.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -47307.1212] [GTR parameters ] . ( 2 sec) [ -46089.0921] [Alpha ][ 0.500960] . ( 2 sec) [ -45896.9668] [10750] [depth= 7] . ( 2 sec) [ -45569.8356] [10652] [depth= 10] . ( 2 sec) [ -45399.8071] [10622] [depth= 6] . ( 3 sec) [ -45175.3987] [10542] [depth= 1] . ( 3 sec) [ -45049.0541] [10502] [depth= 11] . ( 3 sec) [ -45040.1856] [10478] [depth= 3] . ( 3 sec) [ -45022.3454] [10480] [depth= 1] . ( 3 sec) [ -44968.0838] [10463] [depth= 9] . ( 3 sec) [ -44632.7891] [10436] [depth= 2] . ( 3 sec) [ -44084.6260] [10356] [depth= 14] . ( 3 sec) [ -43823.1557] [10263] [depth= 6] . ( 4 sec) [ -43358.1701] [10180] [depth= 15] . ( 4 sec) [ -43020.4906] [10113] [depth= 5] . ( 4 sec) [ -42821.1977] [10038] [depth= 2] . ( 4 sec) [ -42645.0067] [ 9983] [depth= 1] . ( 4 sec) [ -42383.9191] [ 9891] [depth= 2] . ( 4 sec) [ -42159.6772] [ 9852] [depth= 6] . ( 4 sec) [ -42026.9967] [ 9831] [depth= 1] . ( 4 sec) [ -41633.9574] [ 9724] [depth= 6] . ( 4 sec) [ -41239.8853] [ 9673] [depth= 14] . ( 5 sec) [ -41113.3852] [ 9542] [depth= 14] . ( 5 sec) [ -40840.1249] [ 9535] [depth= 1] . ( 5 sec) [ -40711.9142] [ 9462] [depth= 13] . ( 5 sec) [ -40673.6670] [ 9449] [depth= 4] . ( 5 sec) [ -40486.8809] [ 9423] [depth= 1] . ( 5 sec) [ -40247.1966] [ 9295] [depth= 6] . ( 5 sec) [ -40087.4313] [ 9286] [depth= 1] . ( 5 sec) [ -39936.5036] [ 9252] [depth= 10] . ( 5 sec) [ -39913.7094] [ 9221] [depth= 12] . ( 6 sec) [ -39875.6049] [ 9213] [depth= 10] . ( 6 sec) [ -38984.8546] [ 9216] [depth= 11] . ( 6 sec) [ -38826.3499] [ 9201] [depth= 7] . ( 6 sec) [ -38665.7105] [ 9165] [depth= 1] . ( 6 sec) [ -38525.4395] [ 9123] [depth= 7] . ( 6 sec) [ -38321.7862] [ 9095] [depth= 11] . ( 6 sec) [ -38190.6825] [ 9031] [depth= 8] . ( 6 sec) [ -37933.9520] [ 8995] [depth= 4] . ( 6 sec) [ -36689.7313] [ 8990] [depth= 3] . ( 6 sec) [ -36687.0185] [ 8966] [depth= 2] . ( 7 sec) [ -36623.7009] [ 8906] [depth= 1] . ( 7 sec) [ -36258.7741] [ 8896] [depth= 6] . ( 7 sec) [ -36044.4734] [ 8979] [depth= 8] . ( 7 sec) [ -35981.9671] [ 8933] [depth= 4] . ( 7 sec) [ -35641.5135] [ 8852] [depth= 13] . ( 7 sec) [ -35202.1632] [ 8902] [depth= 5] . ( 7 sec) [ -34725.6852] [ 8878] [depth= 4] . ( 7 sec) [ -34414.5701] [ 8867] [depth= 1] . ( 7 sec) [ -34288.2322] [ 8836] [depth= 1] . ( 8 sec) [ -34032.6732] [ 8704] [depth= 13] . ( 8 sec) [ -33985.2963] [ 8707] [depth= 15] . ( 8 sec) [ -33631.7572] [ 8588] [depth= 14] . ( 8 sec) [ -33629.5166] [ 8594] [depth= 1] . ( 8 sec) [ -33362.5139] [ 8573] [depth= 5] . ( 8 sec) [ -33190.8468] [ 8497] [depth= 6] . ( 8 sec) [ -33117.7670] [ 8481] [depth= 1] . ( 8 sec) [ -32854.8373] [ 8367] [depth= 4] . ( 9 sec) [ -32777.1774] [ 8329] [depth= 1] . ( 9 sec) [ -32767.7610] [ 8329] [depth= 1] . ( 9 sec) [ -32643.9058] [ 8263] [depth= 6] . ( 9 sec) [ -32623.9016] [ 8245] [depth= 1] . ( 9 sec) [ -32423.6372] [ 8166] [depth= 8] . ( 9 sec) [ -32244.4035] [ 8115] [depth= 10] . ( 9 sec) [ -32184.4998] [ 8081] [depth= 12] . ( 9 sec) [ -32056.8153] [ 8046] [depth= 14] . ( 9 sec) [ -31816.7157] [ 8030] [depth= 4] . ( 9 sec) [ -31699.8457] [ 8030] [depth= 1] . ( 10 sec) [ -31679.8538] [ 8025] [depth= 1] . ( 10 sec) [ -31610.3562] [ 7980] [depth= 2] . ( 10 sec) [ -31466.2517] [ 7948] [depth= 2] . ( 10 sec) [ -31313.6371] [ 7920] [depth= 4] . ( 10 sec) [ -30698.4272] [ 7776] [depth= 14] . ( 10 sec) [ -30521.9210] [ 7710] [depth= 7] . ( 10 sec) [ -30315.0786] [ 7655] [depth= 2] . ( 10 sec) [ -30047.5755] [ 7561] [depth= 1] . ( 10 sec) [ -29822.7797] [ 7502] [depth= 7] . ( 11 sec) [ -29718.9938] [ 7482] [depth= 2] . ( 11 sec) [ -29395.4679] [ 7409] [depth= 4] . ( 11 sec) [ -29306.4529] [ 7368] [depth= 3] . ( 11 sec) [ -29294.4056] [ 7350] [depth= 5] . ( 11 sec) [ -29244.7799] [ 7331] [depth= 6] . ( 11 sec) [ -29154.1290] [ 7314] [depth= 1] . ( 11 sec) [ -28972.3365] [ 7311] [depth= 1] . ( 11 sec) [ -28875.2897] [ 7264] [depth= 13] . ( 11 sec) [ -28872.2588] [ 7275] [depth= 1] . ( 12 sec) [ -28798.6580] [ 7241] [depth= 1] . ( 12 sec) [ -28702.9804] [ 7197] [depth= 9] . ( 12 sec) [ -28620.6353] [ 7199] [depth= 2] . ( 12 sec) [ -28567.2947] [ 7165] [depth= 3] . ( 12 sec) [ -28494.3591] [ 7145] [depth= 5] . ( 12 sec) [ -28467.5866] [ 7144] [depth= 1] . ( 12 sec) [ -28409.3276] [ 7111] [depth= 1] . ( 12 sec) [ -28332.5042] [ 7088] [depth= 2] . ( 12 sec) [ -27818.4888] [ 6975] [depth= 10] . ( 12 sec) [ -27738.9593] [ 6917] [depth= 1] . ( 13 sec) [ -27737.9815] [ 6920] [depth= 1] . ( 13 sec) [ -27611.4781] [ 6903] [depth= 1] . ( 13 sec) [ -27539.8818] [ 6880] [depth= 2] . ( 13 sec) [ -27452.0990] [ 6882] [depth= 1] . ( 13 sec) [ -27440.5846] [ 6881] [depth= 1] . ( 13 sec) [ -27366.0540] [ 6835] [depth= 1] . ( 13 sec) [ -27254.5422] [ 6813] [depth= 6] . ( 13 sec) [ -27206.6791] [ 6770] [depth= 1] . ( 13 sec) [ -27056.7498] [ 6710] [depth= 8] . ( 14 sec) [ -27029.2711] [ 6683] [depth= 1] . ( 14 sec) [ -27021.0779] [ 6696] [depth= 1] . ( 14 sec) [ -26985.2535] [ 6683] [depth= 1] . ( 14 sec) [ -26798.3011] [ 6633] [depth= 1] . ( 14 sec) [ -26599.0332] [ 6582] [depth= 5] . ( 14 sec) [ -26591.3676] [ 6592] [depth= 1] . ( 14 sec) [ -26587.8882] [ 6584] [depth= 1] . ( 14 sec) [ -26541.4565] [ 6569] [depth= 2] . ( 14 sec) [ -26516.8622] [ 6564] [depth= 3] . ( 14 sec) [ -26505.9409] [ 6557] [depth= 1] . ( 14 sec) [ -26447.0279] [ 6529] [depth= 8] . ( 15 sec) [ -26441.8038] [ 6528] [depth= 1] . ( 15 sec) [ -26403.7458] [ 6517] [depth= 3] . ( 15 sec) [ -26392.8493] [ 6513] [depth= 1] . ( 15 sec) [ -26296.5891] [ 6464] [depth= 2] . ( 15 sec) [ -26262.9815] [ 6443] [depth= 3] . ( 15 sec) [ -26259.7386] [ 6447] [depth= 1] . ( 15 sec) [ -26230.0821] [ 6447] [depth= 5] . ( 16 sec) [ -26211.7650] [ 6452] [depth= 1] . ( 16 sec) [ -26193.5948] [ 6447] [depth= 1] . ( 17 sec) [ -25680.7563] [Branch lengths ] . ( 19 sec) [ -25468.2344] [GTR parameters ] . ( 19 sec) [ -25453.8726] [Alpha ][ 0.417598] . ( 19 sec) [ -25444.7887] [ 6449] [depth= 5] . ( 19 sec) [ -25411.2976] [ 6433] [depth= 4] . ( 20 sec) [ -25341.2972] [ 6400] [depth= 2] . ( 20 sec) [ -25340.3185] [ 6397] [depth= 1] . ( 20 sec) [ -25334.8101] [ 6393] [depth= 3] . ( 20 sec) [ -25331.2595] [ 6392] [depth= 2] . ( 20 sec) [ -25328.6248] [ 6391] [depth= 1] . ( 20 sec) [ -25290.7065] [ 6379] [depth= 1] . ( 21 sec) [ -25290.5610] [ 6382] [depth= 1] . ( 21 sec) [ -25284.4294] [ 6375] [depth= 1] . ( 21 sec) [ -25281.2848] [ 6373] [depth= 1] . ( 21 sec) [ -25281.1052] [ 6373] [depth= 1] . ( 22 sec) [ -25273.9995] [ 6361] [depth= 2] . ( 22 sec) [ -25261.4122] [ 6362] [depth= 1] . ( 22 sec) [ -25230.4206] [ 6346] [depth= 1] . ( 22 sec) [ -25226.2594] [ 6347] [depth= 1] . ( 23 sec) [ -25204.9308] [ 6324] [depth= 1] . ( 23 sec) [ -25204.5892] [ 6328] [depth= 1] . ( 24 sec) [ -25194.7843] [ 6322] [depth= 1] . ( 24 sec) [ -25191.3810] [ 6318] [depth= 1] . ( 25 sec) [ -25191.0491] [ 6321] [depth= 1] . ( 27 sec) [ -25190.1348] [ 6323] [depth= 1] . ( 27 sec) [ -25188.1447] [ 6321] [depth= 1] . ( 28 sec) [ -25187.3363] [ 6323] [depth= 1] . ( 29 sec) [ -25139.9122] [Branch lengths ] . ( 31 sec) [ -25135.1555] [GTR parameters ] . ( 31 sec) [ -25135.1521] [Alpha ][ 0.418731] . ( 31 sec) [ -25133.1905] [ 6315] [depth= 1] . ( 36 sec) [ -25132.7544] [ 6312] [depth= 1] . ( 41 sec) [ -25125.7177] [Branch lengths ] . ( 43 sec) [ -25125.2939] [GTR parameters ] . ( 43 sec) [ -25125.2930] [Alpha ][ 0.419296] . ( 54 sec) [ -25123.2999] [Branch lengths ] . ( 104 sec) [ -25123.2887] [ 6314] [depth= 1] . ( 114 sec) [ -25122.0591] [Branch lengths ] . ( 115 sec) [ -25121.7165] [GTR parameters ] . ( 115 sec) [ -25121.7165] [Alpha ][ 0.419296] . ( 175 sec) [ -25121.2915] [Branch lengths ] . ( 175 sec) [ -25121.2915] [Topology ] . ( 177 sec) [ -25121.2030] [Topology ] . ( 179 sec) [ -25121.1642] [Topology ] . ( 181 sec) [ -25121.1414] [Topology ] . ( 183 sec) [ -25121.1273] [Topology ] . ( 185 sec) [ -25121.1185] [Topology ] . ( 186 sec) [ -25121.1130] [Topology ] . ( 188 sec) [ -25120.9670] [GTR parameters ] . ( 188 sec) [ -25120.9669] [Alpha ][ 0.418876] . ( 188 sec) [ -25120.9669] [Topology ] . ( 190 sec) [ -25120.9216] [Topology ] . ( 192 sec) [ -25120.8970] [Topology ] . ( 193 sec) [ -25120.8818] [Topology ] . ( 195 sec) [ -25120.8721] [Topology ] . ( 197 sec) [ -25120.8659] [Topology ] . ( 199 sec) [ -25120.8620] [Topology ] . ( 200 sec) [ -25120.8333] [GTR parameters ] . ( 200 sec) [ -25120.8333] [Alpha ][ 0.418876] . ( 200 sec) [ -25120.8333] [Topology ] . ( 202 sec) [ -25120.8193] [Topology ] . ( 203 sec) [ -25120.8111] [Topology ] . ( 205 sec) [ -25120.8059] [Topology ] . ( 207 sec) [ -25120.8026] [Topology ] . ( 209 sec) [ -25120.8004] [Topology ] . ( 211 sec) [ -25120.7990] [Topology ] . ( 211 sec) [ -25120.7905] [GTR parameters ] . ( 212 sec) [ -25120.7905] [Alpha ][ 0.418876] . ( 212 sec) [ -25120.7905] [Topology ] . ( 213 sec) [ -25120.7860] [Topology ] . ( 215 sec) [ -25120.7833] [Topology ] . ( 217 sec) [ -25120.7816] [Topology ] . ( 219 sec) [ -25120.7805] [Topology ] . ( 221 sec) [ -25120.7797] [Topology ] . ( 221 sec) [ -25120.7774] [GTR parameters ] . ( 221 sec) [ -25120.7774] [Alpha ][ 0.418876] . ( 221 sec) [ -25120.7774] [Topology ] . ( 223 sec) [ -25120.7758] [Topology ] . ( 225 sec) [ -25120.7747] [Topology ] . ( 227 sec) [ -25120.7741] [Topology ] . ( 227 sec) [ -25120.7736] [GTR parameters ] . ( 228 sec) [ -25120.7736] [Alpha ][ 0.418876] . ( 228 sec) [ -25120.7736] [Topology ] . ( 229 sec) [ -25120.7727] [Topology ] . ( 230 sec) [ -25120.7727] [GTR parameters ] . ( 230 sec) [ -25120.7727] [Alpha ][ 0.418876] . Checking for NNIs, optimizing five branches... . ( 246 sec) [ -25119.8514] [Topology ] . Checking for NNIs, optimizing five branches... . ( 261 sec) [ -25119.1091] [Topology ] . Checking for NNIs, optimizing five branches... . ( 277 sec) [ -25118.0869] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25118.086867. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -46563.5339] [GTR parameters ] . ( 2 sec) [ -45383.2903] [Alpha ][ 0.500960] . ( 2 sec) [ -45359.4196] [10650] [depth= 10] . ( 2 sec) [ -45240.6730] [10612] [depth= 7] . ( 2 sec) [ -45058.3213] [10600] [depth= 1] . ( 2 sec) [ -44946.9944] [10565] [depth= 4] . ( 2 sec) [ -44727.8701] [10477] [depth= 1] . ( 3 sec) [ -44627.6170] [10446] [depth= 10] . ( 3 sec) [ -44284.9922] [10412] [depth= 4] . ( 3 sec) [ -44116.8427] [10370] [depth= 2] . ( 3 sec) [ -43921.1180] [10242] [depth= 7] . ( 3 sec) [ -43764.5603] [10215] [depth= 5] . ( 3 sec) [ -43508.1233] [10174] [depth= 3] . ( 3 sec) [ -43375.0771] [10136] [depth= 3] . ( 3 sec) [ -43073.9117] [10058] [depth= 12] . ( 3 sec) [ -43055.7739] [10012] [depth= 3] . ( 3 sec) [ -43027.0277] [10005] [depth= 2] . ( 3 sec) [ -42603.0846] [ 9965] [depth= 8] . ( 4 sec) [ -41062.3228] [ 9790] [depth= 11] . ( 4 sec) [ -40654.4861] [ 9794] [depth= 6] . ( 4 sec) [ -40637.3312] [ 9764] [depth= 1] . ( 4 sec) [ -40494.8729] [ 9729] [depth= 9] . ( 4 sec) [ -40427.1123] [ 9718] [depth= 2] . ( 4 sec) [ -40369.7616] [ 9626] [depth= 6] . ( 4 sec) [ -39443.5868] [ 9429] [depth= 19] . ( 4 sec) [ -39266.8987] [ 9357] [depth= 13] . ( 4 sec) [ -39116.7050] [ 9341] [depth= 2] . ( 5 sec) [ -38779.0641] [ 9355] [depth= 20] . ( 5 sec) [ -38498.6669] [ 9271] [depth= 5] . ( 5 sec) [ -38320.2126] [ 9265] [depth= 2] . ( 5 sec) [ -38030.2959] [ 9171] [depth= 12] . ( 5 sec) [ -37796.2206] [ 9146] [depth= 3] . ( 5 sec) [ -37768.8974] [ 9164] [depth= 1] . ( 5 sec) [ -37639.5300] [ 9079] [depth= 19] . ( 5 sec) [ -37294.6834] [ 9003] [depth= 12] . ( 5 sec) [ -37171.1859] [ 8930] [depth= 22] . ( 6 sec) [ -36936.0971] [ 8815] [depth= 12] . ( 6 sec) [ -36924.8163] [ 8804] [depth= 1] . ( 6 sec) [ -35919.5104] [ 8814] [depth= 5] . ( 6 sec) [ -35749.1238] [ 8780] [depth= 7] . ( 6 sec) [ -35703.0987] [ 8751] [depth= 1] . ( 6 sec) [ -35399.2616] [ 8678] [depth= 17] . ( 6 sec) [ -35384.7469] [ 8675] [depth= 1] . ( 6 sec) [ -35111.1840] [ 8622] [depth= 12] . ( 7 sec) [ -34262.7982] [ 8539] [depth= 10] . ( 7 sec) [ -34142.9542] [ 8523] [depth= 1] . ( 7 sec) [ -33940.3071] [ 8491] [depth= 4] . ( 7 sec) [ -33805.6210] [ 8440] [depth= 1] . ( 7 sec) [ -33685.5888] [ 8411] [depth= 8] . ( 7 sec) [ -33444.6585] [ 8383] [depth= 1] . ( 7 sec) [ -33038.0744] [ 8290] [depth= 7] . ( 7 sec) [ -32937.4988] [ 8236] [depth= 1] . ( 7 sec) [ -32807.4302] [ 8231] [depth= 2] . ( 8 sec) [ -32540.3529] [ 8131] [depth= 9] . ( 8 sec) [ -32476.9502] [ 8114] [depth= 9] . ( 8 sec) [ -32349.2598] [ 8081] [depth= 4] . ( 8 sec) [ -32338.8944] [ 8066] [depth= 2] . ( 8 sec) [ -32131.1791] [ 8066] [depth= 2] . ( 8 sec) [ -31963.9840] [ 8044] [depth= 5] . ( 8 sec) [ -31912.2597] [ 8005] [depth= 5] . ( 8 sec) [ -31805.3480] [ 7991] [depth= 9] . ( 8 sec) [ -31675.6388] [ 7968] [depth= 3] . ( 9 sec) [ -31672.4185] [ 7971] [depth= 1] . ( 9 sec) [ -31601.0231] [ 7916] [depth= 1] . ( 9 sec) [ -31388.3608] [ 7843] [depth= 14] . ( 9 sec) [ -31328.8536] [ 7814] [depth= 1] . ( 9 sec) [ -31282.1191] [ 7777] [depth= 3] . ( 9 sec) [ -31268.3590] [ 7756] [depth= 1] . ( 9 sec) [ -31034.4070] [ 7736] [depth= 11] . ( 9 sec) [ -31021.0390] [ 7736] [depth= 2] . ( 9 sec) [ -30912.8183] [ 7718] [depth= 12] . ( 10 sec) [ -30788.4106] [ 7685] [depth= 12] . ( 10 sec) [ -30768.2284] [ 7682] [depth= 1] . ( 10 sec) [ -30680.3029] [ 7657] [depth= 3] . ( 10 sec) [ -30679.2378] [ 7656] [depth= 1] . ( 10 sec) [ -30657.7481] [ 7658] [depth= 1] . ( 10 sec) [ -30444.4586] [ 7605] [depth= 3] . ( 10 sec) [ -30368.0767] [ 7608] [depth= 1] . ( 10 sec) [ -29747.4752] [ 7504] [depth= 5] . ( 11 sec) [ -29727.0730] [ 7523] [depth= 9] . ( 11 sec) [ -29535.7258] [ 7400] [depth= 6] . ( 11 sec) [ -29062.2878] [ 7308] [depth= 1] . ( 11 sec) [ -29000.6322] [ 7281] [depth= 1] . ( 11 sec) [ -28988.2544] [ 7274] [depth= 6] . ( 11 sec) [ -28893.7669] [ 7233] [depth= 10] . ( 11 sec) [ -28837.2360] [ 7229] [depth= 1] . ( 11 sec) [ -28806.9318] [ 7221] [depth= 1] . ( 11 sec) [ -28721.3880] [ 7223] [depth= 5] . ( 12 sec) [ -28699.8286] [ 7218] [depth= 1] . ( 12 sec) [ -28580.9376] [ 7133] [depth= 12] . ( 12 sec) [ -28529.8306] [ 7114] [depth= 4] . ( 12 sec) [ -28516.1077] [ 7155] [depth= 1] . ( 12 sec) [ -28498.5946] [ 7114] [depth= 1] . ( 12 sec) [ -28442.3441] [ 7115] [depth= 11] . ( 12 sec) [ -28425.5043] [ 7171] [depth= 1] . ( 12 sec) [ -28347.8847] [ 7132] [depth= 9] . ( 13 sec) [ -28317.3838] [ 7130] [depth= 1] . ( 13 sec) [ -28196.9248] [ 7094] [depth= 4] . ( 13 sec) [ -28174.3753] [ 7098] [depth= 2] . ( 13 sec) [ -28173.5610] [ 7096] [depth= 4] . ( 13 sec) [ -28082.1164] [ 7046] [depth= 3] . ( 13 sec) [ -28013.9387] [ 7038] [depth= 1] . ( 13 sec) [ -27954.8305] [ 6981] [depth= 1] . ( 13 sec) [ -27861.1953] [ 6951] [depth= 3] . ( 13 sec) [ -27833.3511] [ 6964] [depth= 6] . ( 13 sec) [ -27708.2134] [ 6957] [depth= 1] . ( 14 sec) [ -27687.0847] [ 6950] [depth= 5] . ( 14 sec) [ -27641.1404] [ 6948] [depth= 2] . ( 14 sec) [ -27594.5509] [ 6936] [depth= 2] . ( 14 sec) [ -27525.9224] [ 6912] [depth= 2] . ( 14 sec) [ -27493.2330] [ 6906] [depth= 1] . ( 14 sec) [ -27404.4518] [ 6876] [depth= 12] . ( 14 sec) [ -27364.8609] [ 6849] [depth= 2] . ( 14 sec) [ -27336.6135] [ 6816] [depth= 6] . ( 14 sec) [ -27261.5076] [ 6776] [depth= 8] . ( 15 sec) [ -27211.1383] [ 6764] [depth= 1] . ( 15 sec) [ -27205.4253] [ 6781] [depth= 1] . ( 15 sec) [ -27195.9734] [ 6722] [depth= 1] . ( 15 sec) [ -27110.5887] [ 6713] [depth= 5] . ( 15 sec) [ -27102.5470] [ 6714] [depth= 1] . ( 15 sec) [ -27069.2364] [ 6693] [depth= 4] . ( 16 sec) [ -27063.6838] [ 6699] [depth= 1] . ( 16 sec) [ -27032.5593] [ 6691] [depth= 1] . ( 16 sec) [ -26273.9551] [Branch lengths ] . ( 19 sec) [ -26076.0055] [GTR parameters ] . ( 19 sec) [ -26064.1149] [Alpha ][ 0.427315] . ( 19 sec) [ -26048.3097] [ 6671] [depth= 6] . ( 19 sec) [ -26043.4287] [ 6661] [depth= 1] . ( 20 sec) [ -26039.4818] [ 6681] [depth= 5] . ( 20 sec) [ -26035.5756] [ 6677] [depth= 3] . ( 20 sec) [ -25993.9808] [ 6640] [depth= 1] . ( 20 sec) [ -25944.4517] [ 6622] [depth= 10] . ( 20 sec) [ -25938.6272] [ 6621] [depth= 1] . ( 20 sec) [ -25866.8317] [ 6606] [depth= 13] . ( 20 sec) [ -25752.4884] [ 6521] [depth= 10] . ( 21 sec) [ -25750.4047] [ 6522] [depth= 1] . ( 22 sec) [ -25729.2387] [ 6491] [depth= 2] . ( 22 sec) [ -25656.3096] [ 6457] [depth= 4] . ( 22 sec) [ -25653.7396] [ 6455] [depth= 1] . ( 22 sec) [ -25617.6611] [ 6450] [depth= 1] . ( 22 sec) [ -25486.6808] [ 6390] [depth= 4] . ( 23 sec) [ -25481.3575] [ 6394] [depth= 1] . ( 23 sec) [ -25471.9029] [ 6382] [depth= 1] . ( 23 sec) [ -25454.8603] [ 6385] [depth= 2] . ( 24 sec) [ -25454.6454] [ 6386] [depth= 1] . ( 24 sec) [ -25452.9794] [ 6382] [depth= 1] . ( 24 sec) [ -25431.9289] [ 6374] [depth= 2] . ( 24 sec) [ -25404.4508] [ 6357] [depth= 1] . ( 24 sec) [ -25403.2871] [ 6354] [depth= 1] . ( 24 sec) [ -25400.7663] [ 6352] [depth= 1] . ( 25 sec) [ -25398.7579] [ 6351] [depth= 1] . ( 25 sec) [ -25397.8407] [ 6354] [depth= 1] . ( 25 sec) [ -25389.3771] [ 6348] [depth= 1] . ( 25 sec) [ -25372.5532] [ 6342] [depth= 4] . ( 26 sec) [ -25369.0302] [ 6346] [depth= 3] . ( 26 sec) [ -25332.3615] [ 6329] [depth= 1] . ( 26 sec) [ -25304.1720] [ 6308] [depth= 1] . ( 26 sec) [ -25302.3858] [ 6308] [depth= 1] . ( 27 sec) [ -25299.9589] [ 6322] [depth= 1] . ( 27 sec) [ -25283.0100] [ 6326] [depth= 1] . ( 27 sec) [ -25265.3733] [ 6322] [depth= 1] . ( 28 sec) [ -25264.1720] [ 6330] [depth= 1] . ( 28 sec) [ -25261.4134] [ 6339] [depth= 1] . ( 29 sec) [ -25261.2867] [ 6340] [depth= 1] . ( 29 sec) [ -25260.1831] [ 6339] [depth= 1] . ( 31 sec) [ -25190.9170] [Branch lengths ] . ( 32 sec) [ -25186.9824] [GTR parameters ] . ( 32 sec) [ -25186.8637] [Alpha ][ 0.420506] . ( 32 sec) [ -25186.0187] [ 6331] [depth= 1] . ( 33 sec) [ -25169.2312] [ 6322] [depth= 1] . ( 33 sec) [ -25168.6002] [ 6322] [depth= 1] . ( 34 sec) [ -25163.2276] [ 6318] [depth= 4] . ( 36 sec) [ -25163.1451] [ 6321] [depth= 1] . ( 38 sec) [ -25161.4187] [ 6317] [depth= 1] . ( 41 sec) [ -25141.0721] [Branch lengths ] . ( 43 sec) [ -25140.6084] [GTR parameters ] . ( 43 sec) [ -25140.6030] [Alpha ][ 0.418940] . ( 48 sec) [ -25140.5701] [ 6314] [depth= 1] . ( 49 sec) [ -25136.8051] [ 6317] [depth= 1] . ( 50 sec) [ -25136.7586] [ 6316] [depth= 1] . ( 52 sec) [ -25135.9438] [ 6319] [depth= 1] . ( 53 sec) [ -25128.2419] [Branch lengths ] . ( 54 sec) [ -25128.0930] [GTR parameters ] . ( 55 sec) [ -25128.0922] [Alpha ][ 0.418315] . ( 58 sec) [ -25128.0291] [ 6322] [depth= 1] . ( 65 sec) [ -25119.4486] [Branch lengths ] . ( 66 sec) [ -25119.4057] [GTR parameters ] . ( 66 sec) [ -25119.4057] [Alpha ][ 0.418315] . ( 76 sec) [ -25118.6425] [Branch lengths ] . ( 135 sec) [ -25118.5319] [Branch lengths ] . ( 135 sec) [ -25118.5319] [Topology ] . ( 137 sec) [ -25118.2279] [Topology ] . ( 139 sec) [ -25118.1065] [Topology ] . ( 141 sec) [ -25118.0836] [Topology ] . ( 142 sec) [ -25118.0761] [Topology ] . ( 144 sec) [ -25118.0729] [Topology ] . ( 146 sec) [ -25118.0712] [Topology ] . ( 148 sec) [ -25118.0702] [Topology ] . ( 149 sec) [ -25117.9942] [GTR parameters ] . ( 149 sec) [ -25117.9940] [Alpha ][ 0.418734] . ( 149 sec) [ -25117.9940] [Topology ] . ( 151 sec) [ -25117.9777] [Topology ] . ( 153 sec) [ -25117.9696] [Topology ] . ( 154 sec) [ -25117.9646] [Topology ] . ( 156 sec) [ -25117.9615] [Topology ] . ( 158 sec) [ -25117.9596] [Topology ] . ( 160 sec) [ -25117.9583] [Topology ] . ( 161 sec) [ -25117.9503] [GTR parameters ] . ( 161 sec) [ -25117.9503] [Alpha ][ 0.418734] . ( 161 sec) [ -25117.9503] [Topology ] . ( 163 sec) [ -25117.9462] [Topology ] . ( 164 sec) [ -25117.9438] [Topology ] . ( 166 sec) [ -25117.9423] [Topology ] . ( 168 sec) [ -25117.9413] [Topology ] . ( 169 sec) [ -25117.9398] [GTR parameters ] . ( 169 sec) [ -25117.9397] [Alpha ][ 0.418315] . ( 169 sec) [ -25117.9397] [Topology ] . ( 171 sec) [ -25117.9382] [Topology ] . ( 172 sec) [ -25117.9373] [Topology ] . ( 173 sec) [ -25117.9368] [GTR parameters ] . ( 173 sec) [ -25117.9368] [Alpha ][ 0.418315] . ( 173 sec) [ -25117.9368] [Topology ] . ( 175 sec) [ -25117.9358] [Topology ] . ( 175 sec) [ -25117.9358] [GTR parameters ] . ( 175 sec) [ -25117.9358] [Alpha ][ 0.418315] . ( 176 sec) [ -25117.9358] [Topology ] . ( 177 sec) [ -25117.9350] [Topology ] . ( 179 sec) [ -25117.9349] [GTR parameters ] . ( 179 sec) [ -25117.9349] [Alpha ][ 0.418315] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25117.934893. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -43992.1284] [GTR parameters ] . ( 2 sec) [ -42877.0825] [Alpha ][ 0.500960] . ( 2 sec) [ -42778.3642] [10341] [depth= 2] . ( 3 sec) [ -42617.8055] [10285] [depth= 11] . ( 3 sec) [ -42317.7698] [10233] [depth= 9] . ( 3 sec) [ -41946.3299] [10138] [depth= 1] . ( 3 sec) [ -41708.7015] [10115] [depth= 9] . ( 3 sec) [ -41533.2039] [10117] [depth= 3] . ( 3 sec) [ -41303.0433] [10078] [depth= 4] . ( 3 sec) [ -41181.9131] [10040] [depth= 1] . ( 3 sec) [ -41135.5010] [10015] [depth= 8] . ( 3 sec) [ -40882.1016] [ 9974] [depth= 2] . ( 3 sec) [ -40611.8611] [ 9948] [depth= 3] . ( 3 sec) [ -40475.0911] [ 9853] [depth= 5] . ( 4 sec) [ -40223.9142] [ 9843] [depth= 3] . ( 4 sec) [ -40097.6930] [ 9822] [depth= 4] . ( 4 sec) [ -40060.2903] [ 9804] [depth= 6] . ( 4 sec) [ -39425.3177] [ 9607] [depth= 3] . ( 4 sec) [ -39337.4672] [ 9604] [depth= 2] . ( 4 sec) [ -39302.2271] [ 9595] [depth= 1] . ( 4 sec) [ -39175.7895] [ 9531] [depth= 7] . ( 4 sec) [ -38972.0512] [ 9504] [depth= 1] . ( 4 sec) [ -38712.6852] [ 9412] [depth= 2] . ( 4 sec) [ -38490.3153] [ 9386] [depth= 1] . ( 4 sec) [ -38352.7447] [ 9392] [depth= 10] . ( 5 sec) [ -38031.4312] [ 9250] [depth= 11] . ( 5 sec) [ -37878.3547] [ 9241] [depth= 2] . ( 5 sec) [ -37750.3827] [ 9186] [depth= 2] . ( 5 sec) [ -37640.1253] [ 9145] [depth= 6] . ( 5 sec) [ -37458.6622] [ 9156] [depth= 1] . ( 5 sec) [ -37020.0259] [ 9008] [depth= 9] . ( 5 sec) [ -36878.1486] [ 8988] [depth= 1] . ( 5 sec) [ -36780.2113] [ 8961] [depth= 1] . ( 5 sec) [ -36665.1389] [ 8938] [depth= 1] . ( 6 sec) [ -36504.8289] [ 8918] [depth= 5] . ( 6 sec) [ -36438.1284] [ 8899] [depth= 5] . ( 6 sec) [ -35715.9750] [ 8872] [depth= 2] . ( 6 sec) [ -35578.1457] [ 8885] [depth= 1] . ( 6 sec) [ -35443.1326] [ 8863] [depth= 1] . ( 6 sec) [ -35055.3876] [ 8729] [depth= 19] . ( 6 sec) [ -34587.0569] [ 8595] [depth= 15] . ( 6 sec) [ -34148.2959] [ 8487] [depth= 16] . ( 6 sec) [ -34101.4176] [ 8493] [depth= 5] . ( 6 sec) [ -33805.2044] [ 8492] [depth= 2] . ( 7 sec) [ -33475.5731] [ 8437] [depth= 12] . ( 7 sec) [ -33390.9357] [ 8364] [depth= 1] . ( 7 sec) [ -33273.3801] [ 8351] [depth= 14] . ( 7 sec) [ -33186.1328] [ 8338] [depth= 15] . ( 7 sec) [ -32900.7315] [ 8250] [depth= 3] . ( 7 sec) [ -32733.3183] [ 8227] [depth= 12] . ( 7 sec) [ -32698.1874] [ 8225] [depth= 2] . ( 7 sec) [ -32590.7403] [ 8216] [depth= 2] . ( 8 sec) [ -32475.0886] [ 8178] [depth= 12] . ( 8 sec) [ -32326.7833] [ 8172] [depth= 2] . ( 8 sec) [ -32129.8051] [ 8104] [depth= 14] . ( 8 sec) [ -32125.8824] [ 8107] [depth= 1] . ( 8 sec) [ -32100.2731] [ 8094] [depth= 3] . ( 8 sec) [ -31912.0159] [ 8048] [depth= 1] . ( 8 sec) [ -31886.5176] [ 8030] [depth= 1] . ( 8 sec) [ -31877.4742] [ 8034] [depth= 1] . ( 8 sec) [ -31568.0074] [ 7934] [depth= 10] . ( 9 sec) [ -31559.3868] [ 7930] [depth= 1] . ( 9 sec) [ -31343.7061] [ 7912] [depth= 10] . ( 9 sec) [ -31324.1581] [ 7887] [depth= 1] . ( 9 sec) [ -31219.4604] [ 7846] [depth= 1] . ( 9 sec) [ -30911.3370] [ 7698] [depth= 7] . ( 9 sec) [ -30772.6983] [ 7667] [depth= 5] . ( 9 sec) [ -30697.1369] [ 7663] [depth= 8] . ( 9 sec) [ -30491.6657] [ 7580] [depth= 4] . ( 10 sec) [ -30359.2169] [ 7536] [depth= 3] . ( 10 sec) [ -30283.0874] [ 7532] [depth= 1] . ( 10 sec) [ -30090.9912] [ 7467] [depth= 3] . ( 10 sec) [ -29922.7024] [ 7410] [depth= 3] . ( 10 sec) [ -29920.1777] [ 7403] [depth= 1] . ( 10 sec) [ -29891.9618] [ 7383] [depth= 1] . ( 10 sec) [ -29814.2498] [ 7342] [depth= 2] . ( 10 sec) [ -29641.6282] [ 7321] [depth= 1] . ( 10 sec) [ -29573.8814] [ 7287] [depth= 11] . ( 11 sec) [ -29360.0820] [ 7148] [depth= 6] . ( 11 sec) [ -29297.8138] [ 7160] [depth= 2] . ( 11 sec) [ -29093.2492] [ 7065] [depth= 6] . ( 11 sec) [ -29085.6256] [ 7059] [depth= 1] . ( 11 sec) [ -29078.9270] [ 7077] [depth= 1] . ( 11 sec) [ -28935.8818] [ 7041] [depth= 4] . ( 11 sec) [ -28907.9999] [ 7033] [depth= 5] . ( 11 sec) [ -28860.6124] [ 7043] [depth= 1] . ( 12 sec) [ -28821.9066] [ 7051] [depth= 3] . ( 12 sec) [ -28697.4227] [ 7002] [depth= 3] . ( 12 sec) [ -28677.2887] [ 6995] [depth= 1] . ( 12 sec) [ -28500.0785] [ 6981] [depth= 2] . ( 12 sec) [ -28499.9928] [ 6981] [depth= 3] . ( 12 sec) [ -28457.9655] [ 6966] [depth= 4] . ( 13 sec) [ -28442.3269] [ 6966] [depth= 4] . ( 13 sec) [ -28437.0354] [ 6961] [depth= 2] . ( 13 sec) [ -28406.6587] [ 6950] [depth= 1] . ( 13 sec) [ -28346.9882] [ 6930] [depth= 3] . ( 13 sec) [ -28261.1931] [ 6879] [depth= 3] . ( 13 sec) [ -28202.9932] [ 6855] [depth= 1] . ( 13 sec) [ -27415.3186] [ 6809] [depth= 10] . ( 13 sec) [ -27377.0769] [ 6783] [depth= 10] . ( 13 sec) [ -27372.5351] [ 6786] [depth= 3] . ( 13 sec) [ -27280.8337] [ 6724] [depth= 2] . ( 14 sec) [ -27211.4829] [ 6709] [depth= 1] . ( 14 sec) [ -27210.0113] [ 6708] [depth= 2] . ( 14 sec) [ -27180.9028] [ 6704] [depth= 1] . ( 14 sec) [ -27175.8164] [ 6709] [depth= 2] . ( 14 sec) [ -27144.8563] [ 6671] [depth= 2] . ( 14 sec) [ -27144.7558] [ 6671] [depth= 1] . ( 14 sec) [ -27141.8499] [ 6671] [depth= 1] . ( 14 sec) [ -27037.2044] [ 6616] [depth= 9] . ( 14 sec) [ -26747.8357] [ 6619] [depth= 1] . ( 15 sec) [ -26696.9798] [ 6613] [depth= 1] . ( 15 sec) [ -26663.0331] [ 6581] [depth= 3] . ( 15 sec) [ -26649.0120] [ 6586] [depth= 1] . ( 15 sec) [ -26544.6764] [ 6546] [depth= 4] . ( 15 sec) [ -26542.8186] [ 6557] [depth= 1] . ( 15 sec) [ -26512.1265] [ 6546] [depth= 1] . ( 16 sec) [ -26493.5471] [ 6550] [depth= 1] . ( 16 sec) [ -25899.1681] [Branch lengths ] . ( 19 sec) [ -25722.4875] [GTR parameters ] . ( 19 sec) [ -25706.9156] [Alpha ][ 0.414656] . ( 19 sec) [ -25699.7077] [ 6541] [depth= 6] . ( 19 sec) [ -25687.8536] [ 6527] [depth= 1] . ( 19 sec) [ -25660.8175] [ 6523] [depth= 6] . ( 19 sec) [ -25643.1139] [ 6509] [depth= 4] . ( 20 sec) [ -25627.0690] [ 6494] [depth= 1] . ( 20 sec) [ -25582.7681] [ 6469] [depth= 1] . ( 20 sec) [ -25580.6065] [ 6466] [depth= 1] . ( 20 sec) [ -25520.3576] [ 6463] [depth= 11] . ( 20 sec) [ -25519.6066] [ 6464] [depth= 1] . ( 20 sec) [ -25479.9758] [ 6400] [depth= 3] . ( 21 sec) [ -25464.9456] [ 6398] [depth= 1] . ( 21 sec) [ -25463.8775] [ 6398] [depth= 1] . ( 21 sec) [ -25461.0166] [ 6398] [depth= 1] . ( 21 sec) [ -25459.0731] [ 6388] [depth= 4] . ( 22 sec) [ -25455.6897] [ 6393] [depth= 1] . ( 22 sec) [ -25447.2921] [ 6388] [depth= 1] . ( 23 sec) [ -25435.5068] [ 6387] [depth= 1] . ( 23 sec) [ -25357.1303] [ 6349] [depth= 2] . ( 23 sec) [ -25296.0665] [ 6359] [depth= 1] . ( 23 sec) [ -25295.7994] [ 6364] [depth= 1] . ( 23 sec) [ -25290.8946] [ 6361] [depth= 2] . ( 23 sec) [ -25267.9314] [ 6359] [depth= 1] . ( 24 sec) [ -25263.2984] [ 6351] [depth= 1] . ( 24 sec) [ -25262.9088] [ 6350] [depth= 2] . ( 24 sec) [ -25260.6752] [ 6346] [depth= 2] . ( 24 sec) [ -25260.3940] [ 6345] [depth= 1] . ( 25 sec) [ -25260.0119] [ 6350] [depth= 1] . ( 25 sec) [ -25253.2848] [ 6351] [depth= 1] . ( 25 sec) [ -25253.2207] [ 6354] [depth= 1] . ( 25 sec) [ -25243.1514] [ 6346] [depth= 2] . ( 25 sec) [ -25236.7613] [ 6341] [depth= 2] . ( 26 sec) [ -25236.6006] [ 6343] [depth= 2] . ( 26 sec) [ -25235.4406] [ 6335] [depth= 1] . ( 26 sec) [ -25232.8798] [ 6342] [depth= 1] . ( 27 sec) [ -25231.3618] [ 6335] [depth= 1] . ( 27 sec) [ -25227.7633] [ 6334] [depth= 1] . ( 28 sec) [ -25225.7485] [ 6335] [depth= 1] . ( 28 sec) [ -25224.8164] [ 6336] [depth= 2] . ( 30 sec) [ -25222.3775] [ 6335] [depth= 1] . ( 30 sec) [ -25175.1690] [Branch lengths ] . ( 32 sec) [ -25172.0691] [GTR parameters ] . ( 32 sec) [ -25172.0181] [Alpha ][ 0.419171] . ( 32 sec) [ -25169.9678] [ 6334] [depth= 2] . ( 33 sec) [ -25168.6998] [ 6330] [depth= 1] . ( 33 sec) [ -25164.7497] [ 6319] [depth= 3] . ( 34 sec) [ -25164.5592] [ 6324] [depth= 1] . ( 35 sec) [ -25162.6862] [ 6327] [depth= 2] . ( 37 sec) [ -25161.8232] [ 6329] [depth= 1] . ( 37 sec) [ -25161.2520] [ 6331] [depth= 1] . ( 38 sec) [ -25160.8810] [ 6329] [depth= 1] . ( 41 sec) [ -25160.0453] [ 6325] [depth= 1] . ( 43 sec) [ -25150.7906] [Branch lengths ] . ( 45 sec) [ -25150.3545] [GTR parameters ] . ( 45 sec) [ -25150.3523] [Alpha ][ 0.420075] . ( 46 sec) [ -25149.6444] [ 6328] [depth= 1] . ( 46 sec) [ -25149.5630] [ 6329] [depth= 1] . ( 48 sec) [ -25149.5421] [ 6328] [depth= 1] . ( 54 sec) [ -25149.4337] [ 6324] [depth= 2] . ( 57 sec) [ -25136.4562] [Branch lengths ] . ( 58 sec) [ -25136.1552] [GTR parameters ] . ( 59 sec) [ -25136.1544] [Alpha ][ 0.419476] . ( 70 sec) [ -25125.5303] [Branch lengths ] . ( 101 sec) [ -25125.3296] [ 6322] [depth= 2] . ( 130 sec) [ -25122.6262] [Branch lengths ] . ( 131 sec) [ -25122.4803] [GTR parameters ] . ( 131 sec) [ -25122.4781] [Alpha ][ 0.420385] . ( 191 sec) [ -25122.0208] [Branch lengths ] . ( 191 sec) [ -25122.0208] [Topology ] . ( 192 sec) [ -25120.4262] [Topology ] . ( 194 sec) [ -25118.6462] [Topology ] . ( 196 sec) [ -25118.2367] [Topology ] . ( 198 sec) [ -25118.1630] [Topology ] . ( 200 sec) [ -25118.1380] [Topology ] . ( 201 sec) [ -25118.1266] [Topology ] . ( 203 sec) [ -25118.1205] [Topology ] . ( 205 sec) [ -25118.1171] [Topology ] . ( 206 sec) [ -25118.0538] [GTR parameters ] . ( 206 sec) [ -25118.0474] [Alpha ][ 0.418698] . ( 206 sec) [ -25118.0474] [Topology ] . ( 208 sec) [ -25118.0300] [Topology ] . ( 210 sec) [ -25118.0211] [Topology ] . ( 211 sec) [ -25118.0157] [Topology ] . ( 213 sec) [ -25118.0123] [Topology ] . ( 215 sec) [ -25118.0101] [Topology ] . ( 217 sec) [ -25118.0088] [Topology ] . ( 218 sec) [ -25117.9959] [GTR parameters ] . ( 218 sec) [ -25117.9959] [Alpha ][ 0.418698] . ( 218 sec) [ -25117.9959] [Topology ] . ( 220 sec) [ -25117.9904] [Topology ] . ( 221 sec) [ -25117.9872] [Topology ] . ( 223 sec) [ -25117.9852] [Topology ] . ( 225 sec) [ -25117.9839] [Topology ] . ( 227 sec) [ -25117.9831] [Topology ] . ( 227 sec) [ -25117.9803] [GTR parameters ] . ( 227 sec) [ -25117.9803] [Alpha ][ 0.418279] . ( 228 sec) [ -25117.9803] [Topology ] . ( 229 sec) [ -25117.9785] [Topology ] . ( 231 sec) [ -25117.9775] [Topology ] . ( 233 sec) [ -25117.9768] [Topology ] . ( 233 sec) [ -25117.9760] [GTR parameters ] . ( 234 sec) [ -25117.9760] [Alpha ][ 0.418279] . ( 234 sec) [ -25117.9760] [Topology ] . ( 235 sec) [ -25117.9751] [Topology ] . ( 236 sec) [ -25117.9750] [GTR parameters ] . ( 236 sec) [ -25117.9750] [Alpha ][ 0.418279] . ( 236 sec) [ -25117.9750] [Topology ] . ( 238 sec) [ -25117.9742] [Topology ] . ( 238 sec) [ -25117.9742] [GTR parameters ] . ( 239 sec) [ -25117.9742] [Alpha ][ 0.418279] . Checking for NNIs, optimizing five branches... . ( 254 sec) [ -25117.9340] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25117.933959. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -45803.3629] [GTR parameters ] . ( 2 sec) [ -44598.9895] [Alpha ][ 0.500960] . ( 2 sec) [ -44390.6855] [10711] [depth= 8] . ( 2 sec) [ -44152.4415] [10649] [depth= 7] . ( 2 sec) [ -44034.0953] [10624] [depth= 2] . ( 2 sec) [ -43933.5288] [10577] [depth= 8] . ( 2 sec) [ -43773.3615] [10506] [depth= 2] . ( 2 sec) [ -43575.1850] [10479] [depth= 12] . ( 2 sec) [ -43424.2627] [10457] [depth= 3] . ( 3 sec) [ -43355.3736] [10433] [depth= 4] . ( 3 sec) [ -43162.0245] [10361] [depth= 1] . ( 3 sec) [ -43149.4338] [10364] [depth= 1] . ( 3 sec) [ -43133.7916] [10348] [depth= 6] . ( 3 sec) [ -42970.0448] [10334] [depth= 3] . ( 3 sec) [ -42951.0654] [10326] [depth= 1] . ( 3 sec) [ -42871.1857] [10326] [depth= 4] . ( 3 sec) [ -42810.9319] [10294] [depth= 1] . ( 3 sec) [ -42583.2844] [10297] [depth= 2] . ( 3 sec) [ -41701.5541] [10210] [depth= 5] . ( 4 sec) [ -41034.4525] [10177] [depth= 6] . ( 4 sec) [ -40927.4223] [10128] [depth= 1] . ( 4 sec) [ -40852.1630] [10108] [depth= 4] . ( 4 sec) [ -40803.1355] [10100] [depth= 1] . ( 4 sec) [ -40671.1748] [10101] [depth= 4] . ( 4 sec) [ -40659.9840] [10128] [depth= 1] . ( 4 sec) [ -40420.0217] [10100] [depth= 6] . ( 4 sec) [ -38974.9465] [ 9944] [depth= 15] . ( 4 sec) [ -38872.6053] [ 9906] [depth= 1] . ( 4 sec) [ -38427.1989] [ 9817] [depth= 7] . ( 5 sec) [ -38195.1142] [ 9759] [depth= 8] . ( 5 sec) [ -38119.7820] [ 9723] [depth= 15] . ( 5 sec) [ -37953.9446] [ 9705] [depth= 8] . ( 5 sec) [ -37734.9965] [ 9680] [depth= 2] . ( 5 sec) [ -37328.4835] [ 9567] [depth= 3] . ( 5 sec) [ -37208.1792] [ 9560] [depth= 1] . ( 5 sec) [ -37070.8302] [ 9552] [depth= 4] . ( 5 sec) [ -36744.5564] [ 9412] [depth= 4] . ( 5 sec) [ -36703.9892] [ 9397] [depth= 6] . ( 5 sec) [ -36594.5302] [ 9323] [depth= 2] . ( 5 sec) [ -36423.0424] [ 9261] [depth= 13] . ( 6 sec) [ -36357.1696] [ 9245] [depth= 1] . ( 6 sec) [ -36054.8676] [ 9201] [depth= 12] . ( 6 sec) [ -36042.2106] [ 9236] [depth= 1] . ( 6 sec) [ -35786.0881] [ 9137] [depth= 2] . ( 6 sec) [ -35619.9982] [ 9129] [depth= 16] . ( 6 sec) [ -35532.1773] [ 9077] [depth= 1] . ( 6 sec) [ -35391.8561] [ 9055] [depth= 6] . ( 6 sec) [ -34729.9129] [ 8809] [depth= 11] . ( 6 sec) [ -34693.3879] [ 8816] [depth= 1] . ( 7 sec) [ -34666.2780] [ 8802] [depth= 1] . ( 7 sec) [ -34498.6259] [ 8770] [depth= 11] . ( 7 sec) [ -34356.3908] [ 8734] [depth= 6] . ( 7 sec) [ -34281.7310] [ 8719] [depth= 1] . ( 7 sec) [ -34262.0946] [ 8695] [depth= 4] . ( 7 sec) [ -33784.6369] [ 8666] [depth= 11] . ( 7 sec) [ -33587.5538] [ 8569] [depth= 17] . ( 7 sec) [ -33068.0636] [ 8448] [depth= 16] . ( 8 sec) [ -33008.5216] [ 8431] [depth= 1] . ( 8 sec) [ -32924.9549] [ 8367] [depth= 1] . ( 8 sec) [ -32811.2486] [ 8355] [depth= 4] . ( 8 sec) [ -32685.1390] [ 8325] [depth= 6] . ( 8 sec) [ -32579.2664] [ 8313] [depth= 3] . ( 8 sec) [ -32575.2404] [ 8311] [depth= 2] . ( 8 sec) [ -32516.0725] [ 8268] [depth= 10] . ( 8 sec) [ -32367.6489] [ 8262] [depth= 1] . ( 8 sec) [ -32162.3456] [ 8229] [depth= 8] . ( 8 sec) [ -31933.3007] [ 8153] [depth= 9] . ( 9 sec) [ -31772.0410] [ 8099] [depth= 1] . ( 9 sec) [ -31357.7795] [ 7927] [depth= 13] . ( 9 sec) [ -31245.4438] [ 7895] [depth= 1] . ( 9 sec) [ -31238.4793] [ 7910] [depth= 1] . ( 9 sec) [ -30660.2351] [ 7718] [depth= 18] . ( 9 sec) [ -30567.8628] [ 7647] [depth= 14] . ( 9 sec) [ -30274.7545] [ 7626] [depth= 1] . ( 9 sec) [ -29838.3729] [ 7505] [depth= 5] . ( 9 sec) [ -29779.5422] [ 7492] [depth= 1] . ( 9 sec) [ -29721.3485] [ 7495] [depth= 1] . ( 10 sec) [ -29630.7730] [ 7434] [depth= 1] . ( 10 sec) [ -29429.0887] [ 7345] [depth= 7] . ( 10 sec) [ -29406.9100] [ 7345] [depth= 1] . ( 10 sec) [ -29240.6297] [ 7261] [depth= 12] . ( 10 sec) [ -29227.2506] [ 7259] [depth= 2] . ( 10 sec) [ -29137.0309] [ 7243] [depth= 2] . ( 10 sec) [ -29070.4499] [ 7240] [depth= 4] . ( 11 sec) [ -29002.0312] [ 7229] [depth= 2] . ( 11 sec) [ -28928.7377] [ 7208] [depth= 1] . ( 11 sec) [ -28920.3917] [ 7202] [depth= 1] . ( 11 sec) [ -28874.6795] [ 7186] [depth= 1] . ( 11 sec) [ -28869.8410] [ 7182] [depth= 1] . ( 11 sec) [ -28848.0783] [ 7172] [depth= 1] . ( 11 sec) [ -28716.2838] [ 7152] [depth= 4] . ( 11 sec) [ -28687.8371] [ 7149] [depth= 1] . ( 11 sec) [ -28605.8563] [ 7137] [depth= 8] . ( 11 sec) [ -28452.1845] [ 7070] [depth= 3] . ( 12 sec) [ -28427.8245] [ 7078] [depth= 5] . ( 12 sec) [ -28365.8407] [ 7067] [depth= 2] . ( 12 sec) [ -28332.2172] [ 7096] [depth= 2] . ( 12 sec) [ -28271.2719] [ 7055] [depth= 1] . ( 12 sec) [ -28196.4633] [ 7017] [depth= 6] . ( 12 sec) [ -28105.4343] [ 7012] [depth= 1] . ( 12 sec) [ -28093.0734] [ 7010] [depth= 1] . ( 13 sec) [ -28076.9449] [ 7014] [depth= 3] . ( 13 sec) [ -27993.5877] [ 7018] [depth= 1] . ( 13 sec) [ -27931.5379] [ 7002] [depth= 2] . ( 13 sec) [ -27785.7185] [ 7032] [depth= 3] . ( 13 sec) [ -27511.7800] [ 6870] [depth= 7] . ( 13 sec) [ -27489.2356] [ 6865] [depth= 1] . ( 13 sec) [ -27473.8700] [ 6844] [depth= 8] . ( 13 sec) [ -27431.1991] [ 6833] [depth= 1] . ( 13 sec) [ -27180.0808] [ 6790] [depth= 5] . ( 14 sec) [ -27148.3999] [ 6765] [depth= 15] . ( 14 sec) [ -26987.7929] [ 6645] [depth= 9] . ( 14 sec) [ -26944.3875] [ 6632] [depth= 1] . ( 14 sec) [ -26813.1728] [ 6595] [depth= 11] . ( 14 sec) [ -26769.3762] [ 6555] [depth= 4] . ( 14 sec) [ -26762.3448] [ 6554] [depth= 1] . ( 15 sec) [ -26738.5595] [ 6541] [depth= 2] . ( 15 sec) [ -26678.2738] [ 6530] [depth= 8] . ( 15 sec) [ -26673.0484] [ 6533] [depth= 1] . ( 15 sec) [ -26667.4426] [ 6538] [depth= 1] . ( 15 sec) [ -26643.8593] [ 6517] [depth= 7] . ( 15 sec) [ -26612.2087] [ 6514] [depth= 2] . ( 15 sec) [ -26610.7356] [ 6536] [depth= 3] . ( 16 sec) [ -26605.9763] [ 6539] [depth= 1] . ( 16 sec) [ -25909.2326] [Branch lengths ] . ( 18 sec) [ -25711.2531] [GTR parameters ] . ( 18 sec) [ -25698.0259] [Alpha ][ 0.421857] . ( 18 sec) [ -25690.7598] [ 6520] [depth= 9] . ( 18 sec) [ -25611.3445] [ 6490] [depth= 3] . ( 19 sec) [ -25521.3932] [ 6446] [depth= 3] . ( 19 sec) [ -25476.3855] [ 6407] [depth= 4] . ( 19 sec) [ -25452.7529] [ 6386] [depth= 1] . ( 19 sec) [ -25443.6785] [ 6383] [depth= 1] . ( 19 sec) [ -25439.7339] [ 6380] [depth= 1] . ( 19 sec) [ -25434.3199] [ 6376] [depth= 3] . ( 20 sec) [ -25430.3978] [ 6379] [depth= 1] . ( 20 sec) [ -25326.8141] [ 6344] [depth= 3] . ( 20 sec) [ -25326.2014] [ 6346] [depth= 1] . ( 20 sec) [ -25312.5536] [ 6345] [depth= 1] . ( 21 sec) [ -25301.1146] [ 6344] [depth= 2] . ( 21 sec) [ -25289.2105] [ 6340] [depth= 1] . ( 22 sec) [ -25286.4484] [ 6347] [depth= 1] . ( 22 sec) [ -25256.8168] [ 6337] [depth= 1] . ( 23 sec) [ -25254.5069] [ 6343] [depth= 1] . ( 23 sec) [ -25252.1061] [ 6337] [depth= 1] . ( 23 sec) [ -25248.8995] [ 6337] [depth= 1] . ( 24 sec) [ -25248.6495] [ 6340] [depth= 1] . ( 24 sec) [ -25248.0684] [ 6335] [depth= 1] . ( 24 sec) [ -25243.8130] [ 6327] [depth= 2] . ( 25 sec) [ -25228.4788] [ 6320] [depth= 2] . ( 25 sec) [ -25227.8702] [ 6318] [depth= 1] . ( 26 sec) [ -25227.7844] [ 6321] [depth= 1] . ( 26 sec) [ -25221.4448] [ 6321] [depth= 1] . ( 28 sec) [ -25220.4719] [ 6317] [depth= 1] . ( 29 sec) [ -25144.1337] [Branch lengths ] . ( 31 sec) [ -25141.2637] [GTR parameters ] . ( 31 sec) [ -25141.2328] [Alpha ][ 0.418160] . ( 31 sec) [ -25132.3178] [ 6314] [depth= 1] . ( 38 sec) [ -25132.0303] [ 6317] [depth= 1] . ( 42 sec) [ -25123.5275] [Branch lengths ] . ( 43 sec) [ -25123.1106] [GTR parameters ] . ( 43 sec) [ -25123.1106] [Alpha ][ 0.418160] . ( 49 sec) [ -25122.7017] [ 6320] [depth= 1] . ( 54 sec) [ -25119.8383] [Branch lengths ] . ( 55 sec) [ -25119.6686] [GTR parameters ] . ( 55 sec) [ -25119.6684] [Alpha ][ 0.418578] . ( 65 sec) [ -25118.7907] [Branch lengths ] . ( 125 sec) [ -25118.5272] [Branch lengths ] . ( 125 sec) [ -25118.5272] [Topology ] . ( 127 sec) [ -25118.4853] [Topology ] . ( 128 sec) [ -25118.4682] [Topology ] . ( 130 sec) [ -25118.4583] [Topology ] . ( 132 sec) [ -25118.4523] [Topology ] . ( 134 sec) [ -25118.4486] [Topology ] . ( 136 sec) [ -25118.4463] [Topology ] . ( 137 sec) [ -25118.1810] [GTR parameters ] . ( 137 sec) [ -25118.1808] [Alpha ][ 0.418997] . ( 137 sec) [ -25118.1808] [Topology ] . ( 139 sec) [ -25118.1182] [Topology ] . ( 141 sec) [ -25118.0858] [Topology ] . ( 142 sec) [ -25118.0663] [Topology ] . ( 144 sec) [ -25118.0541] [Topology ] . ( 146 sec) [ -25118.0465] [Topology ] . ( 148 sec) [ -25118.0417] [Topology ] . ( 149 sec) [ -25118.0064] [GTR parameters ] . ( 149 sec) [ -25118.0061] [Alpha ][ 0.418578] . ( 149 sec) [ -25118.0061] [Topology ] . ( 151 sec) [ -25117.9889] [Topology ] . ( 153 sec) [ -25117.9790] [Topology ] . ( 154 sec) [ -25117.9729] [Topology ] . ( 156 sec) [ -25117.9690] [Topology ] . ( 158 sec) [ -25117.9666] [Topology ] . ( 160 sec) [ -25117.9650] [Topology ] . ( 160 sec) [ -25117.9550] [GTR parameters ] . ( 160 sec) [ -25117.9550] [Alpha ][ 0.418578] . ( 160 sec) [ -25117.9550] [Topology ] . ( 162 sec) [ -25117.9499] [Topology ] . ( 164 sec) [ -25117.9469] [Topology ] . ( 166 sec) [ -25117.9450] [Topology ] . ( 168 sec) [ -25117.9438] [Topology ] . ( 170 sec) [ -25117.9430] [Topology ] . ( 170 sec) [ -25117.9403] [GTR parameters ] . ( 170 sec) [ -25117.9403] [Alpha ][ 0.418578] . ( 170 sec) [ -25117.9403] [Topology ] . ( 172 sec) [ -25117.9386] [Topology ] . ( 174 sec) [ -25117.9376] [Topology ] . ( 176 sec) [ -25117.9369] [Topology ] . ( 176 sec) [ -25117.9363] [GTR parameters ] . ( 176 sec) [ -25117.9363] [Alpha ][ 0.418578] . ( 176 sec) [ -25117.9363] [Topology ] . ( 178 sec) [ -25117.9354] [Topology ] . ( 179 sec) [ -25117.9354] [GTR parameters ] . ( 179 sec) [ -25117.9354] [Alpha ][ 0.418578] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25117.935369. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -46599.1940] [GTR parameters ] . ( 2 sec) [ -45432.1104] [Alpha ][ 0.500960] . ( 2 sec) [ -45254.3101] [10605] [depth= 11] . ( 2 sec) [ -44096.3864] [10481] [depth= 11] . ( 2 sec) [ -43847.4476] [10428] [depth= 3] . ( 2 sec) [ -43687.8562] [10414] [depth= 8] . ( 3 sec) [ -43552.6276] [10326] [depth= 2] . ( 3 sec) [ -43442.4515] [10306] [depth= 4] . ( 3 sec) [ -43026.8360] [10234] [depth= 6] . ( 3 sec) [ -42845.0982] [10163] [depth= 1] . ( 3 sec) [ -42708.5348] [10154] [depth= 3] . ( 3 sec) [ -42681.1813] [10149] [depth= 1] . ( 3 sec) [ -42664.8073] [10148] [depth= 2] . ( 3 sec) [ -42467.0964] [10075] [depth= 7] . ( 3 sec) [ -42458.2394] [10072] [depth= 1] . ( 3 sec) [ -42452.4113] [10060] [depth= 1] . ( 4 sec) [ -42435.6819] [10059] [depth= 1] . ( 4 sec) [ -42414.5246] [10055] [depth= 1] . ( 4 sec) [ -42376.9812] [10024] [depth= 4] . ( 4 sec) [ -42276.1444] [ 9977] [depth= 3] . ( 4 sec) [ -42102.7129] [ 9883] [depth= 5] . ( 4 sec) [ -42048.9574] [ 9858] [depth= 2] . ( 4 sec) [ -41878.4202] [ 9844] [depth= 1] . ( 4 sec) [ -41695.9029] [ 9753] [depth= 5] . ( 4 sec) [ -41494.5264] [ 9701] [depth= 2] . ( 4 sec) [ -41070.6847] [ 9597] [depth= 1] . ( 4 sec) [ -40823.2690] [ 9510] [depth= 6] . ( 5 sec) [ -40462.8778] [ 9422] [depth= 3] . ( 5 sec) [ -40278.5662] [ 9386] [depth= 2] . ( 5 sec) [ -40076.1687] [ 9263] [depth= 9] . ( 5 sec) [ -39688.8783] [ 9249] [depth= 3] . ( 5 sec) [ -39324.2463] [ 9090] [depth= 12] . ( 5 sec) [ -39276.9056] [ 9083] [depth= 1] . ( 5 sec) [ -38426.2532] [ 9051] [depth= 1] . ( 5 sec) [ -37719.9612] [ 9003] [depth= 16] . ( 6 sec) [ -37115.2793] [ 8899] [depth= 5] . ( 6 sec) [ -36987.2897] [ 8860] [depth= 5] . ( 6 sec) [ -36876.3948] [ 8852] [depth= 1] . ( 6 sec) [ -36655.2641] [ 8817] [depth= 3] . ( 6 sec) [ -36645.7736] [ 8803] [depth= 1] . ( 6 sec) [ -36542.2844] [ 8755] [depth= 12] . ( 6 sec) [ -36515.3010] [ 8733] [depth= 1] . ( 6 sec) [ -36334.4422] [ 8682] [depth= 10] . ( 6 sec) [ -35999.6846] [ 8600] [depth= 14] . ( 7 sec) [ -35713.0488] [ 8507] [depth= 3] . ( 7 sec) [ -35033.0169] [ 8369] [depth= 10] . ( 7 sec) [ -34742.1763] [ 8339] [depth= 15] . ( 7 sec) [ -34481.0833] [ 8291] [depth= 7] . ( 7 sec) [ -34350.5300] [ 8185] [depth= 7] . ( 7 sec) [ -34346.5877] [ 8187] [depth= 1] . ( 7 sec) [ -34345.5091] [ 8192] [depth= 1] . ( 7 sec) [ -34251.6258] [ 8153] [depth= 13] . ( 8 sec) [ -34239.7745] [ 8147] [depth= 1] . ( 8 sec) [ -33842.4667] [ 8106] [depth= 1] . ( 8 sec) [ -33690.5947] [ 8103] [depth= 2] . ( 8 sec) [ -33591.9581] [ 8091] [depth= 1] . ( 8 sec) [ -33573.0979] [ 8087] [depth= 1] . ( 8 sec) [ -33571.0400] [ 8091] [depth= 1] . ( 8 sec) [ -33304.5220] [ 8087] [depth= 8] . ( 8 sec) [ -33265.5197] [ 8067] [depth= 2] . ( 8 sec) [ -33257.5471] [ 8059] [depth= 1] . ( 9 sec) [ -33163.4094] [ 8027] [depth= 5] . ( 9 sec) [ -32852.9506] [ 8013] [depth= 15] . ( 9 sec) [ -31944.1473] [ 7893] [depth= 14] . ( 9 sec) [ -31928.3567] [ 7892] [depth= 1] . ( 9 sec) [ -31747.7669] [ 7848] [depth= 1] . ( 9 sec) [ -31559.7490] [ 7820] [depth= 7] . ( 9 sec) [ -31428.6278] [ 7804] [depth= 2] . ( 9 sec) [ -30884.9158] [ 7754] [depth= 9] . ( 10 sec) [ -30837.7713] [ 7750] [depth= 1] . ( 10 sec) [ -30589.1352] [ 7737] [depth= 6] . ( 10 sec) [ -30349.7834] [ 7639] [depth= 9] . ( 10 sec) [ -29870.5740] [ 7467] [depth= 7] . ( 10 sec) [ -29800.7459] [ 7412] [depth= 1] . ( 10 sec) [ -29749.3067] [ 7406] [depth= 1] . ( 10 sec) [ -29698.8473] [ 7363] [depth= 3] . ( 10 sec) [ -29479.9818] [ 7366] [depth= 3] . ( 10 sec) [ -29205.3411] [ 7237] [depth= 2] . ( 11 sec) [ -28908.8083] [ 7188] [depth= 1] . ( 11 sec) [ -28783.0359] [ 7160] [depth= 2] . ( 11 sec) [ -28494.0570] [ 7043] [depth= 5] . ( 11 sec) [ -28377.8312] [ 7031] [depth= 3] . ( 11 sec) [ -28315.3475] [ 7021] [depth= 3] . ( 11 sec) [ -28063.1971] [ 7016] [depth= 6] . ( 11 sec) [ -27955.9942] [ 6970] [depth= 1] . ( 11 sec) [ -27859.2386] [ 6916] [depth= 6] . ( 11 sec) [ -27827.1176] [ 6901] [depth= 1] . ( 12 sec) [ -27773.1082] [ 6888] [depth= 2] . ( 12 sec) [ -27731.6333] [ 6887] [depth= 1] . ( 12 sec) [ -27642.4865] [ 6854] [depth= 4] . ( 12 sec) [ -27617.4502] [ 6849] [depth= 1] . ( 12 sec) [ -27454.4230] [ 6798] [depth= 3] . ( 12 sec) [ -27437.4383] [ 6800] [depth= 1] . ( 12 sec) [ -27413.5790] [ 6798] [depth= 2] . ( 12 sec) [ -27402.4057] [ 6785] [depth= 1] . ( 13 sec) [ -27232.0119] [ 6730] [depth= 4] . ( 13 sec) [ -27208.6005] [ 6727] [depth= 2] . ( 13 sec) [ -27062.0142] [ 6688] [depth= 2] . ( 13 sec) [ -27055.6623] [ 6692] [depth= 1] . ( 13 sec) [ -27017.0020] [ 6683] [depth= 1] . ( 13 sec) [ -27015.2924] [ 6681] [depth= 1] . ( 14 sec) [ -26992.0624] [ 6677] [depth= 1] . ( 14 sec) [ -26978.0579] [ 6684] [depth= 6] . ( 14 sec) [ -26965.4482] [ 6683] [depth= 1] . ( 14 sec) [ -26918.7260] [ 6634] [depth= 5] . ( 14 sec) [ -26864.5714] [ 6616] [depth= 4] . ( 14 sec) [ -26841.8496] [ 6605] [depth= 1] . ( 14 sec) [ -26806.2780] [ 6605] [depth= 9] . ( 15 sec) [ -26661.4214] [ 6611] [depth= 2] . ( 15 sec) [ -26587.4186] [ 6576] [depth= 3] . ( 15 sec) [ -26566.0414] [ 6567] [depth= 7] . ( 15 sec) [ -26545.5450] [ 6563] [depth= 4] . ( 15 sec) [ -26536.5374] [ 6563] [depth= 2] . ( 15 sec) [ -26530.4426] [ 6562] [depth= 1] . ( 15 sec) [ -26527.2970] [ 6571] [depth= 4] . ( 16 sec) [ -26523.7123] [ 6572] [depth= 1] . ( 17 sec) [ -25995.2795] [Branch lengths ] . ( 19 sec) [ -25795.8034] [GTR parameters ] . ( 19 sec) [ -25782.4444] [Alpha ][ 0.422499] . ( 19 sec) [ -25779.2743] [ 6557] [depth= 2] . ( 19 sec) [ -25705.3065] [ 6547] [depth= 5] . ( 19 sec) [ -25648.8717] [ 6524] [depth= 5] . ( 19 sec) [ -25634.8233] [ 6518] [depth= 4] . ( 20 sec) [ -25629.6423] [ 6504] [depth= 2] . ( 20 sec) [ -25628.5634] [ 6505] [depth= 1] . ( 20 sec) [ -25627.4301] [ 6507] [depth= 1] . ( 20 sec) [ -25550.8588] [ 6492] [depth= 2] . ( 21 sec) [ -25538.1337] [ 6483] [depth= 1] . ( 21 sec) [ -25530.3168] [ 6488] [depth= 1] . ( 22 sec) [ -25501.2364] [ 6479] [depth= 2] . ( 22 sec) [ -25500.2423] [ 6481] [depth= 1] . ( 22 sec) [ -25498.1787] [ 6478] [depth= 2] . ( 23 sec) [ -25491.9319] [ 6469] [depth= 1] . ( 23 sec) [ -25486.2026] [ 6466] [depth= 2] . ( 23 sec) [ -25482.5583] [ 6451] [depth= 2] . ( 24 sec) [ -25407.7881] [ 6412] [depth= 3] . ( 24 sec) [ -25407.7660] [ 6414] [depth= 1] . ( 25 sec) [ -25406.3754] [ 6416] [depth= 1] . ( 26 sec) [ -25351.4936] [ 6403] [depth= 3] . ( 26 sec) [ -25343.5552] [ 6402] [depth= 2] . ( 26 sec) [ -25336.8520] [ 6388] [depth= 3] . ( 26 sec) [ -25330.2475] [ 6380] [depth= 1] . ( 26 sec) [ -25328.7704] [ 6377] [depth= 1] . ( 27 sec) [ -25285.3632] [ 6362] [depth= 1] . ( 28 sec) [ -25281.3437] [ 6359] [depth= 1] . ( 29 sec) [ -25281.3122] [ 6362] [depth= 1] . ( 29 sec) [ -25270.0862] [ 6354] [depth= 1] . ( 30 sec) [ -25267.8543] [ 6356] [depth= 1] . ( 30 sec) [ -25197.7396] [Branch lengths ] . ( 32 sec) [ -25193.3441] [GTR parameters ] . ( 32 sec) [ -25193.3251] [Alpha ][ 0.419611] . ( 32 sec) [ -25148.8502] [ 6317] [depth= 6] . ( 42 sec) [ -25139.8924] [Branch lengths ] . ( 43 sec) [ -25139.3409] [GTR parameters ] . ( 43 sec) [ -25139.3208] [Alpha ][ 0.422477] . ( 53 sec) [ -25136.0612] [Branch lengths ] . ( 58 sec) [ -25135.6091] [ 6312] [depth= 1] . ( 112 sec) [ -25132.1518] [Branch lengths ] . ( 114 sec) [ -25131.5301] [GTR parameters ] . ( 114 sec) [ -25131.5221] [Alpha ][ 0.424262] . ( 174 sec) [ -25124.4329] [Branch lengths ] . ( 174 sec) [ -25124.4329] [Topology ] . ( 175 sec) [ -25122.9154] [Topology ] . ( 177 sec) [ -25122.6257] [Topology ] . ( 179 sec) [ -25122.5303] [Topology ] . ( 181 sec) [ -25122.4882] [Topology ] . ( 183 sec) [ -25122.4648] [Topology ] . ( 184 sec) [ -25122.4497] [Topology ] . ( 186 sec) [ -25122.1576] [GTR parameters ] . ( 186 sec) [ -25122.1568] [Alpha ][ 0.423684] . ( 186 sec) [ -25122.1568] [Topology ] . ( 188 sec) [ -25122.0652] [Topology ] . ( 189 sec) [ -25122.0089] [Topology ] . ( 191 sec) [ -25121.9698] [Topology ] . ( 193 sec) [ -25121.9422] [Topology ] . ( 195 sec) [ -25121.9227] [Topology ] . ( 197 sec) [ -25121.9086] [Topology ] . ( 198 sec) [ -25121.8497] [GTR parameters ] . ( 198 sec) [ -25121.8490] [Alpha ][ 0.423111] . ( 198 sec) [ -25121.8490] [Topology ] . ( 200 sec) [ -25121.8139] [Topology ] . ( 202 sec) [ -25121.7907] [Topology ] . ( 203 sec) [ -25121.7742] [Topology ] . ( 205 sec) [ -25121.7624] [Topology ] . ( 207 sec) [ -25121.7538] [Topology ] . ( 209 sec) [ -25121.7477] [Topology ] . ( 210 sec) [ -25121.7248] [GTR parameters ] . ( 210 sec) [ -25121.7245] [Alpha ][ 0.422688] . ( 210 sec) [ -25121.7245] [Topology ] . ( 212 sec) [ -25121.7100] [Topology ] . ( 214 sec) [ -25121.7004] [Topology ] . ( 215 sec) [ -25121.6934] [Topology ] . ( 217 sec) [ -25121.6884] [Topology ] . ( 219 sec) [ -25121.6847] [Topology ] . ( 221 sec) [ -25121.6821] [Topology ] . ( 222 sec) [ -25121.6726] [GTR parameters ] . ( 222 sec) [ -25121.6726] [Alpha ][ 0.422688] . ( 222 sec) [ -25121.6726] [Topology ] . ( 223 sec) [ -25121.6664] [Topology ] . ( 225 sec) [ -25121.6622] [Topology ] . ( 227 sec) [ -25121.6592] [Topology ] . ( 229 sec) [ -25121.6569] [Topology ] . ( 231 sec) [ -25121.6553] [Topology ] . ( 232 sec) [ -25121.6542] [Topology ] . ( 233 sec) [ -25121.6506] [GTR parameters ] . ( 233 sec) [ -25121.6502] [Alpha ][ 0.422265] . ( 233 sec) [ -25121.6502] [Topology ] . ( 235 sec) [ -25121.6477] [Topology ] . ( 237 sec) [ -25121.6461] [Topology ] . ( 239 sec) [ -25121.6449] [Topology ] . ( 240 sec) [ -25121.6440] [Topology ] . ( 241 sec) [ -25121.6428] [GTR parameters ] . ( 241 sec) [ -25121.6428] [Alpha ][ 0.422265] . ( 241 sec) [ -25121.6428] [Topology ] . ( 243 sec) [ -25121.6415] [Topology ] . ( 245 sec) [ -25121.6405] [Topology ] . ( 245 sec) [ -25121.6403] [GTR parameters ] . ( 245 sec) [ -25121.6403] [Alpha ][ 0.422265] . ( 245 sec) [ -25121.6403] [Topology ] . ( 247 sec) [ -25121.6394] [Topology ] . ( 247 sec) [ -25121.6394] [GTR parameters ] . ( 247 sec) [ -25121.6394] [Alpha ][ 0.422265] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25121.639380. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -26079.2058] [GTR parameters ] . ( 4 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 4 sec) [ -25728.9409] [Topology ] . ( 6 sec) [ -25291.2425] [Topology ] . ( 8 sec) [ -25230.3848] [Topology ] . ( 9 sec) [ -25214.3514] [Topology ] . ( 11 sec) [ -25208.4878] [Topology ] . ( 13 sec) [ -25205.8920] [Topology ] . ( 14 sec) [ -25194.6256] [Topology ] . ( 16 sec) [ -25190.1344] [Topology ] . ( 18 sec) [ -25188.5150] [Topology ] . ( 20 sec) [ -25188.1330] [Topology ] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -25146.5950] [GTR parameters ] . ( 40 sec) [ -25136.1397] [Alpha ][ 0.428858] . ( 40 sec) [ -25136.1397] [Topology ] . ( 42 sec) [ -25131.9942] [Topology ] . ( 44 sec) [ -25130.7501] [Topology ] . ( 46 sec) [ -25130.0910] [Topology ] . ( 47 sec) [ -25129.6974] [Topology ] . ( 49 sec) [ -25129.4521] [Topology ] . ( 51 sec) [ -25129.2950] [Topology ] . Checking for NNIs, optimizing five branches... . ( 69 sec) [ -25126.2391] [GTR parameters ] . ( 69 sec) [ -25126.1947] [Alpha ][ 0.424452] . ( 69 sec) [ -25126.1947] [Topology ] . ( 71 sec) [ -25125.2580] [Topology ] . ( 72 sec) [ -25124.7461] [Topology ] . ( 74 sec) [ -25124.4178] [Topology ] . ( 76 sec) [ -25124.1998] [Topology ] . ( 78 sec) [ -25124.0522] [Topology ] . ( 79 sec) [ -25123.9521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -25123.3318] [GTR parameters ] . ( 97 sec) [ -25123.3317] [Alpha ][ 0.424028] . ( 97 sec) [ -25123.3317] [Topology ] . ( 99 sec) [ -25123.0192] [Topology ] . ( 101 sec) [ -25122.8253] [Topology ] . ( 102 sec) [ -25122.6945] [Topology ] . ( 104 sec) [ -25122.6048] [Topology ] . ( 106 sec) [ -25122.5424] [Topology ] . ( 108 sec) [ -25122.4990] [Topology ] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -25122.3007] [GTR parameters ] . ( 125 sec) [ -25122.3006] [Alpha ][ 0.423604] . ( 125 sec) [ -25122.3006] [Topology ] . ( 127 sec) [ -25122.1866] [Topology ] . ( 129 sec) [ -25122.1127] [Topology ] . ( 131 sec) [ -25122.0612] [Topology ] . ( 132 sec) [ -25122.0251] [Topology ] . ( 134 sec) [ -25121.9995] [Topology ] . ( 136 sec) [ -25121.9812] [Topology ] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -25121.9076] [GTR parameters ] . ( 153 sec) [ -25121.9073] [Alpha ][ 0.423180] . ( 153 sec) [ -25121.9073] [Topology ] . ( 155 sec) [ -25121.8623] [Topology ] . ( 157 sec) [ -25121.8325] [Topology ] . ( 158 sec) [ -25121.8113] [Topology ] . ( 160 sec) [ -25121.7961] [Topology ] . ( 162 sec) [ -25121.7853] [Topology ] . ( 164 sec) [ -25121.7774] [Topology ] . Checking for NNIs, optimizing five branches... . ( 181 sec) [ -25121.7482] [GTR parameters ] . ( 181 sec) [ -25121.7480] [Alpha ][ 0.422757] . ( 181 sec) [ -25121.7480] [Topology ] . ( 183 sec) [ -25121.7303] [Topology ] . ( 185 sec) [ -25121.7185] [Topology ] . ( 186 sec) [ -25121.7100] [Topology ] . ( 188 sec) [ -25121.7039] [Topology ] . ( 190 sec) [ -25121.6994] [Topology ] . ( 192 sec) [ -25121.6962] [Topology ] . Checking for NNIs, optimizing five branches... . ( 209 sec) [ -25121.6832] [GTR parameters ] . ( 209 sec) [ -25121.6832] [Alpha ][ 0.422757] . ( 209 sec) [ -25121.6832] [Topology ] . ( 211 sec) [ -25121.6754] [Topology ] . ( 213 sec) [ -25121.6702] [Topology ] . ( 214 sec) [ -25121.6663] [Topology ] . ( 216 sec) [ -25121.6636] [Topology ] . ( 218 sec) [ -25121.6616] [Topology ] . ( 220 sec) [ -25121.6601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -25121.6553] [GTR parameters ] . ( 237 sec) [ -25121.6549] [Alpha ][ 0.422334] . ( 237 sec) [ -25121.6549] [Topology ] . ( 239 sec) [ -25121.6518] [Topology ] . ( 241 sec) [ -25121.6497] [Topology ] . ( 242 sec) [ -25121.6482] [Topology ] . ( 244 sec) [ -25121.6471] [Topology ] . ( 246 sec) [ -25121.6463] [Topology ] . Checking for NNIs, optimizing five branches... . ( 262 sec) [ -25121.6442] [GTR parameters ] . ( 262 sec) [ -25121.6442] [Alpha ][ 0.422334] . ( 263 sec) [ -25121.6442] [Topology ] . ( 264 sec) [ -25121.6426] [Topology ] . ( 266 sec) [ -25121.6414] [Topology ] . ( 268 sec) [ -25121.6406] [Topology ] . Checking for NNIs, optimizing five branches... . ( 284 sec) [ -25121.6402] [GTR parameters ] . ( 284 sec) [ -25121.6402] [Alpha ][ 0.422334] . ( 284 sec) [ -25121.6402] [Topology ] . ( 286 sec) [ -25121.6393] [Topology ] . Checking for NNIs, optimizing five branches... . ( 302 sec) [ -25121.6393] [GTR parameters ] . ( 302 sec) [ -25121.6393] [Alpha ][ 0.422334] . ( 302 sec) [ -25121.6393] [Topology ] . ( 304 sec) [ -25121.6385] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 338 sec) [ -26079.2058] [GTR parameters ] . ( 338 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 339 sec) [ -25726.2013] [ 6340] [depth= 1] . ( 339 sec) [ -25715.3178] [ 6339] [depth= 1] . ( 340 sec) [ -25709.8673] [ 6334] [depth= 1] . ( 340 sec) [ -25700.1364] [ 6331] [depth= 1] . ( 341 sec) [ -25699.7942] [ 6333] [depth= 1] . ( 341 sec) [ -25695.6843] [ 6329] [depth= 1] . ( 341 sec) [ -25682.5744] [ 6317] [depth= 2] . ( 341 sec) [ -25682.3575] [ 6318] [depth= 1] . ( 341 sec) [ -25681.9471] [ 6322] [depth= 1] . ( 341 sec) [ -25667.9534] [ 6328] [depth= 1] . ( 342 sec) [ -25663.2486] [ 6322] [depth= 1] . ( 342 sec) [ -25645.8279] [ 6321] [depth= 1] . ( 343 sec) [ -25644.8841] [ 6325] [depth= 1] . ( 343 sec) [ -25613.7274] [ 6321] [depth= 1] . ( 343 sec) [ -25610.6254] [ 6315] [depth= 1] . ( 343 sec) [ -25610.2353] [ 6321] [depth= 1] . ( 343 sec) [ -25603.1721] [ 6325] [depth= 2] . ( 343 sec) [ -25601.1863] [ 6319] [depth= 1] . ( 344 sec) [ -25599.5298] [ 6318] [depth= 2] . ( 344 sec) [ -25589.3879] [ 6317] [depth= 1] . ( 344 sec) [ -25587.2064] [ 6323] [depth= 1] . ( 344 sec) [ -25581.9004] [ 6330] [depth= 1] . ( 345 sec) [ -25571.0055] [ 6330] [depth= 1] . ( 345 sec) [ -25568.1439] [ 6337] [depth= 1] . ( 345 sec) [ -25565.1961] [ 6342] [depth= 2] . ( 345 sec) [ -25558.3858] [ 6339] [depth= 1] . ( 346 sec) [ -25547.6821] [ 6342] [depth= 1] . ( 346 sec) [ -25533.3166] [ 6337] [depth= 1] . ( 346 sec) [ -25528.1986] [ 6338] [depth= 2] . ( 346 sec) [ -25519.9391] [ 6345] [depth= 5] . ( 346 sec) [ -25519.3026] [ 6347] [depth= 1] . ( 346 sec) [ -25492.9153] [ 6356] [depth= 1] . ( 347 sec) [ -25480.8205] [ 6347] [depth= 1] . ( 347 sec) [ -25463.5785] [ 6357] [depth= 1] . ( 347 sec) [ -25453.7727] [ 6346] [depth= 3] . ( 347 sec) [ -25444.9652] [ 6355] [depth= 3] . ( 347 sec) [ -25444.2532] [ 6349] [depth= 3] . ( 347 sec) [ -25436.1849] [ 6353] [depth= 1] . ( 347 sec) [ -25428.1178] [ 6348] [depth= 1] . ( 347 sec) [ -25421.3539] [ 6339] [depth= 4] . ( 348 sec) [ -25420.6965] [ 6342] [depth= 1] . ( 348 sec) [ -25419.0576] [ 6343] [depth= 1] . ( 348 sec) [ -25412.3345] [ 6346] [depth= 1] . ( 348 sec) [ -25403.9203] [ 6342] [depth= 1] . ( 348 sec) [ -25403.2716] [ 6346] [depth= 1] . ( 349 sec) [ -25401.0608] [ 6351] [depth= 3] . ( 349 sec) [ -25399.8385] [ 6351] [depth= 1] . ( 349 sec) [ -25398.4449] [ 6345] [depth= 4] . ( 350 sec) [ -25259.6230] [Branch lengths ] . ( 353 sec) [ -25228.8373] [GTR parameters ] . ( 353 sec) [ -25215.1313] [Alpha ][ 0.418957] . ( 356 sec) [ -25213.1995] [ 6341] [depth= 1] . ( 357 sec) [ -25193.9020] [ 6334] [depth= 1] . ( 357 sec) [ -25188.9409] [ 6334] [depth= 1] . ( 357 sec) [ -25186.0249] [ 6333] [depth= 2] . ( 358 sec) [ -25184.5957] [ 6331] [depth= 1] . ( 358 sec) [ -25184.0624] [ 6333] [depth= 1] . ( 359 sec) [ -25177.1292] [ 6332] [depth= 1] . ( 361 sec) [ -25175.9585] [ 6331] [depth= 1] . ( 361 sec) [ -25172.5163] [ 6327] [depth= 1] . ( 362 sec) [ -25172.2133] [ 6329] [depth= 1] . ( 363 sec) [ -25171.0182] [ 6329] [depth= 1] . ( 364 sec) [ -25137.1760] [Branch lengths ] . ( 366 sec) [ -25133.5479] [GTR parameters ] . ( 367 sec) [ -25133.5472] [Alpha ][ 0.419473] . ( 372 sec) [ -25132.8941] [ 6325] [depth= 1] . ( 377 sec) [ -25126.4129] [Branch lengths ] . ( 380 sec) [ -25125.9114] [GTR parameters ] . ( 380 sec) [ -25125.9114] [Alpha ][ 0.419473] . ( 390 sec) [ -25123.7702] [Branch lengths ] . ( 450 sec) [ -25123.1291] [Branch lengths ] . ( 450 sec) [ -25123.1291] [Topology ] . ( 452 sec) [ -25123.0298] [Topology ] . ( 453 sec) [ -25122.9895] [Topology ] . ( 455 sec) [ -25122.9672] [Topology ] . ( 457 sec) [ -25122.9539] [Topology ] . ( 459 sec) [ -25122.9459] [Topology ] . ( 460 sec) [ -25122.9410] [Topology ] . ( 462 sec) [ -25122.2835] [GTR parameters ] . ( 462 sec) [ -25122.2829] [Alpha ][ 0.418928] . ( 462 sec) [ -25122.2829] [Topology ] . ( 464 sec) [ -25122.1370] [Topology ] . ( 466 sec) [ -25122.0636] [Topology ] . ( 468 sec) [ -25122.0194] [Topology ] . ( 469 sec) [ -25121.9923] [Topology ] . ( 471 sec) [ -25121.9755] [Topology ] . ( 473 sec) [ -25121.9650] [Topology ] . ( 475 sec) [ -25121.8839] [GTR parameters ] . ( 475 sec) [ -25121.8834] [Alpha ][ 0.418431] . ( 475 sec) [ -25121.8834] [Topology ] . ( 477 sec) [ -25121.8475] [Topology ] . ( 478 sec) [ -25121.8273] [Topology ] . ( 480 sec) [ -25121.8147] [Topology ] . ( 482 sec) [ -25121.8068] [Topology ] . ( 484 sec) [ -25121.8019] [Topology ] . ( 485 sec) [ -25121.7988] [Topology ] . ( 487 sec) [ -25121.7745] [GTR parameters ] . ( 487 sec) [ -25121.7744] [Alpha ][ 0.418013] . ( 487 sec) [ -25121.7744] [Topology ] . ( 489 sec) [ -25121.7635] [Topology ] . ( 490 sec) [ -25121.7572] [Topology ] . ( 492 sec) [ -25121.7533] [Topology ] . ( 494 sec) [ -25121.7509] [Topology ] . ( 496 sec) [ -25121.7493] [Topology ] . ( 497 sec) [ -25121.7484] [Topology ] . ( 499 sec) [ -25121.7411] [GTR parameters ] . ( 499 sec) [ -25121.7411] [Alpha ][ 0.418013] . ( 499 sec) [ -25121.7411] [Topology ] . ( 501 sec) [ -25121.7376] [Topology ] . ( 503 sec) [ -25121.7356] [Topology ] . ( 504 sec) [ -25121.7343] [Topology ] . ( 506 sec) [ -25121.7335] [Topology ] . ( 507 sec) [ -25121.7324] [GTR parameters ] . ( 507 sec) [ -25121.7324] [Alpha ][ 0.418013] . ( 507 sec) [ -25121.7324] [Topology ] . ( 509 sec) [ -25121.7313] [Topology ] . ( 511 sec) [ -25121.7306] [Topology ] . ( 512 sec) [ -25121.7302] [GTR parameters ] . ( 512 sec) [ -25121.7302] [Alpha ][ 0.418013] . ( 512 sec) [ -25121.7302] [Topology ] . ( 514 sec) [ -25121.7293] [Topology ] . ( 515 sec) [ -25121.7292] [GTR parameters ] . ( 515 sec) [ -25121.7292] [Alpha ][ 0.418013] . ( 515 sec) [ -25121.7292] [Topology ] . ( 516 sec) [ -25121.7287] [Topology ] . ( 517 sec) [ -25121.7287] [GTR parameters ] . ( 517 sec) [ -25121.7287] [Alpha ][ 0.418013] . Checking for NNIs, optimizing five branches... . ( 533 sec) [ -25121.6886] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -25121.638540 . Log likelihood obtained after SPR moves : -25121.688640 . Log likelihood of the current tree: -25121.638540. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Best log likelihood : -25117.933959 . Time used 0h9m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1762.01user 0.00system 29:28.40elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps