] [depth= 1] . ( 16 sec) [ -41818.2398] [ 9091] [depth= 3] . ( 16 sec) [ -41764.5603] [ 9089] [depth= 1] . ( 17 sec) [ -41510.2460] [ 9026] [depth= 3] . ( 17 sec) [ -41465.6752] [ 9018] [depth= 9] . ( 17 sec) [ -41285.6005] [ 8923] [depth= 5] . ( 17 sec) [ -41176.6688] [ 8894] [depth= 17] . ( 17 sec) [ -41052.5731] [ 8887] [depth= 3] . ( 17 sec) [ -40988.6063] [ 8877] [depth= 12] . ( 18 sec) [ -40983.1764] [ 8861] [depth= 9] . ( 18 sec) [ -40772.1747] [ 8821] [depth= 20] . ( 18 sec) [ -40722.5866] [ 8822] [depth= 4] . ( 18 sec) [ -40422.9807] [ 8749] [depth= 22] . ( 18 sec) [ -40283.4731] [ 8721] [depth= 16] . ( 19 sec) [ -40273.0581] [ 8719] [depth= 1] . ( 19 sec) [ -40270.8395] [ 8721] [depth= 1] . ( 19 sec) [ -40183.6467] [ 8715] [depth= 1] . ( 19 sec) [ -40044.6805] [ 8691] [depth= 9] . ( 19 sec) [ -39816.2757] [ 8640] [depth= 19] . ( 20 sec) [ -39816.0805] [ 8638] [depth= 3] . ( 20 sec) [ -39727.1423] [ 8592] [depth= 28] . ( 20 sec) [ -39426.5347] [ 8588] [depth= 1] . ( 20 sec) [ -39193.1329] [ 8469] [depth= 27] . ( 20 sec) [ -39047.7952] [ 8409] [depth= 20] . ( 20 sec) [ -38914.3062] [ 8409] [depth= 18] . ( 21 sec) [ -38594.1376] [ 8337] [depth= 2] . ( 21 sec) [ -38527.0287] [ 8288] [depth= 8] . ( 21 sec) [ -38271.2518] [ 8250] [depth= 4] . ( 21 sec) [ -38252.3962] [ 8255] [depth= 1] . ( 21 sec) [ -38249.9165] [ 8254] [depth= 1] . ( 22 sec) [ -38235.3553] [ 8260] [depth= 2] . ( 22 sec) [ -38006.7642] [ 8250] [depth= 8] . ( 22 sec) [ -37815.1917] [ 8248] [depth= 2] . ( 22 sec) [ -37692.8959] [ 8235] [depth= 17] . ( 23 sec) [ -37624.1672] [ 8218] [depth= 8] . ( 23 sec) [ -37349.5142] [ 8210] [depth= 1] . ( 23 sec) [ -37217.8153] [ 8144] [depth= 25] . ( 23 sec) [ -37111.9788] [ 8107] [depth= 21] . ( 23 sec) [ -36947.7402] [ 8052] [depth= 10] . ( 23 sec) [ -36757.5897] [ 7998] [depth= 5] . ( 24 sec) [ -36680.3142] [ 7977] [depth= 1] . ( 24 sec) [ -36458.6556] [ 7931] [depth= 18] . ( 24 sec) [ -36280.7552] [ 7931] [depth= 9] . ( 24 sec) [ -36254.9287] [ 7932] [depth= 17] . ( 24 sec) [ -36234.4481] [ 7927] [depth= 9] . ( 24 sec) [ -36060.7552] [ 7854] [depth= 7] . ( 25 sec) [ -36049.0414] [ 7809] [depth= 5] . ( 25 sec) [ -36037.0537] [ 7808] [depth= 1] . ( 25 sec) [ -35865.7506] [ 7837] [depth= 6] . ( 25 sec) [ -35653.5371] [ 7795] [depth= 15] . ( 26 sec) [ -35646.6213] [ 7799] [depth= 1] . ( 26 sec) [ -35641.3366] [ 7789] [depth= 1] . ( 26 sec) [ -35640.0748] [ 7789] [depth= 19] . ( 26 sec) [ -35623.5028] [ 7802] [depth= 1] . ( 26 sec) [ -35580.2487] [ 7804] [depth= 1] . ( 26 sec) [ -35401.0239] [ 7803] [depth= 12] . ( 27 sec) [ -35338.2092] [ 7792] [depth= 6] . ( 27 sec) [ -35322.8671] [ 7789] [depth= 13] . ( 27 sec) [ -35320.4970] [ 7790] [depth= 1] . ( 27 sec) [ -35294.9983] [ 7785] [depth= 20] . ( 27 sec) [ -35112.9187] [ 7714] [depth= 17] . ( 27 sec) [ -35108.8951] [ 7714] [depth= 1] . ( 28 sec) [ -34959.4371] [ 7697] [depth= 7] . ( 28 sec) [ -34917.1038] [ 7687] [depth= 7] . ( 28 sec) [ -34785.7513] [ 7677] [depth= 2] . ( 28 sec) [ -34678.7747] [ 7646] [depth= 15] . ( 28 sec) [ -34669.2921] [ 7645] [depth= 1] . ( 28 sec) [ -34442.8107] [ 7547] [depth= 10] . ( 29 sec) [ -34417.5991] [ 7549] [depth= 2] . ( 29 sec) [ -34386.5376] [ 7533] [depth= 2] . ( 29 sec) [ -34378.9940] [ 7528] [depth= 11] . ( 29 sec) [ -34365.7160] [ 7531] [depth= 1] . ( 29 sec) [ -34254.2505] [ 7481] [depth= 1] . ( 29 sec) [ -34109.5091] [ 7467] [depth= 13] . ( 30 sec) [ -34087.7703] [ 7449] [depth= 2] . ( 30 sec) [ -33945.1439] [ 7389] [depth= 5] . ( 30 sec) [ -33916.3312] [ 7387] [depth= 11] . ( 30 sec) [ -33861.7979] [ 7389] [depth= 2] . ( 30 sec) [ -33693.8384] [ 7348] [depth= 13] . ( 30 sec) [ -33626.3565] [ 7339] [depth= 16] . ( 31 sec) [ -33525.1301] [ 7334] [depth= 1] . ( 31 sec) [ -33296.3070] [ 7269] [depth= 14] . ( 31 sec) [ -33251.1775] [ 7259] [depth= 7] . ( 31 sec) [ -33090.4436] [ 7243] [depth= 8] . ( 31 sec) [ -33035.3523] [ 7230] [depth= 1] . ( 32 sec) [ -33016.6277] [ 7204] [depth= 12] . ( 32 sec) [ -32953.2021] [ 7161] [depth= 15] . ( 32 sec) [ -32899.7757] [ 7141] [depth= 17] . ( 32 sec) [ -32885.1601] [ 7125] [depth= 9] . ( 32 sec) [ -32881.0429] [ 7121] [depth= 2] . ( 33 sec) [ -32668.2384] [ 7064] [depth= 1] . ( 33 sec) [ -32664.8342] [ 7061] [depth= 1] . ( 33 sec) [ -32663.2913] [ 7062] [depth= 1] . ( 33 sec) [ -32570.5404] [ 7045] [depth= 12] . ( 33 sec) [ -32470.6624] [ 7039] [depth= 2] . ( 33 sec) [ -32470.1638] [ 7053] [depth= 1] . ( 34 sec) [ -32447.5820] [ 7052] [depth= 3] . ( 34 sec) [ -32431.3593] [ 7050] [depth= 12] . ( 34 sec) [ -32390.9004] [ 7041] [depth= 2] . ( 34 sec) [ -32300.4680] [ 7020] [depth= 5] . ( 34 sec) [ -32290.9678] [ 7016] [depth= 1] . ( 34 sec) [ -32262.8777] [ 6992] [depth= 9] . ( 35 sec) [ -32233.9392] [ 6988] [depth= 8] . ( 35 sec) [ -32229.5866] [ 6993] [depth= 3] . ( 36 sec) [ -32195.4652] [ 6977] [depth= 1] . ( 36 sec) [ -32154.4391] [ 6969] [depth= 6] . ( 36 sec) [ -32037.9119] [ 6943] [depth= 1] . ( 36 sec) [ -32003.4055] [ 6936] [depth= 8] . ( 37 sec) [ -31993.7629] [ 6903] [depth= 2] . ( 38 sec) [ -31969.9375] [ 6891] [depth= 1] . ( 38 sec) [ -31946.8856] [ 6888] [depth= 2] . ( 38 sec) [ -31944.7591] [ 6887] [depth= 1] . ( 38 sec) [ -31903.0792] [ 6878] [depth= 11] . ( 39 sec) [ -31715.4344] [ 6849] [depth= 18] . ( 39 sec) [ -31714.1294] [ 6847] [depth= 1] . ( 39 sec) [ -31650.3300] [ 6782] [depth= 16] . ( 39 sec) [ -31622.4428] [ 6787] [depth= 1] . ( 39 sec) [ -31572.6009] [ 6751] [depth= 1] . ( 40 sec) [ -31449.8885] [ 6731] [depth= 1] . ( 40 sec) [ -31386.4602] [ 6674] [depth= 5] . ( 40 sec) [ -31212.2178] [ 6617] [depth= 3] . ( 40 sec) [ -31179.5521] [ 6612] [depth= 3] . ( 40 sec) [ -31134.5491] [ 6606] [depth= 6] . ( 40 sec) [ -31022.0556] [ 6593] [depth= 2] . ( 41 sec) [ -30732.2649] [ 6506] [depth= 18] . ( 41 sec) [ -30706.1190] [ 6477] [depth= 7] . ( 41 sec) [ -30638.2732] [ 6455] [depth= 2] . ( 41 sec) [ -30620.1443] [ 6445] [depth= 1] . ( 41 sec) [ -30559.8949] [ 6428] [depth= 5] . ( 42 sec) [ -30476.8571] [ 6435] [depth= 10] . ( 42 sec) [ -30379.1934] [ 6424] [depth= 2] . ( 43 sec) [ -30368.7031] [ 6420] [depth= 2] . ( 43 sec) [ -30356.9334] [ 6418] [depth= 1] . ( 43 sec) [ -30307.8493] [ 6393] [depth= 12] . ( 43 sec) [ -30269.6683] [ 6392] [depth= 2] . ( 44 sec) [ -30228.0061] [ 6383] [depth= 1] . ( 44 sec) [ -30200.3486] [ 6381] [depth= 1] . ( 44 sec) [ -30192.6241] [ 6391] [depth= 1] . ( 44 sec) [ -30184.4205] [ 6381] [depth= 1] . ( 44 sec) [ -30167.3915] [ 6357] [depth= 17] . ( 45 sec) [ -30167.0717] [ 6358] [depth= 1] . ( 45 sec) [ -30063.5736] [ 6299] [depth= 11] . ( 45 sec) [ -30061.3438] [ 6337] [depth= 1] . ( 45 sec) [ -29899.9021] [ 6272] [depth= 13] . ( 45 sec) [ -29841.2929] [ 6275] [depth= 13] . ( 46 sec) [ -29789.6338] [ 6264] [depth= 1] . ( 46 sec) [ -29609.3065] [ 6219] [depth= 15] . ( 46 sec) [ -29606.8430] [ 6223] [depth= 1] . ( 46 sec) [ -29604.9019] [ 6223] [depth= 1] . ( 47 sec) [ -29599.0662] [ 6224] [depth= 1] . ( 47 sec) [ -29584.4214] [ 6221] [depth= 1] . ( 47 sec) [ -29584.0066] [ 6221] [depth= 2] . ( 48 sec) [ -29280.1727] [Branch lengths ] . ( 55 sec) [ -28068.4471] [GTR parameters ] . ( 56 sec) [ -28000.8460] [Alpha ][ 0.343957] . ( 56 sec) [ -28000.8224] [ 6220] [depth= 3] . ( 56 sec) [ -27998.2142] [ 6220] [depth= 3] . ( 56 sec) [ -27997.8764] [ 6218] [depth= 1] . ( 58 sec) [ -27990.6339] [ 6208] [depth= 2] . ( 58 sec) [ -27990.6062] [ 6209] [depth= 4] . ( 58 sec) [ -27923.1648] [ 6162] [depth= 9] . ( 58 sec) [ -27917.2990] [ 6165] [depth= 1] . ( 59 sec) [ -27916.6275] [ 6166] [depth= 3] . ( 59 sec) [ -27904.4244] [ 6158] [depth= 5] . ( 59 sec) [ -27894.4462] [ 6144] [depth= 3] . ( 60 sec) [ -27868.4124] [ 6132] [depth= 2] . ( 60 sec) [ -27867.0583] [ 6132] [depth= 1] . ( 60 sec) [ -27749.3567] [ 6086] [depth= 4] . ( 60 sec) [ -27738.1400] [ 6084] [depth= 1] . ( 61 sec) [ -27736.9135] [ 6086] [depth= 1] . ( 62 sec) [ -27730.8295] [ 6081] [depth= 1] . ( 62 sec) [ -27727.9621] [ 6082] [depth= 1] . ( 62 sec) [ -27709.3386] [ 6075] [depth= 1] . ( 63 sec) [ -27708.6493] [ 6070] [depth= 3] . ( 63 sec) [ -27707.4369] [ 6070] [depth= 1] . ( 65 sec) [ -27707.4155] [ 6070] [depth= 1] . ( 65 sec) [ -27706.7516] [ 6068] [depth= 1] . ( 65 sec) [ -27703.2374] [ 6067] [depth= 2] . ( 65 sec) [ -27702.0688] [ 6066] [depth= 3] . ( 65 sec) [ -27698.0717] [ 6065] [depth= 1] . ( 66 sec) [ -27697.0431] [ 6064] [depth= 1] . ( 66 sec) [ -27667.3037] [ 6051] [depth= 9] . ( 66 sec) [ -27663.6305] [ 6050] [depth= 1] . ( 67 sec) [ -27662.5023] [ 6049] [depth= 1] . ( 68 sec) [ -27662.3064] [ 6049] [depth= 1] . ( 68 sec) [ -27659.8582] [ 6048] [depth= 1] . ( 68 sec) [ -27619.5320] [ 6039] [depth= 1] . ( 68 sec) [ -27619.2573] [ 6040] [depth= 1] . ( 68 sec) [ -27615.4366] [ 6039] [depth= 1] . ( 69 sec) [ -27612.4052] [ 6038] [depth= 1] . ( 70 sec) [ -27611.5387] [ 6040] [depth= 1] . ( 70 sec) [ -27600.9448] [ 6033] [depth= 1] . ( 70 sec) [ -27600.8860] [ 6031] [depth= 2] . ( 71 sec) [ -27600.4727] [ 6034] [depth= 2] . ( 72 sec) [ -27531.7914] [ 6004] [depth= 8] . ( 72 sec) [ -27530.2988] [ 5994] [depth= 2] . ( 72 sec) [ -27528.2045] [ 5996] [depth= 2] . ( 73 sec) [ -27475.0892] [ 5990] [depth= 16] . ( 73 sec) [ -27460.2655] [ 5976] [depth= 2] . ( 74 sec) [ -27419.8873] [ 5962] [depth= 18] . ( 74 sec) [ -27342.2422] [ 5914] [depth= 13] . ( 74 sec) [ -27337.0516] [ 5921] [depth= 1] . ( 74 sec) [ -27336.8313] [ 5921] [depth= 5] . ( 75 sec) [ -27336.7644] [ 5922] [depth= 1] . ( 76 sec) [ -27308.3070] [ 5917] [depth= 8] . ( 76 sec) [ -27306.6443] [ 5918] [depth= 2] . ( 76 sec) [ -27301.9897] [ 5919] [depth= 3] . ( 77 sec) [ -27301.5189] [ 5920] [depth= 1] . ( 78 sec) [ -27292.8241] [ 5919] [depth= 1] . ( 78 sec) [ -27292.0853] [ 5917] [depth= 1] . ( 79 sec) [ -27286.0694] [ 5919] [depth= 1] . ( 79 sec) [ -27285.9443] [ 5919] [depth= 2] . ( 79 sec) [ -27277.8522] [ 5911] [depth= 3] . ( 80 sec) [ -27277.4806] [ 5916] [depth= 2] . ( 80 sec) [ -27253.6135] [ 5893] [depth= 2] . ( 80 sec) [ -27252.4067] [ 5895] [depth= 1] . ( 80 sec) [ -27251.9446] [ 5893] [depth= 1] . ( 81 sec) [ -27251.4333] [ 5894] [depth= 1] . ( 81 sec) [ -27246.3231] [ 5893] [depth= 1] . ( 81 sec) [ -27240.5383] [ 5886] [depth= 2] . ( 82 sec) [ -27194.8401] [ 5862] [depth= 2] . ( 82 sec) [ -27194.5588] [ 5861] [depth= 2] . ( 83 sec) [ -27183.6264] [ 5853] [depth= 1] . ( 83 sec) [ -27182.5253] [ 5849] [depth= 2] . ( 84 sec) [ -27180.8936] [ 5852] [depth= 2] . ( 84 sec) [ -27180.3945] [ 5852] [depth= 1] . ( 85 sec) [ -27178.1760] [ 5850] [depth= 1] . ( 85 sec) [ -27176.6082] [ 5852] [depth= 1] . ( 86 sec) [ -27132.5545] [ 5833] [depth= 2] . ( 87 sec) [ -27116.8947] [ 5825] [depth= 1] . ( 88 sec) [ -27115.1425] [ 5827] [depth= 2] . ( 89 sec) [ -27113.9554] [ 5835] [depth= 1] . ( 90 sec) [ -27110.0929] [ 5827] [depth= 1] . ( 90 sec) [ -27107.9280] [ 5823] [depth= 2] . ( 90 sec) [ -27107.6622] [ 5823] [depth= 1] . ( 91 sec) [ -27105.4157] [ 5823] [depth= 1] . ( 91 sec) [ -27101.9943] [ 5820] [depth= 2] . ( 91 sec) [ -27100.1411] [ 5819] [depth= 1] . ( 92 sec) [ -27097.1777] [ 5817] [depth= 1] . ( 92 sec) [ -27070.8875] [ 5802] [depth= 2] . ( 92 sec) [ -27067.1922] [ 5801] [depth= 1] . ( 92 sec) [ -27066.8173] [ 5801] [depth= 1] . ( 93 sec) [ -27066.7689] [ 5800] [depth= 1] . ( 94 sec) [ -27064.9912] [ 5800] [depth= 1] . ( 96 sec) [ -27000.0693] [Branch lengths ] . ( 100 sec) [ -26996.6773] [GTR parameters ] . ( 101 sec) [ -26995.5940] [Alpha ][ 0.327089] . ( 102 sec) [ -26995.1003] [ 5799] [depth= 1] . ( 102 sec) [ -26994.5549] [ 5799] [depth= 1] . ( 103 sec) [ -26994.4723] [ 5799] [depth= 1] . ( 104 sec) [ -26994.3917] [ 5798] [depth= 1] . ( 107 sec) [ -26994.3352] [ 5798] [depth= 1] . ( 110 sec) [ -26994.2893] [ 5802] [depth= 1] . ( 110 sec) [ -26993.8704] [ 5801] [depth= 2] . ( 112 sec) [ -26993.3336] [ 5801] [depth= 1] . ( 112 sec) [ -26993.0988] [ 5801] [depth= 1] . ( 115 sec) [ -26987.7534] [ 5801] [depth= 2] . ( 118 sec) [ -26974.5987] [ 5791] [depth= 4] . ( 119 sec) [ -26974.4176] [ 5791] [depth= 1] . ( 119 sec) [ -26974.4005] [ 5791] [depth= 1] . ( 122 sec) [ -26973.0935] [ 5788] [depth= 1] . ( 123 sec) [ -26971.0545] [ 5786] [depth= 3] . ( 127 sec) [ -26969.6094] [ 5787] [depth= 1] . ( 128 sec) [ -26969.4802] [ 5788] [depth= 1] . ( 134 sec) [ -26966.6829] [ 5790] [depth= 1] . ( 134 sec) [ -26966.5373] [ 5796] [depth= 1] . ( 137 sec) [ -26964.3153] [ 5797] [depth= 1] . ( 140 sec) [ -26954.2410] [Branch lengths ] . ( 145 sec) [ -26954.1632] [GTR parameters ] . ( 145 sec) [ -26953.7765] [Alpha ][ 0.317383] . ( 161 sec) [ -26953.7094] [ 5798] [depth= 1] . ( 182 sec) [ -26950.8613] [ 5803] [depth= 3] . ( 189 sec) [ -26947.5642] [Branch lengths ] . ( 194 sec) [ -26947.4772] [GTR parameters ] . ( 194 sec) [ -26947.2252] [Alpha ][ 0.309733] . ( 238 sec) [ -26946.8258] [Branch lengths ] . ( 375 sec) [ -26946.7887] [Branch lengths ] . ( 376 sec) [ -26946.7887] [Topology ] . ( 379 sec) [ -26946.1574] [Topology ] . ( 382 sec) [ -26945.0515] [Topology ] . ( 385 sec) [ -26944.8916] [Topology ] . ( 388 sec) [ -26944.8450] [Topology ] . ( 392 sec) [ -26944.8290] [Topology ] . ( 395 sec) [ -26944.8229] [Topology ] . ( 398 sec) [ -26944.8205] [Topology ] . ( 402 sec) [ -26944.7752] [GTR parameters ] . ( 402 sec) [ -26944.5446] [Alpha ][ 0.302518] . ( 402 sec) [ -26944.5446] [Topology ] . ( 405 sec) [ -26944.4610] [Topology ] . ( 408 sec) [ -26944.4359] [Topology ] . ( 412 sec) [ -26944.4273] [Topology ] . ( 415 sec) [ -26944.4243] [Topology ] . ( 418 sec) [ -26944.4232] [Topology ] . ( 421 sec) [ -26944.4229] [Topology ] . ( 425 sec) [ -26944.4193] [GTR parameters ] . ( 425 sec) [ -26944.3508] [Alpha ][ 0.298460] . ( 425 sec) [ -26944.3508] [Topology ] . ( 428 sec) [ -26944.3219] [Topology ] . ( 432 sec) [ -26944.3133] [Topology ] . ( 435 sec) [ -26944.3104] [Topology ] . ( 438 sec) [ -26944.3094] [Topology ] . ( 441 sec) [ -26944.3090] [Topology ] . ( 445 sec) [ -26944.3075] [GTR parameters ] . ( 445 sec) [ -26944.2878] [Alpha ][ 0.296290] . ( 445 sec) [ -26944.2878] [Topology ] . ( 448 sec) [ -26944.2783] [Topology ] . ( 452 sec) [ -26944.2755] [Topology ] . ( 455 sec) [ -26944.2745] [Topology ] . ( 458 sec) [ -26944.2743] [GTR parameters ] . ( 458 sec) [ -26944.2696] [Alpha ][ 0.295229] . ( 459 sec) [ -26944.2696] [Topology ] . ( 462 sec) [ -26944.2660] [Topology ] . ( 465 sec) [ -26944.2649] [Topology ] . ( 468 sec) [ -26944.2645] [Topology ] . ( 470 sec) [ -26944.2644] [GTR parameters ] . ( 470 sec) [ -26944.2626] [Alpha ][ 0.294573] . ( 470 sec) [ -26944.2626] [Topology ] . ( 473 sec) [ -26944.2612] [Topology ] . ( 477 sec) [ -26944.2608] [Topology ] . ( 480 sec) [ -26944.2606] [GTR parameters ] . ( 480 sec) [ -26944.2600] [Alpha ][ 0.294204] . ( 480 sec) [ -26944.2600] [Topology ] . ( 483 sec) [ -26944.2593] [Topology ] . ( 484 sec) [ -26944.2593] [GTR parameters ] . ( 484 sec) [ -26944.2593] [Alpha ][ 0.294204] . Checking for NNIs, optimizing five branches... . ( 508 sec) [ -26944.1692] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26944.169193. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -55932.4431] [GTR parameters ] . ( 2 sec) [ -54379.3570] [Alpha ][ 0.500960] . ( 3 sec) [ -54223.3162] [11301] [depth= 15] . ( 3 sec) [ -53827.8909] [11252] [depth= 19] . ( 3 sec) [ -53609.2123] [11256] [depth= 1] . ( 3 sec) [ -53293.6912] [11239] [depth= 12] . ( 3 sec) [ -52986.5385] [11162] [depth= 3] . ( 3 sec) [ -52938.0918] [11160] [depth= 7] . ( 3 sec) [ -52773.0756] [11134] [depth= 2] . ( 4 sec) [ -52682.2980] [11122] [depth= 8] . ( 4 sec) [ -52589.4354] [11105] [depth= 1] . ( 4 sec) [ -52449.3898] [11069] [depth= 10] . ( 4 sec) [ -52249.8239] [11049] [depth= 2] . ( 4 sec) [ -52242.1699] [11048] [depth= 3] . ( 4 sec) [ -52183.5927] [11044] [depth= 1] . ( 5 sec) [ -52100.5299] [11034] [depth= 15] . ( 5 sec) [ -52045.2391] [11029] [depth= 4] . ( 5 sec) [ -51980.8140] [11035] [depth= 1] . ( 5 sec) [ -51857.0484] [11020] [depth= 19] . ( 5 sec) [ -51850.5233] [11009] [depth= 21] . ( 6 sec) [ -51831.8600] [11006] [depth= 2] . ( 6 sec) [ -51784.2061] [11004] [depth= 3] . ( 6 sec) [ -51650.6481] [10984] [depth= 14] . ( 6 sec) [ -51536.8718] [10948] [depth= 2] . ( 6 sec) [ -51490.8163] [10943] [depth= 21] . ( 6 sec) [ -51397.1230] [10903] [depth= 2] . ( 6 sec) [ -50831.6821] [10802] [depth= 21] . ( 7 sec) [ -50583.7330] [10762] [depth= 19] . ( 7 sec) [ -49932.0863] [10644] [depth= 8] . ( 7 sec) [ -49653.5895] [10546] [depth= 23] . ( 7 sec) [ -49543.4676] [10525] [depth= 1] . ( 7 sec) [ -49311.1245] [10471] [depth= 7] . ( 8 sec) [ -49233.5185] [10467] [depth= 26] . ( 8 sec) [ -49192.5419] [10434] [depth= 2] . ( 8 sec) [ -48979.6880] [10408] [depth= 16] . ( 8 sec) [ -48645.7230] [10333] [depth= 14] . ( 8 sec) [ -48240.0694] [10237] [depth= 12] . ( 8 sec) [ -48139.7901] [10211] [depth= 2] . ( 8 sec) [ -48101.2602] [10210] [depth= 2] . ( 9 sec) [ -48062.7010] [10194] [depth= 3] . ( 9 sec) [ -47914.8361] [10190] [depth= 1] . ( 9 sec) [ -47803.4025] [10154] [depth= 1] . ( 9 sec) [ -47717.3305] [10162] [depth= 1] . ( 9 sec) [ -47563.5685] [10119] [depth= 2] . ( 9 sec) [ -47493.3803] [10107] [depth= 20] . ( 9 sec) [ -47320.2038] [10072] [depth= 13] . ( 10 sec) [ -47114.4649] [10032] [depth= 10] . ( 10 sec) [ -46801.0188] [ 9941] [depth= 24] . ( 10 sec) [ -46794.7089] [ 9938] [depth= 5] . ( 10 sec) [ -46788.9925] [ 9937] [depth= 1] . ( 10 sec) [ -46611.1606] [ 9910] [depth= 1] . ( 10 sec) [ -46543.9059] [ 9907] [depth= 1] . ( 11 sec) [ -46363.4493] [ 9864] [depth= 1] . ( 11 sec) [ -46362.5854] [ 9863] [depth= 3] . ( 11 sec) [ -46353.5829] [ 9861] [depth= 2] . ( 11 sec) [ -46064.9002] [ 9773] [depth= 21] . ( 11 sec) [ -46034.1798] [ 9771] [depth= 1] . ( 11 sec) [ -45665.5483] [ 9712] [depth= 23] . ( 12 sec) [ -45661.4281] [ 9713] [depth= 7] . ( 12 sec) [ -45659.4548] [ 9712] [depth= 1] . ( 12 sec) [ -45559.5501] [ 9666] [depth= 18] . ( 12 sec) [ -45538.4887] [ 9663] [depth= 3] . ( 12 sec) [ -45092.7445] [ 9592] [depth= 2] . ( 13 sec) [ -44932.0274] [ 9555] [depth= 22] . ( 13 sec) [ -44712.3924] [ 9533] [depth= 17] . ( 13 sec) [ -44695.1752] [ 9534] [depth= 1] . ( 13 sec) [ -44589.1998] [ 9514] [depth= 4] . ( 13 sec) [ -44397.0548] [ 9481] [depth= 11] . ( 13 sec) [ -44244.9382] [ 9483] [depth= 1] . ( 14 sec) [ -43828.6358] [ 9394] [depth= 11] . ( 14 sec) [ -43799.1567] [ 9395] [depth= 1] . ( 14 sec) [ -43229.2685] [ 9310] [depth= 7] . ( 14 sec) [ -43226.4351] [ 9295] [depth= 19] . ( 14 sec) [ -42957.9251] [ 9217] [depth= 3] . ( 14 sec) [ -42601.2323] [ 9192] [depth= 7] . ( 15 sec) [ -42531.8603] [ 9149] [depth= 1] . ( 15 sec) [ -42337.2318] [ 9116] [depth= 1] . ( 15 sec) [ -42289.7318] [ 9115] [depth= 6] . ( 15 sec) [ -42224.8912] [ 9099] [depth= 1] . ( 15 sec) [ -42054.2322] [ 9059] [depth= 6] . ( 15 sec) [ -41748.9740] [ 8978] [depth= 5] . ( 16 sec) [ -41341.2260] [ 8951] [depth= 11] . ( 16 sec) [ -41131.0631] [ 8917] [depth= 14] . ( 16 sec) [ -41048.7746] [ 8884] [depth= 1] . ( 16 sec) [ -40977.2027] [ 8879] [depth= 1] . ( 16 sec) [ -40680.9894] [ 8866] [depth= 7] . ( 16 sec) [ -40630.5126] [ 8849] [depth= 10] . ( 17 sec) [ -40399.8490] [ 8869] [depth= 1] . ( 17 sec) [ -40265.8904] [ 8819] [depth= 2] . ( 17 sec) [ -40063.8892] [ 8764] [depth= 7] . ( 17 sec) [ -39914.4477] [ 8686] [depth= 17] . ( 17 sec) [ -39812.4721] [ 8670] [depth= 21] . ( 17 sec) [ -39749.3309] [ 8651] [depth= 1] . ( 18 sec) [ -39688.6180] [ 8650] [depth= 4] . ( 18 sec) [ -39500.7495] [ 8582] [depth= 21] . ( 18 sec) [ -39314.7227] [ 8541] [depth= 6] . ( 18 sec) [ -39261.3800] [ 8541] [depth= 1] . ( 18 sec) [ -39253.8974] [ 8546] [depth= 1] . ( 18 sec) [ -39196.1656] [ 8535] [depth= 7] . ( 18 sec) [ -39162.7880] [ 8518] [depth= 1] . ( 19 sec) [ -38823.2561] [ 8522] [depth= 1] . ( 19 sec) [ -38821.2499] [ 8524] [depth= 1] . ( 19 sec) [ -38801.7987] [ 8500] [depth= 1] . ( 19 sec) [ -38729.3089] [ 8489] [depth= 9] . ( 19 sec) [ -38391.1256] [ 8383] [depth= 8] . ( 19 sec) [ -38329.7129] [ 8381] [depth= 2] . ( 20 sec) [ -38126.4400] [ 8336] [depth= 17] . ( 20 sec) [ -38109.1441] [ 8324] [depth= 1] . ( 20 sec) [ -37998.3867] [ 8339] [depth= 1] . ( 20 sec) [ -37932.0624] [ 8287] [depth= 8] . ( 20 sec) [ -37921.1511] [ 8276] [depth= 1] . ( 20 sec) [ -37920.8300] [ 8268] [depth= 15] . ( 21 sec) [ -37732.2781] [ 8235] [depth= 7] . ( 21 sec) [ -37663.5254] [ 8223] [depth= 2] . ( 21 sec) [ -37593.9400] [ 8212] [depth= 1] . ( 21 sec) [ -37480.8113] [ 8153] [depth= 3] . ( 21 sec) [ -37430.9254] [ 8149] [depth= 1] . ( 22 sec) [ -37172.7085] [ 8105] [depth= 15] . ( 22 sec) [ -37048.9207] [ 8059] [depth= 9] . ( 22 sec) [ -37021.2417] [ 8063] [depth= 1] . ( 22 sec) [ -36556.0384] [ 7976] [depth= 5] . ( 22 sec) [ -36513.7817] [ 7970] [depth= 10] . ( 22 sec) [ -36378.9930] [ 7984] [depth= 1] . ( 23 sec) [ -36097.6527] [ 7880] [depth= 12] . ( 23 sec) [ -36096.0960] [ 7885] [depth= 2] . ( 23 sec) [ -36047.3289] [ 7849] [depth= 18] . ( 23 sec) [ -35609.7373] [ 7781] [depth= 15] . ( 23 sec) [ -35240.9388] [ 7677] [depth= 13] . ( 23 sec) [ -35148.8684] [ 7671] [depth= 1] . ( 24 sec) [ -35078.2095] [ 7646] [depth= 12] . ( 24 sec) [ -34802.1986] [ 7584] [depth= 16] . ( 24 sec) [ -34789.0632] [ 7572] [depth= 1] . ( 24 sec) [ -34780.4303] [ 7571] [depth= 2] . ( 24 sec) [ -34708.0374] [ 7577] [depth= 4] . ( 25 sec) [ -34690.4006] [ 7571] [depth= 3] . ( 25 sec) [ -34648.6296] [ 7553] [depth= 8] . ( 25 sec) [ -34627.3949] [ 7548] [depth= 1] . ( 25 sec) [ -34485.8024] [ 7523] [depth= 5] . ( 25 sec) [ -34416.0893] [ 7506] [depth= 4] . ( 25 sec) [ -34394.1033] [ 7503] [depth= 3] . ( 25 sec) [ -34338.9701] [ 7500] [depth= 4] . ( 26 sec) [ -34236.3024] [ 7444] [depth= 17] . ( 26 sec) [ -34185.4102] [ 7434] [depth= 1] . ( 26 sec) [ -33944.9234] [ 7399] [depth= 9] . ( 26 sec) [ -33873.9547] [ 7387] [depth= 1] . ( 26 sec) [ -33644.5419] [ 7351] [depth= 8] . ( 26 sec) [ -33456.2947] [ 7284] [depth= 15] . ( 26 sec) [ -33393.8492] [ 7282] [depth= 1] . ( 27 sec) [ -33269.9044] [ 7246] [depth= 1] . ( 27 sec) [ -33267.2122] [ 7245] [depth= 4] . ( 27 sec) [ -33264.2795] [ 7245] [depth= 2] . ( 27 sec) [ -33111.6354] [ 7166] [depth= 13] . ( 27 sec) [ -33023.9648] [ 7161] [depth= 1] . ( 27 sec) [ -32997.4283] [ 7154] [depth= 15] . ( 28 sec) [ -32774.6409] [ 7096] [depth= 18] . ( 28 sec) [ -32669.9726] [ 7101] [depth= 16] . ( 28 sec) [ -32669.2476] [ 7102] [depth= 1] . ( 28 sec) [ -32667.4996] [ 7101] [depth= 1] . ( 28 sec) [ -32660.3574] [ 7098] [depth= 2] . ( 29 sec) [ -32522.4690] [ 7066] [depth= 15] . ( 29 sec) [ -32469.3007] [ 7050] [depth= 3] . ( 29 sec) [ -32467.5175] [ 7046] [depth= 6] . ( 29 sec) [ -32406.5985] [ 7021] [depth= 3] . ( 29 sec) [ -32319.6603] [ 7010] [depth= 3] . ( 30 sec) [ -32249.5313] [ 6987] [depth= 3] . ( 31 sec) [ -32203.0570] [ 6946] [depth= 7] . ( 31 sec) [ -31870.1557] [ 6927] [depth= 6] . ( 31 sec) [ -31701.6751] [ 6903] [depth= 18] . ( 32 sec) [ -31691.1170] [ 6903] [depth= 1] . ( 32 sec) [ -31666.3665] [ 6885] [depth= 1] . ( 32 sec) [ -31552.7972] [ 6837] [depth= 12] . ( 33 sec) [ -31426.4233] [ 6782] [depth= 16] . ( 33 sec) [ -31353.0436] [ 6775] [depth= 6] . ( 34 sec) [ -31350.6392] [ 6777] [depth= 1] . ( 34 sec) [ -31343.8327] [ 6777] [depth= 2] . ( 34 sec) [ -31312.7750] [ 6775] [depth= 4] . ( 34 sec) [ -31288.6288] [ 6767] [depth= 3] . ( 34 sec) [ -31274.2883] [ 6772] [depth= 1] . ( 34 sec) [ -31273.6903] [ 6773] [depth= 2] . ( 34 sec) [ -31270.5891] [ 6770] [depth= 1] . ( 35 sec) [ -31270.3999] [ 6772] [depth= 1] . ( 35 sec) [ -31268.9063] [ 6771] [depth= 1] . ( 35 sec) [ -30968.1838] [ 6714] [depth= 11] . ( 35 sec) [ -30906.2272] [ 6679] [depth= 11] . ( 35 sec) [ -30903.2203] [ 6685] [depth= 14] . ( 36 sec) [ -30818.3312] [ 6622] [depth= 10] . ( 36 sec) [ -30791.6325] [ 6616] [depth= 1] . ( 36 sec) [ -30702.5593] [ 6559] [depth= 10] . ( 36 sec) [ -30612.8788] [ 6545] [depth= 11] . ( 36 sec) [ -30602.2077] [ 6537] [depth= 1] . ( 36 sec) [ -30577.3783] [ 6536] [depth= 1] . ( 37 sec) [ -30524.0219] [ 6495] [depth= 1] . ( 37 sec) [ -30494.6956] [ 6493] [depth= 2] . ( 37 sec) [ -30387.3586] [ 6435] [depth= 7] . ( 37 sec) [ -30314.6353] [ 6427] [depth= 3] . ( 37 sec) [ -30085.0610] [ 6334] [depth= 2] . ( 38 sec) [ -30079.1432] [ 6331] [depth= 1] . ( 38 sec) [ -30056.5293] [ 6321] [depth= 3] . ( 38 sec) [ -30055.1039] [ 6317] [depth= 1] . ( 38 sec) [ -29973.3377] [ 6293] [depth= 2] . ( 38 sec) [ -29891.0132] [ 6263] [depth= 4] . ( 38 sec) [ -29809.6292] [ 6226] [depth= 4] . ( 39 sec) [ -29808.8930] [ 6225] [depth= 1] . ( 39 sec) [ -29785.7755] [ 6222] [depth= 2] . ( 39 sec) [ -29738.2738] [ 6200] [depth= 2] . ( 39 sec) [ -29730.2879] [ 6197] [depth= 3] . ( 40 sec) [ -29693.3040] [ 6192] [depth= 3] . ( 40 sec) [ -29639.6431] [ 6170] [depth= 1] . ( 40 sec) [ -29631.1379] [ 6178] [depth= 1] . ( 40 sec) [ -29630.9004] [ 6181] [depth= 1] . ( 40 sec) [ -29623.7982] [ 6179] [depth= 1] . ( 41 sec) [ -29602.3102] [ 6173] [depth= 3] . ( 41 sec) [ -29581.9384] [ 6179] [depth= 2] . ( 41 sec) [ -29519.0389] [ 6155] [depth= 4] . ( 41 sec) [ -29517.9938] [ 6159] [depth= 1] . ( 42 sec) [ -29415.7022] [ 6133] [depth= 3] . ( 42 sec) [ -29401.1595] [ 6129] [depth= 2] . ( 42 sec) [ -29368.3435] [ 6128] [depth= 4] . ( 43 sec) [ -29368.2248] [ 6128] [depth= 3] . ( 43 sec) [ -29363.8000] [ 6127] [depth= 1] . ( 43 sec) [ -29325.5346] [ 6118] [depth= 1] . ( 43 sec) [ -29318.1900] [ 6109] [depth= 2] . ( 44 sec) [ -29317.0340] [ 6108] [depth= 1] . ( 44 sec) [ -29316.8734] [ 6113] [depth= 1] . ( 44 sec) [ -29256.9638] [ 6089] [depth= 4] . ( 44 sec) [ -29253.8360] [ 6088] [depth= 1] . ( 44 sec) [ -29233.7460] [ 6089] [depth= 1] . ( 44 sec) [ -29201.1042] [ 6082] [depth= 2] . ( 45 sec) [ -29113.6494] [ 6056] [depth= 8] . ( 45 sec) [ -29019.3699] [ 6006] [depth= 7] . ( 45 sec) [ -29018.5458] [ 6008] [depth= 1] . ( 46 sec) [ -29014.8652] [ 6007] [depth= 1] . ( 46 sec) [ -29013.7988] [ 6007] [depth= 1] . ( 47 sec) [ -28764.3246] [Branch lengths ] . ( 54 sec) [ -27563.2398] [GTR parameters ] . ( 54 sec) [ -27511.8390] [Alpha ][ 0.360133] . ( 54 sec) [ -27511.7470] [ 6007] [depth= 2] . ( 55 sec) [ -27510.9676] [ 6006] [depth= 4] . ( 55 sec) [ -27508.8187] [ 6005] [depth= 1] . ( 55 sec) [ -27461.5338] [ 5970] [depth= 7] . ( 55 sec) [ -27451.4977] [ 5966] [depth= 2] . ( 55 sec) [ -27450.9104] [ 5967] [depth= 1] . ( 57 sec) [ -27434.7346] [ 5959] [depth= 8] . ( 57 sec) [ -27422.6984] [ 5953] [depth= 1] . ( 58 sec) [ -27414.2276] [ 5951] [depth= 1] . ( 59 sec) [ -27413.3320] [ 5951] [depth= 2] . ( 60 sec) [ -27411.1676] [ 5951] [depth= 5] . ( 60 sec) [ -27401.1779] [ 5947] [depth= 1] . ( 60 sec) [ -27366.6758] [ 5932] [depth= 1] . ( 61 sec) [ -27365.9855] [ 5932] [depth= 1] . ( 61 sec) [ -27286.7759] [ 5894] [depth= 7] . ( 61 sec) [ -27285.0863] [ 5891] [depth= 1] . ( 61 sec) [ -27273.1809] [ 5889] [depth= 5] . ( 62 sec) [ -27272.3869] [ 5889] [depth= 1] . ( 62 sec) [ -27272.3181] [ 5890] [depth= 1] . ( 62 sec) [ -27270.7197] [ 5887] [depth= 1] . ( 62 sec) [ -27270.2558] [ 5887] [depth= 1] . ( 62 sec) [ -27267.9918] [ 5892] [depth= 1] . ( 64 sec) [ -27267.0274] [ 5886] [depth= 1] . ( 64 sec) [ -27243.7784] [ 5876] [depth= 1] . ( 65 sec) [ -27195.4439] [ 5860] [depth= 1] . ( 66 sec) [ -27192.2426] [ 5858] [depth= 1] . ( 66 sec) [ -27188.5269] [ 5857] [depth= 1] . ( 66 sec) [ -27187.6171] [ 5857] [depth= 1] . ( 68 sec) [ -27185.3904] [ 5848] [depth= 1] . ( 68 sec) [ -27185.0304] [ 5851] [depth= 1] . ( 69 sec) [ -27184.8175] [ 5856] [depth= 1] . ( 69 sec) [ -27178.4108] [ 5849] [depth= 2] . ( 70 sec) [ -27149.6239] [ 5840] [depth= 4] . ( 71 sec) [ -27143.5636] [ 5837] [depth= 1] . ( 72 sec) [ -27142.0993] [ 5840] [depth= 1] . ( 73 sec) [ -27142.0302] [ 5842] [depth= 1] . ( 73 sec) [ -27141.0790] [ 5841] [depth= 1] . ( 74 sec) [ -27128.6056] [ 5834] [depth= 2] . ( 74 sec) [ -27127.0982] [ 5831] [depth= 1] . ( 76 sec) [ -27120.5917] [ 5830] [depth= 2] . ( 76 sec) [ -27117.7910] [ 5832] [depth= 1] . ( 76 sec) [ -27116.6194] [ 5837] [depth= 2] . ( 77 sec) [ -27115.9416] [ 5836] [depth= 1] . ( 77 sec) [ -27114.4203] [ 5837] [depth= 1] . ( 78 sec) [ -27109.0073] [ 5834] [depth= 1] . ( 78 sec) [ -27094.5428] [ 5826] [depth= 3] . ( 78 sec) [ -27091.4831] [ 5820] [depth= 3] . ( 79 sec) [ -27091.3069] [ 5820] [depth= 1] . ( 79 sec) [ -27090.8158] [ 5820] [depth= 1] . ( 79 sec) [ -27085.0692] [ 5812] [depth= 2] . ( 80 sec) [ -27082.1776] [ 5816] [depth= 1] . ( 80 sec) [ -27073.6778] [ 5810] [depth= 1] . ( 81 sec) [ -27072.7893] [ 5808] [depth= 1] . ( 81 sec) [ -27066.8469] [ 5804] [depth= 2] . ( 82 sec) [ -27066.8191] [ 5804] [depth= 1] . ( 82 sec) [ -27063.3320] [ 5803] [depth= 2] . ( 82 sec) [ -27061.1224] [ 5803] [depth= 1] . ( 83 sec) [ -27060.1572] [ 5800] [depth= 2] . ( 84 sec) [ -27060.0028] [ 5800] [depth= 1] . ( 84 sec) [ -27055.7945] [ 5801] [depth= 1] . ( 85 sec) [ -27053.1056] [ 5803] [depth= 1] . ( 85 sec) [ -27052.7756] [ 5808] [depth= 1] . ( 85 sec) [ -27050.0115] [ 5808] [depth= 1] . ( 86 sec) [ -27049.8010] [ 5805] [depth= 2] . ( 86 sec) [ -27048.1239] [ 5809] [depth= 1] . ( 86 sec) [ -27048.0220] [ 5805] [depth= 1] . ( 87 sec) [ -27046.4190] [ 5806] [depth= 1] . ( 88 sec) [ -27045.8921] [ 5805] [depth= 1] . ( 88 sec) [ -27045.6778] [ 5809] [depth= 1] . ( 90 sec) [ -27045.5639] [ 5811] [depth= 1] . ( 90 sec) [ -27042.4434] [ 5810] [depth= 5] . ( 90 sec) [ -27041.0418] [ 5803] [depth= 1] . ( 91 sec) [ -27040.8203] [ 5798] [depth= 1] . ( 91 sec) [ -27040.8027] [ 5797] [depth= 1] . ( 91 sec) [ -27035.8802] [ 5796] [depth= 2] . ( 92 sec) [ -27033.8322] [ 5795] [depth= 1] . ( 92 sec) [ -27033.1181] [ 5798] [depth= 1] . ( 93 sec) [ -27032.8450] [ 5796] [depth= 1] . ( 94 sec) [ -27032.3352] [ 5795] [depth= 1] . ( 95 sec) [ -26981.9973] [Branch lengths ] . ( 99 sec) [ -26979.4105] [GTR parameters ] . ( 100 sec) [ -26976.4203] [Alpha ][ 0.331430] . ( 107 sec) [ -26975.4150] [ 5794] [depth= 1] . ( 111 sec) [ -26970.4902] [ 5790] [depth= 1] . ( 116 sec) [ -26969.2178] [ 5784] [depth= 1] . ( 118 sec) [ -26968.9209] [ 5787] [depth= 1] . ( 118 sec) [ -26968.8673] [ 5788] [depth= 1] . ( 121 sec) [ -26965.7569] [ 5788] [depth= 1] . ( 123 sec) [ -26965.3868] [ 5788] [depth= 1] . ( 124 sec) [ -26965.2467] [ 5791] [depth= 1] . ( 137 sec) [ -26964.6800] [ 5792] [depth= 1] . ( 141 sec) [ -26956.1078] [Branch lengths ] . ( 146 sec) [ -26956.0086] [GTR parameters ] . ( 146 sec) [ -26955.3710] [Alpha ][ 0.318825] . ( 159 sec) [ -26952.4037] [ 5797] [depth= 3] . ( 162 sec) [ -26952.1275] [ 5796] [depth= 1] . ( 178 sec) [ -26952.0267] [ 5796] [depth= 1] . ( 188 sec) [ -26948.0836] [Branch lengths ] . ( 192 sec) [ -26948.0242] [GTR parameters ] . ( 192 sec) [ -26947.7405] [Alpha ][ 0.310698] . ( 234 sec) [ -26946.4114] [Branch lengths ] . ( 370 sec) [ -26946.3681] [Branch lengths ] . ( 370 sec) [ -26946.3681] [Topology ] . ( 374 sec) [ -26945.6344] [Topology ] . ( 377 sec) [ -26944.4466] [Topology ] . ( 380 sec) [ -26944.2831] [Topology ] . ( 383 sec) [ -26944.2336] [Topology ] . ( 387 sec) [ -26944.2158] [Topology ] . ( 390 sec) [ -26944.2090] [Topology ] . ( 393 sec) [ -26944.2063] [Topology ] . ( 396 sec) [ -26944.1827] [GTR parameters ] . ( 397 sec) [ -26943.9083] [Alpha ][ 0.302804] . ( 397 sec) [ -26943.9083] [Topology ] . ( 400 sec) [ -26943.8116] [Topology ] . ( 403 sec) [ -26943.7834] [Topology ] . ( 406 sec) [ -26943.7740] [Topology ] . ( 409 sec) [ -26943.7708] [Topology ] . ( 413 sec) [ -26943.7697] [Topology ] . ( 416 sec) [ -26943.7693] [Topology ] . ( 419 sec) [ -26943.7650] [GTR parameters ] . ( 419 sec) [ -26943.6893] [Alpha ][ 0.298551] . ( 419 sec) [ -26943.6893] [Topology ] . ( 422 sec) [ -26943.6594] [Topology ] . ( 425 sec) [ -26943.6508] [Topology ] . ( 429 sec) [ -26943.6480] [Topology ] . ( 432 sec) [ -26943.6470] [Topology ] . ( 434 sec) [ -26943.6459] [GTR parameters ] . ( 435 sec) [ -26943.6288] [Alpha ][ 0.296533] . ( 435 sec) [ -26943.6288] [Topology ] . ( 438 sec) [ -26943.6194] [Topology ] . ( 441 sec) [ -26943.6166] [Topology ] . ( 444 sec) [ -26943.6157] [Topology ] . ( 446 sec) [ -26943.6156] [GTR parameters ] . ( 446 sec) [ -26943.6111] [Alpha ][ 0.295509] . ( 446 sec) [ -26943.6111] [Topology ] . ( 450 sec) [ -26943.6080] [Topology ] . ( 453 sec) [ -26943.6071] [Topology ] . ( 454 sec) [ -26943.6071] [GTR parameters ] . ( 454 sec) [ -26943.6061] [Alpha ][ 0.295015] . ( 454 sec) [ -26943.6061] [Topology ] . ( 457 sec) [ -26943.6048] [Topology ] . ( 461 sec) [ -26943.6044] [Topology ] . ( 462 sec) [ -26943.6040] [GTR parameters ] . ( 463 sec) [ -26943.6035] [Alpha ][ 0.294658] . ( 463 sec) [ -26943.6035] [Topology ] . ( 466 sec) [ -26943.6029] [Topology ] . ( 468 sec) [ -26943.6027] [GTR parameters ] . ( 468 sec) [ -26943.6027] [Alpha ][ 0.294658] . Checking for NNIs, optimizing five branches... . ( 492 sec) [ -26943.5325] [Topology ] . Checking for NNIs, optimizing five branches... . ( 516 sec) [ -26943.5106] [Topology ] . Checking for NNIs, optimizing five branches... . ( 540 sec) [ -26943.4333] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26943.433340. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -56121.1109] [GTR parameters ] . ( 2 sec) [ -54567.6333] [Alpha ][ 0.500960] . ( 2 sec) [ -54465.3810] [11335] [depth= 15] . ( 2 sec) [ -54275.2638] [11323] [depth= 7] . ( 2 sec) [ -53952.5528] [11281] [depth= 8] . ( 2 sec) [ -53946.7964] [11277] [depth= 1] . ( 3 sec) [ -53730.0162] [11220] [depth= 7] . ( 3 sec) [ -53596.6573] [11213] [depth= 1] . ( 3 sec) [ -53471.6176] [11173] [depth= 10] . ( 3 sec) [ -53427.7237] [11155] [depth= 1] . ( 3 sec) [ -52728.7266] [11146] [depth= 9] . ( 3 sec) [ -52433.0026] [11130] [depth= 1] . ( 3 sec) [ -52047.9416] [11119] [depth= 5] . ( 4 sec) [ -51916.4365] [11052] [depth= 2] . ( 4 sec) [ -51825.7224] [11032] [depth= 10] . ( 4 sec) [ -51421.1403] [10998] [depth= 2] . ( 4 sec) [ -51213.6954] [10952] [depth= 14] . ( 4 sec) [ -51033.8026] [10894] [depth= 1] . ( 4 sec) [ -50822.5499] [10862] [depth= 4] . ( 4 sec) [ -50803.2789] [10852] [depth= 3] . ( 5 sec) [ -50566.8425] [10840] [depth= 8] . ( 5 sec) [ -50459.9219] [10781] [depth= 4] . ( 5 sec) [ -50183.2969] [10709] [depth= 17] . ( 5 sec) [ -50172.0144] [10707] [depth= 1] . ( 5 sec) [ -50131.9128] [10701] [depth= 1] . ( 5 sec) [ -50086.6843] [10698] [depth= 2] . ( 5 sec) [ -49994.9443] [10697] [depth= 5] . ( 6 sec) [ -49840.7519] [10668] [depth= 6] . ( 6 sec) [ -49767.2732] [10664] [depth= 10] . ( 6 sec) [ -49405.5278] [10629] [depth= 5] . ( 6 sec) [ -48977.7685] [10618] [depth= 3] . ( 6 sec) [ -48737.4018] [10579] [depth= 2] . ( 6 sec) [ -48357.4267] [10529] [depth= 24] . ( 6 sec) [ -48140.7764] [10508] [depth= 8] . ( 7 sec) [ -48024.6764] [10471] [depth= 10] . ( 7 sec) [ -47974.5030] [10467] [depth= 1] . ( 7 sec) [ -47598.1033] [10452] [depth= 30] . ( 7 sec) [ -47331.4434] [10388] [depth= 3] . ( 7 sec) [ -47257.8075] [10378] [depth= 35] . ( 7 sec) [ -47218.9158] [10381] [depth= 2] . ( 7 sec) [ -47078.2978] [10346] [depth= 5] . ( 8 sec) [ -46997.9859] [10306] [depth= 1] . ( 8 sec) [ -46782.2851] [10271] [depth= 15] . ( 8 sec) [ -46681.1548] [10263] [depth= 25] . ( 8 sec) [ -46548.7594] [10265] [depth= 1] . ( 8 sec) [ -46503.2324] [10261] [depth= 2] . ( 8 sec) [ -46487.3520] [10260] [depth= 1] . ( 8 sec) [ -46316.4160] [10269] [depth= 27] . ( 9 sec) [ -46082.8043] [10190] [depth= 6] . ( 9 sec) [ -46062.1524] [10188] [depth= 1] . ( 9 sec) [ -45975.8393] [10191] [depth= 29] . ( 9 sec) [ -45877.3862] [10161] [depth= 18] . ( 9 sec) [ -45650.6285] [10153] [depth= 1] . ( 9 sec) [ -45330.0127] [10143] [depth= 19] . ( 10 sec) [ -44844.1908] [10050] [depth= 20] . ( 10 sec) [ -44779.2019] [10033] [depth= 1] . ( 10 sec) [ -44712.1812] [10013] [depth= 16] . ( 10 sec) [ -44635.8868] [10017] [depth= 21] . ( 10 sec) [ -44539.5500] [ 9971] [depth= 18] . ( 10 sec) [ -44273.8042] [ 9919] [depth= 18] . ( 11 sec) [ -44103.9509] [ 9901] [depth= 7] . ( 11 sec) [ -43888.8338] [ 9892] [depth= 19] . ( 11 sec) [ -43807.9815] [ 9853] [depth= 23] . ( 11 sec) [ -43794.5492] [ 9844] [depth= 1] . ( 11 sec) [ -43754.8456] [ 9841] [depth= 2] . ( 11 sec) [ -43051.9902] [ 9740] [depth= 9] . ( 12 sec) [ -42954.1113] [ 9685] [depth= 3] . ( 12 sec) [ -42819.3227] [ 9659] [depth= 30] . ( 12 sec) [ -42646.4903] [ 9597] [depth= 21] . ( 12 sec) [ -42567.5748] [ 9597] [depth= 5] . ( 12 sec) [ -42485.2079] [ 9569] [depth= 6] . ( 12 sec) [ -42479.4399] [ 9556] [depth= 5] . ( 12 sec) [ -42371.9086] [ 9528] [depth= 19] . ( 13 sec) [ -42175.6558] [ 9495] [depth= 6] . ( 13 sec) [ -42173.2202] [ 9488] [depth= 1] . ( 13 sec) [ -42043.2830] [ 9443] [depth= 20] . ( 13 sec) [ -42035.4101] [ 9446] [depth= 1] . ( 13 sec) [ -41812.3713] [ 9377] [depth= 21] . ( 13 sec) [ -41670.4208] [ 9317] [depth= 5] . ( 14 sec) [ -41577.1652] [ 9279] [depth= 6] . ( 14 sec) [ -41426.5007] [ 9262] [depth= 1] . ( 14 sec) [ -41124.5575] [ 9139] [depth= 10] . ( 14 sec) [ -41105.4570] [ 9115] [depth= 1] . ( 14 sec) [ -40980.8215] [ 9057] [depth= 1] . ( 14 sec) [ -40409.5661] [ 8975] [depth= 28] . ( 15 sec) [ -40246.1621] [ 8969] [depth= 4] . ( 15 sec) [ -39905.7021] [ 8915] [depth= 6] . ( 15 sec) [ -39734.3851] [ 8844] [depth= 19] . ( 15 sec) [ -39722.0259] [ 8840] [depth= 1] . ( 15 sec) [ -39704.8256] [ 8844] [depth= 1] . ( 15 sec) [ -39441.4398] [ 8790] [depth= 8] . ( 15 sec) [ -39254.8874] [ 8740] [depth= 12] . ( 16 sec) [ -39165.1694] [ 8711] [depth= 3] . ( 16 sec) [ -39160.8978] [ 8715] [depth= 1] . ( 16 sec) [ -38980.6332] [ 8675] [depth= 21] . ( 16 sec) [ -38831.4235] [ 8673] [depth= 4] . ( 16 sec) [ -38556.6019] [ 8616] [depth= 1] . ( 17 sec) [ -38289.6161] [ 8531] [depth= 7] . ( 17 sec) [ -38269.0929] [ 8533] [depth= 1] . ( 17 sec) [ -37973.1246] [ 8497] [depth= 23] . ( 17 sec) [ -37812.7612] [ 8468] [depth= 20] . ( 17 sec) [ -37794.4527] [ 8465] [depth= 4] . ( 18 sec) [ -37782.1164] [ 8462] [depth= 1] . ( 18 sec) [ -37734.1677] [ 8441] [depth= 14] . ( 18 sec) [ -37711.3776] [ 8437] [depth= 1] . ( 18 sec) [ -37617.6381] [ 8405] [depth= 10] . ( 18 sec) [ -37497.4015] [ 8344] [depth= 8] . ( 18 sec) [ -37458.4631] [ 8349] [depth= 1] . ( 19 sec) [ -37408.6729] [ 8340] [depth= 5] . ( 19 sec) [ -37408.3352] [ 8338] [depth= 3] . ( 19 sec) [ -37191.7521] [ 8302] [depth= 7] . ( 19 sec) [ -37178.5638] [ 8295] [depth= 3] . ( 19 sec) [ -36982.3573] [ 8219] [depth= 12] . ( 19 sec) [ -36662.2454] [ 8181] [depth= 10] . ( 20 sec) [ -36374.2264] [ 8031] [depth= 8] . ( 20 sec) [ -36353.7478] [ 8036] [depth= 1] . ( 20 sec) [ -35942.7645] [ 8014] [depth= 7] . ( 20 sec) [ -35800.7331] [ 7961] [depth= 5] . ( 20 sec) [ -35779.2083] [ 7961] [depth= 1] . ( 21 sec) [ -35680.9845] [ 7957] [depth= 1] . ( 21 sec) [ -35467.9405] [ 7869] [depth= 11] . ( 21 sec) [ -35377.4278] [ 7864] [depth= 9] . ( 21 sec) [ -35375.7970] [ 7863] [depth= 1] . ( 21 sec) [ -35225.5791] [ 7830] [depth= 19] . ( 21 sec) [ -35208.9450] [ 7827] [depth= 4] . ( 22 sec) [ -35123.0105] [ 7809] [depth= 3] . ( 22 sec) [ -35120.0757] [ 7810] [depth= 1] . ( 22 sec) [ -34989.2386] [ 7778] [depth= 3] . ( 22 sec) [ -34974.7510] [ 7773] [depth= 1] . ( 22 sec) [ -34931.5345] [ 7771] [depth= 5] . ( 22 sec) [ -34765.2041] [ 7730] [depth= 5] . ( 22 sec) [ -34297.6648] [ 7589] [depth= 9] . ( 23 sec) [ -34260.0230] [ 7606] [depth= 14] . ( 23 sec) [ -34024.8295] [ 7532] [depth= 13] . ( 23 sec) [ -34017.6401] [ 7529] [depth= 1] . ( 23 sec) [ -33994.1870] [ 7528] [depth= 3] . ( 23 sec) [ -33978.8746] [ 7524] [depth= 9] . ( 23 sec) [ -33846.9913] [ 7527] [depth= 10] . ( 24 sec) [ -33821.4800] [ 7522] [depth= 8] . ( 24 sec) [ -33774.6576] [ 7516] [depth= 8] . ( 24 sec) [ -33700.8273] [ 7516] [depth= 7] . ( 24 sec) [ -33683.2653] [ 7514] [depth= 8] . ( 25 sec) [ -33491.5923] [ 7446] [depth= 9] . ( 25 sec) [ -33481.1717] [ 7443] [depth= 1] . ( 25 sec) [ -33431.3626] [ 7432] [depth= 22] . ( 25 sec) [ -33430.2600] [ 7441] [depth= 1] . ( 25 sec) [ -33304.7274] [ 7401] [depth= 8] . ( 26 sec) [ -33256.3657] [ 7376] [depth= 4] . ( 26 sec) [ -33203.6809] [ 7360] [depth= 5] . ( 26 sec) [ -33140.9192] [ 7336] [depth= 1] . ( 26 sec) [ -33030.9923] [ 7312] [depth= 21] . ( 26 sec) [ -33019.5613] [ 7316] [depth= 2] . ( 27 sec) [ -33018.7602] [ 7320] [depth= 1] . ( 27 sec) [ -32966.4248] [ 7320] [depth= 4] . ( 27 sec) [ -32963.7745] [ 7318] [depth= 4] . ( 27 sec) [ -32869.3738] [ 7307] [depth= 2] . ( 27 sec) [ -32710.3096] [ 7263] [depth= 5] . ( 28 sec) [ -32678.8714] [ 7250] [depth= 10] . ( 28 sec) [ -32613.6250] [ 7220] [depth= 2] . ( 28 sec) [ -32560.5943] [ 7240] [depth= 8] . ( 28 sec) [ -32552.1714] [ 7234] [depth= 1] . ( 28 sec) [ -32542.4280] [ 7228] [depth= 3] . ( 28 sec) [ -32482.9021] [ 7216] [depth= 7] . ( 29 sec) [ -32402.4209] [ 7171] [depth= 4] . ( 29 sec) [ -32308.9917] [ 7136] [depth= 12] . ( 29 sec) [ -32282.0190] [ 7134] [depth= 2] . ( 29 sec) [ -32259.5513] [ 7130] [depth= 9] . ( 30 sec) [ -32209.9413] [ 7117] [depth= 3] . ( 30 sec) [ -32155.3602] [ 7108] [depth= 18] . ( 30 sec) [ -32107.0534] [ 7079] [depth= 1] . ( 30 sec) [ -32094.3092] [ 7072] [depth= 8] . ( 30 sec) [ -32086.6396] [ 7099] [depth= 2] . ( 30 sec) [ -32010.8701] [ 7067] [depth= 3] . ( 31 sec) [ -32005.4582] [ 7066] [depth= 1] . ( 31 sec) [ -31913.5411] [ 7032] [depth= 5] . ( 31 sec) [ -31875.0097] [ 7031] [depth= 7] . ( 31 sec) [ -31746.8641] [ 6982] [depth= 9] . ( 31 sec) [ -31703.3497] [ 6926] [depth= 7] . ( 31 sec) [ -31694.0763] [ 6926] [depth= 1] . ( 32 sec) [ -31654.1823] [ 6928] [depth= 1] . ( 33 sec) [ -31553.1505] [ 6894] [depth= 9] . ( 33 sec) [ -31544.9309] [ 6896] [depth= 1] . ( 33 sec) [ -31541.7690] [ 6895] [depth= 1] . ( 33 sec) [ -31541.6931] [ 6896] [depth= 1] . ( 33 sec) [ -31473.4635] [ 6872] [depth= 1] . ( 33 sec) [ -31373.7383] [ 6821] [depth= 7] . ( 33 sec) [ -31304.1935] [ 6784] [depth= 6] . ( 34 sec) [ -31267.4997] [ 6781] [depth= 5] . ( 34 sec) [ -31261.6641] [ 6782] [depth= 3] . ( 34 sec) [ -31251.2021] [ 6778] [depth= 1] . ( 35 sec) [ -31246.7008] [ 6782] [depth= 6] . ( 35 sec) [ -31237.2224] [ 6783] [depth= 1] . ( 35 sec) [ -31232.7850] [ 6783] [depth= 2] . ( 35 sec) [ -31226.4800] [ 6780] [depth= 3] . ( 36 sec) [ -31160.3358] [ 6754] [depth= 6] . ( 36 sec) [ -31044.6739] [ 6786] [depth= 1] . ( 36 sec) [ -30938.1754] [ 6703] [depth= 9] . ( 36 sec) [ -30773.4837] [ 6629] [depth= 1] . ( 36 sec) [ -30652.7548] [ 6591] [depth= 6] . ( 36 sec) [ -30619.9195] [ 6587] [depth= 2] . ( 37 sec) [ -30574.0652] [ 6576] [depth= 4] . ( 37 sec) [ -30569.0884] [ 6574] [depth= 1] . ( 37 sec) [ -30563.6992] [ 6570] [depth= 3] . ( 37 sec) [ -30555.9234] [ 6568] [depth= 2] . ( 38 sec) [ -30546.7421] [ 6564] [depth= 1] . ( 38 sec) [ -30545.0979] [ 6564] [depth= 2] . ( 38 sec) [ -30526.1876] [ 6561] [depth= 1] . ( 38 sec) [ -30523.0255] [ 6560] [depth= 3] . ( 38 sec) [ -30514.9384] [ 6565] [depth= 1] . ( 39 sec) [ -30514.7591] [ 6565] [depth= 1] . ( 39 sec) [ -30506.4455] [ 6566] [depth= 1] . ( 39 sec) [ -30489.9109] [ 6561] [depth= 1] . ( 40 sec) [ -30489.4125] [ 6562] [depth= 2] . ( 40 sec) [ -30435.5835] [ 6522] [depth= 2] . ( 40 sec) [ -30434.1282] [ 6522] [depth= 1] . ( 40 sec) [ -30431.8389] [ 6524] [depth= 2] . ( 41 sec) [ -30374.8995] [ 6510] [depth= 10] . ( 41 sec) [ -30300.9332] [ 6460] [depth= 12] . ( 41 sec) [ -30264.3177] [ 6452] [depth= 3] . ( 41 sec) [ -30259.6411] [ 6450] [depth= 2] . ( 42 sec) [ -30256.5759] [ 6451] [depth= 1] . ( 42 sec) [ -30253.9203] [ 6453] [depth= 1] . ( 42 sec) [ -30121.2740] [ 6434] [depth= 13] . ( 42 sec) [ -30103.3131] [ 6426] [depth= 1] . ( 43 sec) [ -30088.7606] [ 6429] [depth= 8] . ( 43 sec) [ -30087.8541] [ 6400] [depth= 7] . ( 43 sec) [ -30086.3801] [ 6394] [depth= 3] . ( 43 sec) [ -29986.4381] [ 6365] [depth= 16] . ( 43 sec) [ -29986.1398] [ 6365] [depth= 1] . ( 44 sec) [ -29854.0676] [ 6353] [depth= 7] . ( 44 sec) [ -29847.7740] [ 6349] [depth= 3] . ( 44 sec) [ -29796.0129] [ 6345] [depth= 1] . ( 44 sec) [ -29755.3689] [ 6344] [depth= 10] . ( 45 sec) [ -29751.1744] [ 6342] [depth= 1] . ( 45 sec) [ -29745.5782] [ 6342] [depth= 7] . ( 46 sec) [ -29422.9473] [Branch lengths ] . ( 53 sec) [ -28185.2888] [GTR parameters ] . ( 53 sec) [ -28131.5446] [Alpha ][ 0.362530] . ( 56 sec) [ -28129.3064] [ 6341] [depth= 6] . ( 56 sec) [ -28127.1950] [ 6335] [depth= 1] . ( 57 sec) [ -28124.7015] [ 6302] [depth= 1] . ( 57 sec) [ -28124.1564] [ 6301] [depth= 4] . ( 57 sec) [ -28029.5414] [ 6246] [depth= 14] . ( 57 sec) [ -28017.2315] [ 6245] [depth= 7] . ( 58 sec) [ -27868.9809] [ 6176] [depth= 6] . ( 59 sec) [ -27824.5376] [ 6148] [depth= 3] . ( 59 sec) [ -27824.3944] [ 6149] [depth= 3] . ( 59 sec) [ -27794.2296] [ 6141] [depth= 1] . ( 59 sec) [ -27792.5758] [ 6146] [depth= 1] . ( 61 sec) [ -27785.4174] [ 6143] [depth= 1] . ( 61 sec) [ -27776.2750] [ 6139] [depth= 1] . ( 61 sec) [ -27776.0795] [ 6138] [depth= 1] . ( 61 sec) [ -27770.8713] [ 6115] [depth= 4] . ( 61 sec) [ -27752.2892] [ 6111] [depth= 8] . ( 62 sec) [ -27720.0169] [ 6076] [depth= 1] . ( 62 sec) [ -27698.3493] [ 6070] [depth= 1] . ( 62 sec) [ -27687.6826] [ 6068] [depth= 2] . ( 62 sec) [ -27659.0496] [ 6049] [depth= 10] . ( 63 sec) [ -27658.8919] [ 6050] [depth= 1] . ( 63 sec) [ -27656.1854] [ 6049] [depth= 1] . ( 63 sec) [ -27649.0786] [ 6044] [depth= 1] . ( 64 sec) [ -27633.3571] [ 6038] [depth= 1] . ( 64 sec) [ -27616.7812] [ 6051] [depth= 8] . ( 64 sec) [ -27616.4635] [ 6056] [depth= 1] . ( 64 sec) [ -27603.4887] [ 6045] [depth= 3] . ( 64 sec) [ -27601.8426] [ 6040] [depth= 1] . ( 65 sec) [ -27531.4943] [ 6007] [depth= 7] . ( 65 sec) [ -27428.7130] [ 5962] [depth= 3] . ( 66 sec) [ -27427.0006] [ 5964] [depth= 1] . ( 66 sec) [ -27425.1888] [ 5966] [depth= 4] . ( 66 sec) [ -27421.0636] [ 5964] [depth= 1] . ( 66 sec) [ -27412.1836] [ 5962] [depth= 2] . ( 67 sec) [ -27392.1581] [ 5952] [depth= 1] . ( 67 sec) [ -27391.9636] [ 5955] [depth= 1] . ( 68 sec) [ -27390.0084] [ 5957] [depth= 1] . ( 68 sec) [ -27389.5486] [ 5957] [depth= 1] . ( 69 sec) [ -27389.2535] [ 5957] [depth= 1] . ( 69 sec) [ -27388.7428] [ 5961] [depth= 1] . ( 70 sec) [ -27387.9693] [ 5961] [depth= 1] . ( 70 sec) [ -27372.0898] [ 5947] [depth= 2] . ( 70 sec) [ -27371.4997] [ 5950] [depth= 1] . ( 71 sec) [ -27342.3393] [ 5942] [depth= 2] . ( 72 sec) [ -27337.4600] [ 5937] [depth= 1] . ( 72 sec) [ -27319.9670] [ 5931] [depth= 1] . ( 72 sec) [ -27309.9475] [ 5926] [depth= 1] . ( 73 sec) [ -27308.1145] [ 5924] [depth= 3] . ( 73 sec) [ -27300.8360] [ 5916] [depth= 2] . ( 74 sec) [ -27293.1250] [ 5895] [depth= 7] . ( 74 sec) [ -27290.1987] [ 5895] [depth= 2] . ( 75 sec) [ -27289.6561] [ 5897] [depth= 2] . ( 76 sec) [ -27259.9241] [ 5891] [depth= 1] . ( 77 sec) [ -27259.0140] [ 5891] [depth= 1] . ( 77 sec) [ -27257.9314] [ 5890] [depth= 1] . ( 77 sec) [ -27257.5646] [ 5889] [depth= 1] . ( 78 sec) [ -27257.1405] [ 5891] [depth= 1] . ( 78 sec) [ -27251.2674] [ 5889] [depth= 1] . ( 78 sec) [ -27236.9466] [ 5880] [depth= 1] . ( 79 sec) [ -27226.3537] [ 5874] [depth= 6] . ( 80 sec) [ -27204.2990] [ 5875] [depth= 1] . ( 80 sec) [ -27185.5572] [ 5862] [depth= 1] . ( 80 sec) [ -27127.4552] [ 5823] [depth= 7] . ( 80 sec) [ -27127.4144] [ 5826] [depth= 1] . ( 82 sec) [ -27127.3196] [ 5826] [depth= 1] . ( 83 sec) [ -27126.7423] [ 5832] [depth= 1] . ( 83 sec) [ -27126.7241] [ 5832] [depth= 1] . ( 84 sec) [ -27122.1424] [ 5831] [depth= 2] . ( 88 sec) [ -27121.7882] [ 5831] [depth= 1] . ( 89 sec) [ -27099.3023] [ 5803] [depth= 10] . ( 89 sec) [ -27083.5477] [ 5792] [depth= 1] . ( 90 sec) [ -27083.4552] [ 5792] [depth= 1] . ( 92 sec) [ -27078.9448] [ 5792] [depth= 1] . ( 92 sec) [ -27078.8333] [ 5792] [depth= 1] . ( 93 sec) [ -27062.3754] [ 5790] [depth= 4] . ( 94 sec) [ -27060.2835] [ 5788] [depth= 1] . ( 94 sec) [ -27058.9025] [ 5791] [depth= 1] . ( 96 sec) [ -27058.7229] [ 5792] [depth= 1] . ( 98 sec) [ -26983.3653] [Branch lengths ] . ( 103 sec) [ -26980.1947] [GTR parameters ] . ( 103 sec) [ -26979.5197] [Alpha ][ 0.348772] . ( 108 sec) [ -26979.3937] [ 5792] [depth= 1] . ( 110 sec) [ -26979.2826] [ 5788] [depth= 1] . ( 111 sec) [ -26975.9968] [ 5788] [depth= 1] . ( 111 sec) [ -26974.8793] [ 5791] [depth= 1] . ( 115 sec) [ -26974.3287] [ 5789] [depth= 1] . ( 115 sec) [ -26973.7520] [ 5790] [depth= 1] . ( 115 sec) [ -26972.2564] [ 5791] [depth= 1] . ( 119 sec) [ -26968.5287] [ 5791] [depth= 1] . ( 128 sec) [ -26968.2235] [ 5795] [depth= 1] . ( 144 sec) [ -26967.7087] [ 5796] [depth= 1] . ( 148 sec) [ -26955.3023] [Branch lengths ] . ( 152 sec) [ -26955.1647] [GTR parameters ] . ( 152 sec) [ -26953.6778] [Alpha ][ 0.328769] . ( 159 sec) [ -26953.5623] [ 5795] [depth= 1] . ( 161 sec) [ -26950.4779] [ 5800] [depth= 3] . ( 196 sec) [ -26947.2459] [Branch lengths ] . ( 200 sec) [ -26947.1542] [GTR parameters ] . ( 200 sec) [ -26946.5689] [Alpha ][ 0.316725] . ( 244 sec) [ -26945.6146] [Branch lengths ] . ( 381 sec) [ -26945.4915] [Branch lengths ] . ( 381 sec) [ -26945.4915] [Topology ] . ( 384 sec) [ -26945.4844] [Topology ] . ( 387 sec) [ -26945.4827] [Topology ] . ( 391 sec) [ -26945.4822] [Topology ] . ( 395 sec) [ -26945.4670] [GTR parameters ] . ( 395 sec) [ -26944.9893] [Alpha ][ 0.306096] . ( 395 sec) [ -26944.9893] [Topology ] . ( 398 sec) [ -26944.8130] [Topology ] . ( 402 sec) [ -26944.7582] [Topology ] . ( 405 sec) [ -26944.7391] [Topology ] . ( 408 sec) [ -26944.7119] [Topology ] . ( 411 sec) [ -26944.5731] [Topology ] . ( 415 sec) [ -26944.5500] [Topology ] . ( 418 sec) [ -26944.5417] [Topology ] . ( 421 sec) [ -26944.5386] [Topology ] . ( 424 sec) [ -26944.5373] [Topology ] . ( 430 sec) [ -26944.5233] [GTR parameters ] . ( 430 sec) [ -26944.3304] [Alpha ][ 0.299252] . ( 430 sec) [ -26944.3304] [Topology ] . ( 434 sec) [ -26944.2554] [Topology ] . ( 437 sec) [ -26944.2337] [Topology ] . ( 440 sec) [ -26944.2264] [Topology ] . ( 443 sec) [ -26944.2238] [Topology ] . ( 447 sec) [ -26944.2229] [Topology ] . ( 450 sec) [ -26944.2198] [GTR parameters ] . ( 451 sec) [ -26944.1700] [Alpha ][ 0.295806] . ( 451 sec) [ -26944.1700] [Topology ] . ( 454 sec) [ -26944.1462] [Topology ] . ( 457 sec) [ -26944.1393] [Topology ] . ( 460 sec) [ -26944.1370] [Topology ] . ( 464 sec) [ -26944.1361] [Topology ] . ( 466 sec) [ -26944.1357] [GTR parameters ] . ( 466 sec) [ -26944.1220] [Alpha ][ 0.294001] . ( 466 sec) [ -26944.1220] [Topology ] . ( 469 sec) [ -26944.1142] [Topology ] . ( 472 sec) [ -26944.1118] [Topology ] . ( 476 sec) [ -26944.1111] [Topology ] . ( 479 sec) [ -26944.1097] [GTR parameters ] . ( 479 sec) [ -26944.1053] [Alpha ][ 0.292972] . ( 479 sec) [ -26944.1053] [Topology ] . ( 482 sec) [ -26944.1021] [Topology ] . ( 485 sec) [ -26944.1011] [Topology ] . ( 486 sec) [ -26944.1010] [GTR parameters ] . ( 486 sec) [ -26944.0999] [Alpha ][ 0.292449] . ( 486 sec) [ -26944.0999] [Topology ] . ( 490 sec) [ -26944.0985] [Topology ] . ( 493 sec) [ -26944.0981] [Topology ] . ( 494 sec) [ -26944.0981] [GTR parameters ] . ( 494 sec) [ -26944.0976] [Alpha ][ 0.292125] . ( 494 sec) [ -26944.0976] [Topology ] . ( 497 sec) [ -26944.0970] [Topology ] . ( 499 sec) [ -26944.0968] [GTR parameters ] . ( 499 sec) [ -26944.0968] [Alpha ][ 0.291833] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26944.096816. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -55016.6924] [GTR parameters ] . ( 2 sec) [ -53434.3784] [Alpha ][ 0.500960] . ( 2 sec) [ -52991.5851] [11434] [depth= 14] . ( 2 sec) [ -52772.0567] [11381] [depth= 10] . ( 2 sec) [ -52519.9863] [11363] [depth= 14] . ( 2 sec) [ -52435.1610] [11317] [depth= 1] . ( 2 sec) [ -52196.6656] [11294] [depth= 11] . ( 3 sec) [ -52179.8599] [11285] [depth= 1] . ( 3 sec) [ -51934.6375] [11273] [depth= 6] . ( 3 sec) [ -51850.0132] [11235] [depth= 2] . ( 3 sec) [ -51763.5345] [11203] [depth= 7] . ( 3 sec) [ -51737.4099] [11199] [depth= 2] . ( 3 sec) [ -51636.6632] [11195] [depth= 9] . ( 3 sec) [ -51316.9264] [11153] [depth= 5] . ( 4 sec) [ -50937.9509] [11132] [depth= 8] . ( 4 sec) [ -50923.6120] [11114] [depth= 2] . ( 4 sec) [ -50834.0708] [11111] [depth= 10] . ( 4 sec) [ -50393.5304] [11078] [depth= 3] . ( 4 sec) [ -50288.3710] [11069] [depth= 8] . ( 4 sec) [ -49972.8871] [11061] [depth= 7] . ( 4 sec) [ -49964.9667] [11057] [depth= 4] . ( 5 sec) [ -49886.3388] [11040] [depth= 1] . ( 5 sec) [ -49877.5276] [11038] [depth= 1] . ( 5 sec) [ -49729.5311] [11017] [depth= 17] . ( 5 sec) [ -49696.5680] [11025] [depth= 1] . ( 5 sec) [ -49592.4831] [11013] [depth= 8] . ( 5 sec) [ -49566.2650] [10987] [depth= 1] . ( 5 sec) [ -49372.8249] [10961] [depth= 14] . ( 6 sec) [ -49185.0292] [10934] [depth= 9] . ( 6 sec) [ -49005.2094] [10881] [depth= 1] . ( 6 sec) [ -48915.2677] [10838] [depth= 7] . ( 6 sec) [ -48791.1236] [10833] [depth= 4] . ( 6 sec) [ -48722.5833] [10823] [depth= 11] . ( 6 sec) [ -48436.2174] [10785] [depth= 1] . ( 7 sec) [ -48326.0188] [10755] [depth= 15] . ( 7 sec) [ -48282.0806] [10756] [depth= 12] . ( 7 sec) [ -48272.7483] [10757] [depth= 2] . ( 7 sec) [ -48135.8140] [10720] [depth= 11] . ( 7 sec) [ -48064.9840] [10719] [depth= 1] . ( 7 sec) [ -47547.0646] [10630] [depth= 20] . ( 7 sec) [ -47523.0757] [10631] [depth= 2] . ( 8 sec) [ -47331.5315] [10580] [depth= 11] . ( 8 sec) [ -47047.9250] [10460] [depth= 10] . ( 8 sec) [ -46861.2460] [10373] [depth= 17] . ( 8 sec) [ -46857.1467] [10372] [depth= 1] . ( 8 sec) [ -46674.7137] [10331] [depth= 14] . ( 9 sec) [ -46580.9522] [10323] [depth= 17] . ( 9 sec) [ -46439.6117] [10312] [depth= 1] . ( 9 sec) [ -46333.6917] [10290] [depth= 1] . ( 9 sec) [ -46065.4259] [10252] [depth= 15] . ( 9 sec) [ -46056.3254] [10242] [depth= 1] . ( 9 sec) [ -46053.2633] [10255] [depth= 17] . ( 9 sec) [ -45795.0529] [10138] [depth= 18] . ( 10 sec) [ -45682.1513] [10125] [depth= 11] . ( 10 sec) [ -45536.4060] [10099] [depth= 12] . ( 10 sec) [ -45533.2337] [10101] [depth= 1] . ( 10 sec) [ -45344.9473] [10070] [depth= 14] . ( 10 sec) [ -44562.8502] [ 9994] [depth= 17] . ( 11 sec) [ -44148.4699] [ 9898] [depth= 15] . ( 11 sec) [ -43863.3646] [ 9864] [depth= 5] . ( 11 sec) [ -43534.8777] [ 9824] [depth= 9] . ( 11 sec) [ -43438.1661] [ 9802] [depth= 11] . ( 11 sec) [ -43421.6128] [ 9801] [depth= 2] . ( 11 sec) [ -43421.2657] [ 9799] [depth= 1] . ( 11 sec) [ -43239.5430] [ 9738] [depth= 10] . ( 12 sec) [ -43152.2642] [ 9723] [depth= 9] . ( 12 sec) [ -43017.4898] [ 9745] [depth= 15] . ( 12 sec) [ -42861.3894] [ 9656] [depth= 7] . ( 12 sec) [ -42737.1578] [ 9652] [depth= 4] . ( 12 sec) [ -42580.0567] [ 9590] [depth= 5] . ( 13 sec) [ -42311.8769] [ 9517] [depth= 8] . ( 13 sec) [ -42296.4578] [ 9512] [depth= 2] . ( 13 sec) [ -42205.1385] [ 9505] [depth= 3] . ( 13 sec) [ -42088.0997] [ 9430] [depth= 5] . ( 13 sec) [ -42040.8898] [ 9431] [depth= 8] . ( 13 sec) [ -42026.8077] [ 9430] [depth= 1] . ( 13 sec) [ -41946.7382] [ 9423] [depth= 8] . ( 13 sec) [ -41826.8389] [ 9409] [depth= 3] . ( 14 sec) [ -41712.6073] [ 9383] [depth= 15] . ( 14 sec) [ -41600.4731] [ 9312] [depth= 14] . ( 14 sec) [ -41586.9543] [ 9310] [depth= 1] . ( 14 sec) [ -41485.2693] [ 9282] [depth= 1] . ( 14 sec) [ -40639.5895] [ 9125] [depth= 17] . ( 14 sec) [ -40620.0839] [ 9126] [depth= 19] . ( 15 sec) [ -40481.9541] [ 9075] [depth= 11] . ( 15 sec) [ -40481.0798] [ 9075] [depth= 1] . ( 15 sec) [ -40361.3571] [ 9065] [depth= 9] . ( 15 sec) [ -40344.2401] [ 9054] [depth= 1] . ( 15 sec) [ -40261.4559] [ 9036] [depth= 19] . ( 15 sec) [ -40235.4267] [ 9028] [depth= 1] . ( 16 sec) [ -40159.6530] [ 9004] [depth= 16] . ( 16 sec) [ -39856.0398] [ 8916] [depth= 17] . ( 16 sec) [ -39748.2794] [ 8894] [depth= 1] . ( 16 sec) [ -39665.5569] [ 8887] [depth= 10] . ( 16 sec) [ -39566.8399] [ 8871] [depth= 7] . ( 17 sec) [ -39531.1666] [ 8860] [depth= 1] . ( 17 sec) [ -39529.5123] [ 8858] [depth= 1] . ( 17 sec) [ -39485.5647] [ 8858] [depth= 7] . ( 17 sec) [ -39417.5458] [ 8819] [depth= 17] . ( 17 sec) [ -39185.0710] [ 8811] [depth= 1] . ( 17 sec) [ -38794.7855] [ 8734] [depth= 14] . ( 17 sec) [ -38658.9418] [ 8725] [depth= 13] . ( 18 sec) [ -38563.3546] [ 8700] [depth= 15] . ( 18 sec) [ -38399.5760] [ 8654] [depth= 6] . ( 18 sec) [ -38065.9758] [ 8612] [depth= 3] . ( 18 sec) [ -37998.9317] [ 8593] [depth= 1] . ( 18 sec) [ -37910.3164] [ 8572] [depth= 1] . ( 18 sec) [ -37816.7767] [ 8539] [depth= 1] . ( 19 sec) [ -37648.7108] [ 8486] [depth= 12] . ( 19 sec) [ -37483.5493] [ 8443] [depth= 17] . ( 19 sec) [ -37343.5974] [ 8387] [depth= 1] . ( 19 sec) [ -37263.3635] [ 8353] [depth= 9] . ( 19 sec) [ -37023.6967] [ 8315] [depth= 10] . ( 20 sec) [ -36853.5096] [ 8291] [depth= 13] . ( 20 sec) [ -36491.5911] [ 8188] [depth= 9] . ( 20 sec) [ -36428.8106] [ 8190] [depth= 1] . ( 20 sec) [ -36336.1158] [ 8149] [depth= 7] . ( 20 sec) [ -36322.0143] [ 8147] [depth= 4] . ( 21 sec) [ -36222.2318] [ 8120] [depth= 8] . ( 21 sec) [ -36180.4376] [ 8118] [depth= 1] . ( 21 sec) [ -36088.3904] [ 8089] [depth= 9] . ( 21 sec) [ -36059.3484] [ 8083] [depth= 1] . ( 21 sec) [ -35913.6855] [ 8010] [depth= 6] . ( 21 sec) [ -35875.6667] [ 8010] [depth= 1] . ( 21 sec) [ -35829.2418] [ 7989] [depth= 1] . ( 22 sec) [ -35736.8244] [ 7972] [depth= 15] . ( 22 sec) [ -35685.9965] [ 7979] [depth= 5] . ( 22 sec) [ -35663.6606] [ 7984] [depth= 1] . ( 22 sec) [ -35659.7507] [ 7983] [depth= 1] . ( 22 sec) [ -35657.5561] [ 7983] [depth= 1] . ( 22 sec) [ -35401.3547] [ 7942] [depth= 8] . ( 23 sec) [ -35311.6693] [ 7926] [depth= 11] . ( 23 sec) [ -35277.8342] [ 7926] [depth= 2] . ( 23 sec) [ -35230.5308] [ 7917] [depth= 10] . ( 23 sec) [ -35096.5653] [ 7875] [depth= 9] . ( 23 sec) [ -34920.6339] [ 7875] [depth= 11] . ( 24 sec) [ -34827.8522] [ 7861] [depth= 1] . ( 24 sec) [ -34820.4566] [ 7838] [depth= 8] . ( 24 sec) [ -34816.9744] [ 7834] [depth= 2] . ( 24 sec) [ -34445.5100] [ 7780] [depth= 10] . ( 24 sec) [ -34186.8462] [ 7719] [depth= 14] . ( 25 sec) [ -34174.1950] [ 7717] [depth= 2] . ( 25 sec) [ -34140.0186] [ 7719] [depth= 1] . ( 25 sec) [ -33961.8016] [ 7666] [depth= 4] . ( 25 sec) [ -33857.7350] [ 7651] [depth= 3] . ( 25 sec) [ -33689.9350] [ 7598] [depth= 9] . ( 25 sec) [ -33674.3852] [ 7588] [depth= 4] . ( 25 sec) [ -33636.9782] [ 7566] [depth= 1] . ( 26 sec) [ -33614.0436] [ 7555] [depth= 13] . ( 26 sec) [ -33589.7291] [ 7523] [depth= 10] . ( 26 sec) [ -33584.5395] [ 7556] [depth= 1] . ( 26 sec) [ -33580.6577] [ 7556] [depth= 1] . ( 26 sec) [ -33273.5921] [ 7491] [depth= 10] . ( 26 sec) [ -33237.1686] [ 7470] [depth= 1] . ( 27 sec) [ -33218.1936] [ 7457] [depth= 1] . ( 27 sec) [ -33208.5276] [ 7452] [depth= 4] . ( 27 sec) [ -33166.9198] [ 7421] [depth= 1] . ( 27 sec) [ -33127.8231] [ 7408] [depth= 4] . ( 27 sec) [ -33113.8389] [ 7404] [depth= 5] . ( 27 sec) [ -32998.0782] [ 7385] [depth= 15] . ( 28 sec) [ -32952.1303] [ 7373] [depth= 3] . ( 28 sec) [ -32929.1406] [ 7365] [depth= 4] . ( 28 sec) [ -32773.0810] [ 7321] [depth= 11] . ( 28 sec) [ -32720.9884] [ 7311] [depth= 1] . ( 28 sec) [ -32581.0015] [ 7278] [depth= 14] . ( 28 sec) [ -32572.1602] [ 7279] [depth= 2] . ( 28 sec) [ -32566.8589] [ 7279] [depth= 2] . ( 29 sec) [ -32566.4840] [ 7280] [depth= 1] . ( 29 sec) [ -32563.1604] [ 7280] [depth= 1] . ( 29 sec) [ -32278.7718] [ 7149] [depth= 9] . ( 29 sec) [ -32278.2172] [ 7149] [depth= 1] . ( 29 sec) [ -32227.2988] [ 7099] [depth= 2] . ( 30 sec) [ -32033.9968] [ 7047] [depth= 22] . ( 30 sec) [ -31967.3175] [ 6994] [depth= 8] . ( 30 sec) [ -31918.4214] [ 6981] [depth= 1] . ( 30 sec) [ -31875.9363] [ 6976] [depth= 9] . ( 30 sec) [ -31830.4463] [ 6954] [depth= 1] . ( 31 sec) [ -31827.4127] [ 6959] [depth= 9] . ( 32 sec) [ -31781.7476] [ 6958] [depth= 17] . ( 32 sec) [ -31752.1480] [ 6944] [depth= 14] . ( 32 sec) [ -31638.7355] [ 6936] [depth= 1] . ( 32 sec) [ -31614.5124] [ 6937] [depth= 2] . ( 32 sec) [ -31606.1877] [ 6934] [depth= 2] . ( 32 sec) [ -31589.0116] [ 6936] [depth= 7] . ( 33 sec) [ -31582.5483] [ 6934] [depth= 1] . ( 33 sec) [ -31558.1793] [ 6910] [depth= 12] . ( 33 sec) [ -31556.4393] [ 6912] [depth= 2] . ( 33 sec) [ -31555.4338] [ 6917] [depth= 2] . ( 33 sec) [ -31535.6833] [ 6910] [depth= 12] . ( 34 sec) [ -31425.1888] [ 6881] [depth= 7] . ( 34 sec) [ -31400.0848] [ 6882] [depth= 1] . ( 34 sec) [ -31378.6799] [ 6882] [depth= 1] . ( 34 sec) [ -31314.6300] [ 6867] [depth= 10] . ( 34 sec) [ -31261.0963] [ 6857] [depth= 1] . ( 34 sec) [ -31256.3848] [ 6854] [depth= 1] . ( 35 sec) [ -31195.2871] [ 6816] [depth= 8] . ( 35 sec) [ -31187.0288] [ 6814] [depth= 2] . ( 37 sec) [ -31178.7675] [ 6812] [depth= 2] . ( 37 sec) [ -31164.1755] [ 6813] [depth= 2] . ( 37 sec) [ -31153.5531] [ 6811] [depth= 3] . ( 37 sec) [ -31152.9962] [ 6812] [depth= 2] . ( 38 sec) [ -31150.7162] [ 6812] [depth= 1] . ( 38 sec) [ -31150.6844] [ 6811] [depth= 5] . ( 38 sec) [ -31143.4902] [ 6808] [depth= 5] . ( 38 sec) [ -31058.1384] [ 6775] [depth= 9] . ( 39 sec) [ -31042.1048] [ 6739] [depth= 4] . ( 39 sec) [ -30997.1211] [ 6726] [depth= 8] . ( 39 sec) [ -30972.5747] [ 6724] [depth= 1] . ( 39 sec) [ -30931.7726] [ 6716] [depth= 12] . ( 40 sec) [ -30870.0141] [ 6670] [depth= 10] . ( 40 sec) [ -30854.9814] [ 6652] [depth= 3] . ( 40 sec) [ -30844.5030] [ 6641] [depth= 1] . ( 40 sec) [ -30646.2938] [ 6571] [depth= 1] . ( 40 sec) [ -30632.5360] [ 6565] [depth= 2] . ( 40 sec) [ -30571.7886] [ 6548] [depth= 5] . ( 41 sec) [ -30363.7151] [ 6486] [depth= 7] . ( 41 sec) [ -30309.5349] [ 6475] [depth= 1] . ( 41 sec) [ -30308.5996] [ 6476] [depth= 5] . ( 42 sec) [ -30307.5869] [ 6476] [depth= 1] . ( 42 sec) [ -30306.5825] [ 6476] [depth= 1] . ( 42 sec) [ -30303.7730] [ 6477] [depth= 2] . ( 42 sec) [ -30298.5521] [ 6477] [depth= 2] . ( 42 sec) [ -30292.2275] [ 6475] [depth= 1] . ( 43 sec) [ -30278.1999] [ 6476] [depth= 4] . ( 43 sec) [ -30273.7582] [ 6461] [depth= 6] . ( 43 sec) [ -30251.3432] [ 6454] [depth= 1] . ( 43 sec) [ -30243.3096] [ 6449] [depth= 1] . ( 43 sec) [ -30214.1935] [ 6443] [depth= 2] . ( 43 sec) [ -30193.8872] [ 6435] [depth= 4] . ( 44 sec) [ -30190.8944] [ 6438] [depth= 2] . ( 44 sec) [ -30121.1929] [ 6412] [depth= 11] . ( 44 sec) [ -30074.2730] [ 6409] [depth= 1] . ( 45 sec) [ -30073.9221] [ 6409] [depth= 2] . ( 45 sec) [ -30072.6825] [ 6408] [depth= 1] . ( 45 sec) [ -30039.3315] [ 6396] [depth= 2] . ( 45 sec) [ -29765.4910] [ 6296] [depth= 14] . ( 45 sec) [ -29736.0672] [ 6308] [depth= 1] . ( 47 sec) [ -29494.7535] [Branch lengths ] . ( 52 sec) [ -28268.2329] [GTR parameters ] . ( 53 sec) [ -28207.2590] [Alpha ][ 0.353647] . ( 54 sec) [ -28143.4596] [ 6280] [depth= 7] . ( 54 sec) [ -28127.3705] [ 6272] [depth= 4] . ( 54 sec) [ -28126.7437] [ 6272] [depth= 1] . ( 54 sec) [ -28120.3233] [ 6264] [depth= 3] . ( 54 sec) [ -28042.8201] [ 6220] [depth= 12] . ( 54 sec) [ -28034.1942] [ 6214] [depth= 3] . ( 55 sec) [ -28032.0439] [ 6213] [depth= 1] . ( 55 sec) [ -28021.8467] [ 6206] [depth= 2] . ( 55 sec) [ -28019.7315] [ 6206] [depth= 2] . ( 55 sec) [ -28019.3656] [ 6210] [depth= 1] . ( 55 sec) [ -28000.5088] [ 6201] [depth= 2] . ( 56 sec) [ -27998.8805] [ 6205] [depth= 2] . ( 56 sec) [ -27998.8065] [ 6206] [depth= 1] . ( 56 sec) [ -27986.0351] [ 6210] [depth= 1] . ( 56 sec) [ -27976.9939] [ 6196] [depth= 1] . ( 56 sec) [ -27973.1274] [ 6193] [depth= 1] . ( 56 sec) [ -27883.7965] [ 6131] [depth= 8] . ( 57 sec) [ -27871.5761] [ 6125] [depth= 2] . ( 57 sec) [ -27870.1247] [ 6124] [depth= 1] . ( 58 sec) [ -27817.4810] [ 6103] [depth= 2] . ( 58 sec) [ -27815.3673] [ 6102] [depth= 4] . ( 58 sec) [ -27714.1063] [ 6064] [depth= 6] . ( 58 sec) [ -27707.8056] [ 6065] [depth= 1] . ( 58 sec) [ -27704.6534] [ 6063] [depth= 1] . ( 58 sec) [ -27679.4987] [ 6052] [depth= 2] . ( 59 sec) [ -27675.9618] [ 6051] [depth= 3] . ( 59 sec) [ -27635.4066] [ 6032] [depth= 13] . ( 60 sec) [ -27633.5663] [ 6032] [depth= 2] . ( 60 sec) [ -27612.7082] [ 6025] [depth= 2] . ( 61 sec) [ -27612.6044] [ 6025] [depth= 1] . ( 61 sec) [ -27611.4603] [ 6025] [depth= 2] . ( 61 sec) [ -27574.7554] [ 6020] [depth= 4] . ( 62 sec) [ -27572.9725] [ 6022] [depth= 1] . ( 62 sec) [ -27517.3392] [ 6006] [depth= 2] . ( 63 sec) [ -27513.6042] [ 6005] [depth= 4] . ( 63 sec) [ -27471.4479] [ 5972] [depth= 6] . ( 63 sec) [ -27470.0917] [ 5971] [depth= 1] . ( 64 sec) [ -27469.7058] [ 5971] [depth= 1] . ( 65 sec) [ -27434.6148] [ 5941] [depth= 8] . ( 65 sec) [ -27428.8046] [ 5941] [depth= 6] . ( 65 sec) [ -27405.5964] [ 5930] [depth= 3] . ( 65 sec) [ -27390.6487] [ 5922] [depth= 4] . ( 66 sec) [ -27376.0811] [ 5920] [depth= 7] . ( 67 sec) [ -27342.7185] [ 5921] [depth= 1] . ( 67 sec) [ -27338.4058] [ 5918] [depth= 4] . ( 67 sec) [ -27334.7917] [ 5917] [depth= 1] . ( 68 sec) [ -27333.7031] [ 5917] [depth= 1] . ( 68 sec) [ -27302.6794] [ 5899] [depth= 6] . ( 68 sec) [ -27287.0264] [ 5891] [depth= 5] . ( 69 sec) [ -27284.2593] [ 5891] [depth= 1] . ( 69 sec) [ -27277.4653] [ 5888] [depth= 1] . ( 70 sec) [ -27277.2317] [ 5887] [depth= 1] . ( 70 sec) [ -27276.4152] [ 5888] [depth= 1] . ( 71 sec) [ -27264.8140] [ 5877] [depth= 1] . ( 72 sec) [ -27259.5620] [ 5882] [depth= 1] . ( 72 sec) [ -27257.5413] [ 5883] [depth= 1] . ( 72 sec) [ -27254.8927] [ 5885] [depth= 2] . ( 72 sec) [ -27230.7899] [ 5871] [depth= 7] . ( 72 sec) [ -27228.8832] [ 5873] [depth= 1] . ( 74 sec) [ -27212.4436] [ 5866] [depth= 1] . ( 75 sec) [ -27210.9441] [ 5869] [depth= 1] . ( 75 sec) [ -27210.0562] [ 5866] [depth= 1] . ( 77 sec) [ -27201.0659] [ 5868] [depth= 1] . ( 78 sec) [ -27191.1965] [ 5863] [depth= 1] . ( 79 sec) [ -27186.6965] [ 5859] [depth= 1] . ( 79 sec) [ -27186.5808] [ 5855] [depth= 1] . ( 81 sec) [ -27182.6800] [ 5853] [depth= 4] . ( 81 sec) [ -27179.2939] [ 5854] [depth= 1] . ( 83 sec) [ -27168.5794] [ 5850] [depth= 1] . ( 83 sec) [ -27119.3801] [ 5830] [depth= 3] . ( 83 sec) [ -27115.8848] [ 5830] [depth= 2] . ( 84 sec) [ -27113.5180] [ 5833] [depth= 1] . ( 84 sec) [ -27112.3200] [ 5836] [depth= 1] . ( 84 sec) [ -27111.8747] [ 5838] [depth= 1] . ( 84 sec) [ -27110.3079] [ 5841] [depth= 1] . ( 85 sec) [ -27109.6662] [ 5841] [depth= 1] . ( 85 sec) [ -27104.1140] [ 5840] [depth= 1] . ( 85 sec) [ -27103.0564] [ 5840] [depth= 1] . ( 86 sec) [ -27092.6243] [ 5826] [depth= 1] . ( 86 sec) [ -27092.2584] [ 5826] [depth= 1] . ( 88 sec) [ -27091.7078] [ 5825] [depth= 1] . ( 89 sec) [ -27059.2043] [ 5810] [depth= 4] . ( 90 sec) [ -27058.0661] [ 5811] [depth= 1] . ( 90 sec) [ -27057.8530] [ 5813] [depth= 1] . ( 90 sec) [ -27057.6939] [ 5816] [depth= 1] . ( 90 sec) [ -27046.5602] [ 5807] [depth= 1] . ( 91 sec) [ -27039.3220] [ 5805] [depth= 2] . ( 92 sec) [ -27037.0463] [ 5805] [depth= 1] . ( 92 sec) [ -27036.9618] [ 5809] [depth= 1] . ( 93 sec) [ -27036.4845] [ 5811] [depth= 1] . ( 93 sec) [ -27035.5957] [ 5808] [depth= 1] . ( 94 sec) [ -27034.4893] [ 5807] [depth= 1] . ( 95 sec) [ -26977.8767] [Branch lengths ] . ( 101 sec) [ -26973.2383] [GTR parameters ] . ( 102 sec) [ -26971.9905] [Alpha ][ 0.335284] . ( 103 sec) [ -26968.7909] [ 5808] [depth= 1] . ( 116 sec) [ -26968.1097] [ 5809] [depth= 1] . ( 119 sec) [ -26966.9079] [ 5803] [depth= 1] . ( 123 sec) [ -26966.8903] [ 5806] [depth= 1] . ( 124 sec) [ -26965.3038] [ 5805] [depth= 2] . ( 125 sec) [ -26964.0558] [ 5803] [depth= 2] . ( 128 sec) [ -26961.3188] [ 5807] [depth= 3] . ( 134 sec) [ -26960.1205] [ 5805] [depth= 1] . ( 140 sec) [ -26959.4414] [ 5801] [depth= 1] . ( 140 sec) [ -26959.4139] [ 5799] [depth= 1] . ( 145 sec) [ -26949.4109] [Branch lengths ] . ( 150 sec) [ -26949.1775] [GTR parameters ] . ( 150 sec) [ -26948.5290] [Alpha ][ 0.322503] . ( 184 sec) [ -26948.4957] [ 5803] [depth= 1] . ( 195 sec) [ -26946.7464] [Branch lengths ] . ( 198 sec) [ -26946.7351] [GTR parameters ] . ( 198 sec) [ -26946.4478] [Alpha ][ 0.314281] . ( 244 sec) [ -26945.9990] [Branch lengths ] . ( 381 sec) [ -26945.9451] [Branch lengths ] . ( 381 sec) [ -26945.9451] [Topology ] . ( 385 sec) [ -26945.3433] [Topology ] . ( 388 sec) [ -26945.0329] [Topology ] . ( 391 sec) [ -26944.7985] [Topology ] . ( 394 sec) [ -26945.2378] [Topology ] . Moving backward . ( 395 sec) [ -26944.7717] [Topology ] . ( 398 sec) [ -26944.7490] [Topology ] . ( 401 sec) [ -26944.9577] [Topology ] . Moving backward . ( 401 sec) [ -26944.5767] [Topology ] . ( 405 sec) [ -26944.5007] [Topology ] . ( 412 sec) [ -26944.4646] [GTR parameters ] . ( 413 sec) [ -26944.1745] [Alpha ][ 0.306120] . ( 413 sec) [ -26944.1745] [Topology ] . ( 416 sec) [ -26944.0685] [Topology ] . ( 419 sec) [ -26944.0359] [Topology ] . ( 422 sec) [ -26944.0245] [Topology ] . ( 426 sec) [ -26944.0204] [Topology ] . ( 429 sec) [ -26944.0189] [Topology ] . ( 432 sec) [ -26944.0183] [Topology ] . ( 436 sec) [ -26944.0133] [GTR parameters ] . ( 436 sec) [ -26943.9282] [Alpha ][ 0.301584] . ( 437 sec) [ -26943.9282] [Topology ] . ( 440 sec) [ -26943.8925] [Topology ] . ( 443 sec) [ -26943.8816] [Topology ] . ( 446 sec) [ -26943.8778] [Topology ] . ( 449 sec) [ -26943.8765] [Topology ] . ( 453 sec) [ -26943.8609] [Topology ] . ( 456 sec) [ -26943.7352] [Topology ] . ( 459 sec) [ -26943.7161] [Topology ] . ( 462 sec) [ -26943.7095] [Topology ] . ( 466 sec) [ -26943.7070] [Topology ] . ( 473 sec) [ -26943.7011] [GTR parameters ] . ( 473 sec) [ -26943.6562] [Alpha ][ 0.298310] . ( 474 sec) [ -26943.6562] [Topology ] . ( 477 sec) [ -26943.6370] [Topology ] . ( 480 sec) [ -26943.6313] [Topology ] . ( 483 sec) [ -26943.6293] [Topology ] . ( 487 sec) [ -26943.6286] [Topology ] . ( 489 sec) [ -26943.6281] [GTR parameters ] . ( 489 sec) [ -26943.6172] [Alpha ][ 0.296698] . ( 489 sec) [ -26943.6172] [Topology ] . ( 492 sec) [ -26943.6112] [Topology ] . ( 495 sec) [ -26943.6094] [Topology ] . ( 499 sec) [ -26943.6088] [Topology ] . ( 501 sec) [ -26943.6070] [GTR parameters ] . ( 501 sec) [ -26943.6036] [Alpha ][ 0.295789] . ( 501 sec) [ -26943.6036] [Topology ] . ( 504 sec) [ -26943.6013] [Topology ] . ( 508 sec) [ -26943.6005] [Topology ] . ( 511 sec) [ -26943.6003] [GTR parameters ] . ( 511 sec) [ -26943.5995] [Alpha ][ 0.295349] . ( 511 sec) [ -26943.5995] [Topology ] . ( 515 sec) [ -26943.5985] [Topology ] . ( 518 sec) [ -26943.5981] [Topology ] . ( 519 sec) [ -26943.5981] [GTR parameters ] . ( 519 sec) [ -26943.5978] [Alpha ][ 0.295054] . ( 519 sec) [ -26943.5978] [Topology ] . ( 522 sec) [ -26943.5974] [Topology ] . ( 524 sec) [ -26943.5973] [GTR parameters ] . ( 524 sec) [ -26943.5973] [Alpha ][ 0.295054] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26943.597286. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -29176.8561] [GTR parameters ] . ( 2 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 2 sec) [ -28718.2078] [Topology ] . ( 5 sec) [ -28358.1403] [Topology ] . ( 8 sec) [ -28287.7496] [Topology ] . ( 12 sec) [ -28272.6038] [Topology ] . ( 15 sec) [ -28264.6408] [Topology ] . ( 18 sec) [ -28262.2033] [Topology ] . ( 21 sec) [ -28260.6583] [Topology ] . ( 24 sec) [ -28260.9603] [Topology ] . Moving backward . ( 24 sec) [ -28257.1897] [Topology ] . ( 27 sec) [ -28256.3358] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -28255.2392] [Topology ] . ( 60 sec) [ -27042.7798] [GTR parameters ] . ( 61 sec) [ -26994.3318] [Alpha ][ 0.359977] . ( 61 sec) [ -26994.3318] [Topology ] . ( 64 sec) [ -26978.7021] [Topology ] . ( 67 sec) [ -26973.8576] [Topology ] . ( 70 sec) [ -26970.8549] [Topology ] . ( 74 sec) [ -26965.9230] [Topology ] . ( 77 sec) [ -26964.8842] [Topology ] . ( 80 sec) [ -26964.6376] [Topology ] . ( 83 sec) [ -26964.5529] [Topology ] . ( 86 sec) [ -26964.5265] [Topology ] . ( 89 sec) [ -26964.5174] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -26964.3230] [Topology ] . ( 122 sec) [ -26962.6025] [GTR parameters ] . ( 122 sec) [ -26958.2517] [Alpha ][ 0.325279] . ( 122 sec) [ -26958.2517] [Topology ] . ( 125 sec) [ -26956.9976] [Topology ] . ( 128 sec) [ -26956.5920] [Topology ] . ( 132 sec) [ -26956.4431] [Topology ] . ( 135 sec) [ -26956.3755] [Topology ] . ( 138 sec) [ -26955.4347] [Topology ] . ( 141 sec) [ -26955.3374] [Topology ] . ( 144 sec) [ -26955.3272] [Topology ] . ( 147 sec) [ -26955.3253] [Topology ] . ( 151 sec) [ -26955.3249] [Topology ] . Checking for NNIs, optimizing five branches... . ( 175 sec) [ -26955.2670] [Topology ] . ( 180 sec) [ -26955.1035] [GTR parameters ] . ( 180 sec) [ -26954.1330] [Alpha ][ 0.309800] . ( 180 sec) [ -26954.1330] [Topology ] . ( 184 sec) [ -26953.6506] [Topology ] . ( 187 sec) [ -26953.5250] [Topology ] . ( 190 sec) [ -26953.4835] [Topology ] . ( 193 sec) [ -26953.4690] [Topology ] . ( 196 sec) [ -26953.4637] [Topology ] . ( 199 sec) [ -26953.4617] [Topology ] . Checking for NNIs, optimizing five branches... . ( 227 sec) [ -26953.4424] [GTR parameters ] . ( 228 sec) [ -26953.1895] [Alpha ][ 0.302220] . ( 228 sec) [ -26953.1895] [Topology ] . ( 231 sec) [ -26953.0886] [Topology ] . ( 234 sec) [ -26953.0576] [Topology ] . ( 237 sec) [ -26953.0468] [Topology ] . ( 240 sec) [ -26953.0429] [Topology ] . ( 243 sec) [ -26953.0415] [Topology ] . ( 247 sec) [ -26953.0409] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -26953.0148] [Topology ] . ( 273 sec) [ -26953.0054] [GTR parameters ] . ( 273 sec) [ -26952.9089] [Alpha ][ 0.297401] . ( 273 sec) [ -26952.9089] [Topology ] . ( 277 sec) [ -26952.8427] [Topology ] . ( 280 sec) [ -26952.8242] [Topology ] . ( 283 sec) [ -26952.8180] [Topology ] . ( 286 sec) [ -26952.8158] [Topology ] . ( 289 sec) [ -26952.8150] [Topology ] . Checking for NNIs, optimizing five branches... . ( 317 sec) [ -26952.8136] [GTR parameters ] . ( 317 sec) [ -26952.7720] [Alpha ][ 0.294258] . ( 317 sec) [ -26952.7720] [Topology ] . ( 320 sec) [ -26952.7518] [Topology ] . ( 324 sec) [ -26952.7458] [Topology ] . ( 327 sec) [ -26952.7438] [Topology ] . ( 330 sec) [ -26952.7431] [Topology ] . Checking for NNIs, optimizing five branches... . ( 355 sec) [ -26952.7430] [GTR parameters ] . ( 355 sec) [ -26952.7312] [Alpha ][ 0.292591] . ( 355 sec) [ -26952.7312] [Topology ] . ( 358 sec) [ -26952.7242] [Topology ] . ( 361 sec) [ -26952.7221] [Topology ] . ( 365 sec) [ -26952.7214] [Topology ] . Checking for NNIs, optimizing five branches... . ( 393 sec) [ -26952.7198] [GTR parameters ] . ( 394 sec) [ -26952.7156] [Alpha ][ 0.291594] . ( 394 sec) [ -26952.7156] [Topology ] . ( 397 sec) [ -26952.7128] [Topology ] . ( 400 sec) [ -26952.7119] [Topology ] . Checking for NNIs, optimizing five branches... . ( 426 sec) [ -26952.7119] [GTR parameters ] . ( 426 sec) [ -26952.7109] [Alpha ][ 0.291108] . ( 426 sec) [ -26952.7109] [Topology ] . ( 429 sec) [ -26952.7096] [Topology ] . ( 432 sec) [ -26952.7092] [Topology ] . Checking for NNIs, optimizing five branches... . ( 458 sec) [ -26952.7091] [GTR parameters ] . ( 459 sec) [ -26952.7086] [Alpha ][ 0.290762] . ( 459 sec) [ -26952.7086] [Topology ] . ( 462 sec) [ -26952.7079] [Topology ] . Checking for NNIs, optimizing five branches... . ( 489 sec) [ -26952.7078] [GTR parameters ] . ( 490 sec) [ -26952.7078] [Alpha ][ 0.290471] . ( 490 sec) [ -26952.7078] [Topology ] . ( 493 sec) [ -26952.7072] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 545 sec) [ -29176.8561] [GTR parameters ] . ( 546 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 547 sec) [ -28715.8595] [ 5819] [depth= 1] . ( 548 sec) [ -28709.8159] [ 5824] [depth= 1] . ( 548 sec) [ -28697.5201] [ 5819] [depth= 1] . ( 549 sec) [ -28696.6045] [ 5823] [depth= 1] . ( 549 sec) [ -28683.6351] [ 5819] [depth= 1] . ( 550 sec) [ -28681.3289] [ 5822] [depth= 1] . ( 550 sec) [ -28679.2730] [ 5819] [depth= 1] . ( 550 sec) [ -28672.1645] [ 5820] [depth= 1] . ( 552 sec) [ -28670.8541] [ 5822] [depth= 1] . ( 552 sec) [ -28669.3735] [ 5824] [depth= 1] . ( 552 sec) [ -28667.7191] [ 5823] [depth= 1] . ( 553 sec) [ -28664.6733] [ 5818] [depth= 1] . ( 553 sec) [ -28658.0320] [ 5822] [depth= 1] . ( 553 sec) [ -28635.3083] [ 5811] [depth= 4] . ( 554 sec) [ -28627.6068] [ 5812] [depth= 1] . ( 554 sec) [ -28627.4745] [ 5811] [depth= 1] . ( 554 sec) [ -28624.7292] [ 5812] [depth= 1] . ( 555 sec) [ -28618.7177] [ 5809] [depth= 1] . ( 555 sec) [ -28618.1073] [ 5811] [depth= 1] . ( 556 sec) [ -28616.9607] [ 5809] [depth= 1] . ( 556 sec) [ -28608.6871] [ 5800] [depth= 1] . ( 556 sec) [ -28605.2953] [ 5801] [depth= 1] . ( 557 sec) [ -28603.7189] [ 5806] [depth= 1] . ( 557 sec) [ -28603.2967] [ 5805] [depth= 1] . ( 557 sec) [ -28596.6809] [ 5802] [depth= 1] . ( 558 sec) [ -28581.8849] [ 5812] [depth= 1] . ( 558 sec) [ -28556.9955] [ 5802] [depth= 1] . ( 559 sec) [ -28553.6707] [ 5805] [depth= 1] . ( 559 sec) [ -28550.7503] [ 5805] [depth= 1] . ( 560 sec) [ -28532.9785] [ 5811] [depth= 2] . ( 560 sec) [ -28505.2161] [ 5801] [depth= 2] . ( 560 sec) [ -28494.7125] [ 5801] [depth= 1] . ( 560 sec) [ -28493.8834] [ 5801] [depth= 1] . ( 560 sec) [ -28484.6717] [ 5800] [depth= 1] . ( 561 sec) [ -28481.3638] [ 5802] [depth= 1] . ( 561 sec) [ -28479.5954] [ 5800] [depth= 1] . ( 561 sec) [ -28475.0670] [ 5797] [depth= 2] . ( 562 sec) [ -28471.8349] [ 5798] [depth= 1] . ( 562 sec) [ -28471.0611] [ 5799] [depth= 2] . ( 562 sec) [ -28470.1203] [ 5801] [depth= 1] . ( 562 sec) [ -28465.6616] [ 5796] [depth= 1] . ( 563 sec) [ -28456.6326] [ 5803] [depth= 1] . ( 563 sec) [ -28454.4766] [ 5803] [depth= 1] . ( 563 sec) [ -28452.0039] [ 5805] [depth= 2] . ( 563 sec) [ -28450.9616] [ 5805] [depth= 1] . ( 564 sec) [ -28449.4810] [ 5805] [depth= 1] . ( 564 sec) [ -28448.4225] [ 5805] [depth= 1] . ( 565 sec) [ -28442.1678] [ 5798] [depth= 1] . ( 565 sec) [ -28441.6328] [ 5799] [depth= 1] . ( 566 sec) [ -28439.7610] [ 5797] [depth= 1] . ( 566 sec) [ -28436.0051] [ 5799] [depth= 1] . ( 567 sec) [ -28421.7718] [ 5791] [depth= 3] . ( 567 sec) [ -28418.4526] [ 5794] [depth= 1] . ( 567 sec) [ -28415.5810] [ 5791] [depth= 1] . ( 568 sec) [ -28414.3279] [ 5792] [depth= 1] . ( 568 sec) [ -28411.2934] [ 5791] [depth= 1] . ( 568 sec) [ -28408.9258] [ 5788] [depth= 2] . ( 569 sec) [ -28408.0051] [ 5790] [depth= 1] . ( 569 sec) [ -28405.2591] [ 5791] [depth= 1] . ( 569 sec) [ -28404.9784] [ 5791] [depth= 1] . ( 569 sec) [ -28404.3581] [ 5790] [depth= 2] . ( 570 sec) [ -28401.9181] [ 5788] [depth= 1] . ( 571 sec) [ -28401.4738] [ 5788] [depth= 1] . ( 572 sec) [ -28398.8514] [ 5786] [depth= 1] . ( 574 sec) [ -28395.7868] [ 5785] [depth= 1] . ( 576 sec) [ -28393.1605] [ 5784] [depth= 1] . ( 577 sec) [ -28391.5912] [ 5784] [depth= 1] . ( 580 sec) [ -28389.0516] [ 5784] [depth= 4] . ( 582 sec) [ -28385.4871] [ 5783] [depth= 1] . ( 593 sec) [ -28286.9092] [Branch lengths ] . ( 600 sec) [ -27076.2807] [GTR parameters ] . ( 601 sec) [ -27006.2899] [Alpha ][ 0.332427] . ( 604 sec) [ -27005.0990] [ 5785] [depth= 1] . ( 604 sec) [ -27004.5914] [ 5790] [depth= 1] . ( 607 sec) [ -27004.3819] [ 5788] [depth= 1] . ( 607 sec) [ -27003.5448] [ 5785] [depth= 1] . ( 608 sec) [ -26996.9663] [ 5784] [depth= 2] . ( 609 sec) [ -26996.4399] [ 5787] [depth= 1] . ( 610 sec) [ -26994.6504] [ 5788] [depth= 1] . ( 610 sec) [ -26992.4700] [ 5788] [depth= 1] . ( 613 sec) [ -26981.6455] [ 5790] [depth= 1] . ( 614 sec) [ -26981.0775] [ 5792] [depth= 1] . ( 614 sec) [ -26981.0141] [ 5790] [depth= 1] . ( 614 sec) [ -26980.5630] [ 5791] [depth= 1] . ( 615 sec) [ -26977.0447] [ 5793] [depth= 1] . ( 615 sec) [ -26976.5660] [ 5795] [depth= 1] . ( 618 sec) [ -26974.1025] [ 5798] [depth= 1] . ( 647 sec) [ -26954.7785] [Branch lengths ] . ( 652 sec) [ -26952.1491] [GTR parameters ] . ( 652 sec) [ -26951.4636] [Alpha ][ 0.319341] . ( 662 sec) [ -26948.4777] [ 5802] [depth= 3] . ( 699 sec) [ -26946.4044] [Branch lengths ] . ( 704 sec) [ -26946.3229] [GTR parameters ] . ( 704 sec) [ -26946.1128] [Alpha ][ 0.312384] . ( 751 sec) [ -26945.7659] [Branch lengths ] . ( 896 sec) [ -26945.7305] [Branch lengths ] . ( 896 sec) [ -26945.7305] [Topology ] . ( 899 sec) [ -26945.7283] [Topology ] . ( 903 sec) [ -26945.7277] [Topology ] . ( 907 sec) [ -26945.7225] [GTR parameters ] . ( 908 sec) [ -26945.5805] [Alpha ][ 0.306476] . ( 908 sec) [ -26945.5805] [Topology ] . ( 912 sec) [ -26945.5235] [Topology ] . ( 915 sec) [ -26945.5055] [Topology ] . ( 919 sec) [ -26945.4991] [Topology ] . ( 922 sec) [ -26945.4967] [Topology ] . ( 925 sec) [ -26945.4959] [Topology ] . ( 929 sec) [ -26945.4921] [GTR parameters ] . ( 929 sec) [ -26945.4538] [Alpha ][ 0.303429] . ( 929 sec) [ -26945.4538] [Topology ] . ( 933 sec) [ -26945.4361] [Topology ] . ( 936 sec) [ -26945.4305] [Topology ] . ( 939 sec) [ -26945.4285] [Topology ] . ( 943 sec) [ -26945.4277] [Topology ] . ( 947 sec) [ -26945.4266] [GTR parameters ] . ( 947 sec) [ -26945.4159] [Alpha ][ 0.301819] . ( 947 sec) [ -26945.4159] [Topology ] . ( 951 sec) [ -26945.4099] [Topology ] . ( 954 sec) [ -26945.4079] [Topology ] . ( 958 sec) [ -26945.4072] [Topology ] . ( 964 sec) [ -26945.4070] [GTR parameters ] . ( 965 sec) [ -26945.4041] [Alpha ][ 0.300970] . ( 965 sec) [ -26945.4041] [Topology ] . ( 968 sec) [ -26945.4018] [Topology ] . ( 972 sec) [ -26945.4011] [Topology ] . ( 973 sec) [ -26945.4010] [GTR parameters ] . ( 973 sec) [ -26945.4003] [Alpha ][ 0.300543] . ( 973 sec) [ -26945.4003] [Topology ] . ( 977 sec) [ -26945.3992] [Topology ] . ( 980 sec) [ -26945.3989] [Topology ] . ( 984 sec) [ -26945.3988] [GTR parameters ] . ( 984 sec) [ -26945.3985] [Alpha ][ 0.300242] . ( 984 sec) [ -26945.3985] [Topology ] . ( 987 sec) [ -26945.3980] [Topology ] . ( 990 sec) [ -26945.3978] [GTR parameters ] . ( 990 sec) [ -26945.3978] [Alpha ][ 0.300242] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -26952.707180 . Log likelihood obtained after SPR moves : -26945.397843 . Log likelihood of the current tree: -26945.397843. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Best log likelihood : -26943.433340 . Time used 0h16m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3705.45user 0.00system 1:02:19elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps