.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2477_39x888_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 638 patterns found. (out of a total of 888 sites) . 262 sites without polymorphism (29.50%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -36406.7499] [Alpha ][ 0.500960] . ( 3 sec) [ -36000.0020] [ 6243] [depth= 5] . ( 4 sec) [ -35488.1491] [ 6136] [depth= 12] . ( 4 sec) [ -35441.5958] [ 6122] [depth= 1] . ( 5 sec) [ -35386.5451] [ 6113] [depth= 4] . ( 6 sec) [ -35042.6251] [ 5994] [depth= 6] . ( 6 sec) [ -34761.8365] [ 6004] [depth= 4] . ( 7 sec) [ -34648.2389] [ 5996] [depth= 11] . ( 8 sec) [ -34527.2907] [ 5972] [depth= 1] . ( 8 sec) [ -33768.9504] [ 5941] [depth= 6] . ( 9 sec) [ -33374.7232] [ 5926] [depth= 1] . ( 10 sec) [ -32726.7098] [ 5844] [depth= 12] . ( 11 sec) [ -31660.4533] [ 5771] [depth= 12] . ( 11 sec) [ -31432.0798] [ 5730] [depth= 5] . ( 12 sec) [ -31375.4029] [ 5734] [depth= 1] . ( 13 sec) [ -31232.6061] [ 5700] [depth= 2] . ( 14 sec) [ -31165.0017] [ 5670] [depth= 3] . ( 15 sec) [ -30893.3698] [ 5595] [depth= 2] . ( 15 sec) [ -30806.7910] [ 5605] [depth= 1] . ( 16 sec) [ -30611.8068] [ 5570] [depth= 2] . ( 17 sec) [ -30370.0092] [ 5546] [depth= 17] . ( 18 sec) [ -30279.6640] [ 5522] [depth= 1] . ( 18 sec) [ -30173.2778] [ 5502] [depth= 13] . ( 19 sec) [ -29760.5260] [ 5431] [depth= 11] . ( 20 sec) [ -29369.4245] [ 5357] [depth= 1] . ( 21 sec) [ -29330.4020] [ 5345] [depth= 1] . ( 22 sec) [ -28932.9400] [ 5266] [depth= 9] . ( 23 sec) [ -28572.5635] [ 5178] [depth= 11] . ( 23 sec) [ -28213.0317] [ 5095] [depth= 1] . ( 24 sec) [ -28189.0035] [ 5074] [depth= 5] . ( 25 sec) [ -27809.9479] [ 4986] [depth= 6] . ( 26 sec) [ -27264.2140] [ 4859] [depth= 4] . ( 27 sec) [ -26708.6303] [ 4809] [depth= 8] . ( 28 sec) [ -26533.4387] [ 4738] [depth= 3] . ( 29 sec) [ -26325.1539] [ 4750] [depth= 1] . ( 29 sec) [ -26153.4807] [ 4683] [depth= 1] . ( 30 sec) [ -25771.7598] [ 4610] [depth= 2] . ( 31 sec) [ -25699.6853] [ 4603] [depth= 9] . ( 32 sec) [ -25406.6415] [ 4534] [depth= 5] . ( 33 sec) [ -25307.7818] [ 4525] [depth= 5] . ( 34 sec) [ -25114.2279] [ 4558] [depth= 1] . ( 34 sec) [ -24921.0353] [ 4492] [depth= 1] . ( 35 sec) [ -24805.4434] [ 4448] [depth= 1] . ( 36 sec) [ -24780.6416] [ 4446] [depth= 1] . ( 37 sec) [ -24529.7377] [ 4413] [depth= 2] . ( 37 sec) [ -24514.0426] [ 4429] [depth= 1] . ( 38 sec) [ -24188.3086] [ 4327] [depth= 2] . ( 39 sec) [ -24167.0041] [ 4318] [depth= 1] . ( 40 sec) [ -24114.0340] [ 4292] [depth= 2] . ( 40 sec) [ -23929.0840] [ 4270] [depth= 4] . ( 41 sec) [ -23851.5020] [ 4258] [depth= 4] . ( 42 sec) [ -23674.6743] [ 4207] [depth= 2] . ( 43 sec) [ -23670.8058] [ 4207] [depth= 1] . ( 44 sec) [ -23632.3805] [ 4186] [depth= 4] . ( 45 sec) [ -23627.3560] [ 4183] [depth= 1] . ( 45 sec) [ -23296.3173] [ 4097] [depth= 3] . ( 46 sec) [ -23211.3932] [ 4058] [depth= 2] . ( 47 sec) [ -23161.3701] [ 4039] [depth= 2] . ( 47 sec) [ -23154.1452] [ 4039] [depth= 1] . ( 48 sec) [ -23041.5209] [ 4008] [depth= 2] . ( 49 sec) [ -23021.0738] [ 4005] [depth= 1] . ( 51 sec) [ -22883.0495] [ 3964] [depth= 1] . ( 51 sec) [ -22556.0067] [ 3920] [depth= 3] . ( 52 sec) [ -22514.6042] [ 3916] [depth= 2] . ( 53 sec) [ -22510.1438] [ 3921] [depth= 1] . ( 54 sec) [ -22315.1228] [ 3860] [depth= 4] . ( 55 sec) [ -22012.2016] [ 3857] [depth= 5] . ( 55 sec) [ -22002.5240] [ 3861] [depth= 1] . ( 56 sec) [ -21989.7097] [ 3873] [depth= 1] . ( 57 sec) [ -21905.3301] [ 3851] [depth= 1] . ( 58 sec) [ -21843.9861] [ 3840] [depth= 2] . ( 58 sec) [ -21765.8789] [ 3806] [depth= 1] . ( 59 sec) [ -21672.3121] [ 3779] [depth= 1] . ( 60 sec) [ -21611.2659] [ 3780] [depth= 1] . ( 61 sec) [ -21583.8756] [ 3770] [depth= 2] . ( 63 sec) [ -21534.4669] [ 3753] [depth= 2] . ( 63 sec) [ -21487.1457] [ 3743] [depth= 1] . ( 65 sec) [ -21485.2322] [ 3747] [depth= 1] . ( 69 sec) [ -21327.3957] [Branch lengths ] . ( 70 sec) [ -21327.3817] [Alpha ][ 0.504722] . ( 71 sec) [ -21321.4257] [ 3742] [depth= 1] . ( 74 sec) [ -21216.2407] [ 3678] [depth= 6] . ( 77 sec) [ -21216.1019] [ 3678] [depth= 1] . ( 77 sec) [ -21214.5508] [ 3677] [depth= 1] . ( 84 sec) [ -21191.9068] [ 3663] [depth= 1] . ( 96 sec) [ -21191.2739] [ 3660] [depth= 1] . ( 110 sec) [ -21190.0175] [ 3665] [depth= 1] . ( 112 sec) [ -21189.4703] [ 3670] [depth= 1] . ( 113 sec) [ -21187.9215] [ 3665] [depth= 1] . ( 121 sec) [ -21171.5983] [Branch lengths ] . ( 121 sec) [ -21171.4579] [Alpha ][ 0.516551] . ( 125 sec) [ -21167.3919] [ 3665] [depth= 1] . ( 172 sec) [ -21164.7587] [Branch lengths ] . ( 173 sec) [ -21164.7484] [Alpha ][ 0.519888] . ( 223 sec) [ -21164.2432] [Branch lengths ] . ( 223 sec) [ -21164.2432] [Topology ] . ( 229 sec) [ -21164.1834] [Topology ] . ( 234 sec) [ -21164.1611] [Topology ] . ( 239 sec) [ -21164.1491] [Topology ] . ( 245 sec) [ -21164.1425] [Topology ] . ( 250 sec) [ -21164.1388] [Topology ] . ( 255 sec) [ -21164.1366] [Topology ] . ( 256 sec) [ -21164.1353] [Alpha ][ 0.521044] . ( 256 sec) [ -21164.1353] [Topology ] . ( 262 sec) [ -21164.1340] [Topology ] . ( 267 sec) [ -21164.1332] [Topology ] . ( 268 sec) [ -21164.1332] [Alpha ][ 0.521044] . ( 268 sec) [ -21164.1332] [Topology ] . ( 273 sec) [ -21164.1328] [Topology ] . ( 274 sec) [ -21164.1328] [Alpha ][ 0.521044] . Checking for NNIs, optimizing five branches... . ( 319 sec) [ -21163.4742] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -21163.474186. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -36283.1279] [Alpha ][ 0.500960] . ( 3 sec) [ -35799.7383] [ 6333] [depth= 14] . ( 3 sec) [ -35411.4642] [ 6259] [depth= 7] . ( 4 sec) [ -35266.7024] [ 6228] [depth= 8] . ( 5 sec) [ -35047.0668] [ 6165] [depth= 1] . ( 5 sec) [ -34769.4134] [ 6123] [depth= 11] . ( 6 sec) [ -34261.4500] [ 6082] [depth= 2] . ( 7 sec) [ -34127.4331] [ 6066] [depth= 2] . ( 7 sec) [ -33926.3368] [ 6002] [depth= 1] . ( 8 sec) [ -33617.6067] [ 5984] [depth= 3] . ( 9 sec) [ -33603.1256] [ 5984] [depth= 2] . ( 9 sec) [ -33343.2640] [ 5966] [depth= 9] . ( 10 sec) [ -33111.7848] [ 5904] [depth= 4] . ( 11 sec) [ -33003.9869] [ 5899] [depth= 5] . ( 11 sec) [ -32826.8659] [ 5878] [depth= 8] . ( 12 sec) [ -32450.5440] [ 5791] [depth= 5] . ( 13 sec) [ -32068.6470] [ 5674] [depth= 1] . ( 14 sec) [ -31732.0758] [ 5641] [depth= 5] . ( 15 sec) [ -31583.3176] [ 5586] [depth= 7] . ( 15 sec) [ -31507.5076] [ 5582] [depth= 1] . ( 17 sec) [ -31477.7328] [ 5537] [depth= 11] . ( 17 sec) [ -31423.7780] [ 5521] [depth= 1] . ( 18 sec) [ -31196.5222] [ 5445] [depth= 15] . ( 19 sec) [ -30911.4071] [ 5387] [depth= 3] . ( 20 sec) [ -30477.8471] [ 5336] [depth= 7] . ( 20 sec) [ -30428.8816] [ 5327] [depth= 1] . ( 21 sec) [ -29823.0514] [ 5173] [depth= 4] . ( 22 sec) [ -29382.3102] [ 5038] [depth= 10] . ( 23 sec) [ -28651.6115] [ 5036] [depth= 2] . ( 24 sec) [ -28648.3453] [ 5041] [depth= 1] . ( 25 sec) [ -28513.8606] [ 4986] [depth= 5] . ( 26 sec) [ -28326.5791] [ 4950] [depth= 5] . ( 27 sec) [ -28196.1252] [ 4924] [depth= 1] . ( 28 sec) [ -28067.5573] [ 4901] [depth= 7] . ( 29 sec) [ -27928.3233] [ 4890] [depth= 4] . ( 29 sec) [ -27885.0019] [ 4869] [depth= 11] . ( 30 sec) [ -27874.9411] [ 4869] [depth= 1] . ( 31 sec) [ -27864.5965] [ 4869] [depth= 1] . ( 32 sec) [ -27794.7705] [ 4847] [depth= 5] . ( 33 sec) [ -27422.6487] [ 4748] [depth= 3] . ( 34 sec) [ -26838.0476] [ 4669] [depth= 10] . ( 35 sec) [ -26810.2524] [ 4655] [depth= 1] . ( 35 sec) [ -26634.9285] [ 4630] [depth= 1] . ( 36 sec) [ -26634.0972] [ 4632] [depth= 1] . ( 37 sec) [ -26537.1949] [ 4617] [depth= 5] . ( 38 sec) [ -26406.7568] [ 4582] [depth= 9] . ( 38 sec) [ -26365.2824] [ 4575] [depth= 2] . ( 39 sec) [ -25906.6680] [ 4465] [depth= 4] . ( 40 sec) [ -25766.7470] [ 4432] [depth= 3] . ( 42 sec) [ -25762.9842] [ 4431] [depth= 1] . ( 44 sec) [ -25761.4573] [ 4434] [depth= 1] . ( 44 sec) [ -25397.5569] [ 4446] [depth= 8] . ( 45 sec) [ -25263.5930] [ 4405] [depth= 4] . ( 46 sec) [ -25056.7617] [ 4325] [depth= 3] . ( 46 sec) [ -24839.6901] [ 4298] [depth= 2] . ( 47 sec) [ -24342.6387] [ 4309] [depth= 1] . ( 48 sec) [ -24282.5995] [ 4299] [depth= 1] . ( 48 sec) [ -23732.2972] [ 4129] [depth= 6] . ( 49 sec) [ -22972.2369] [ 4000] [depth= 2] . ( 51 sec) [ -22839.3786] [ 3986] [depth= 2] . ( 53 sec) [ -22524.8998] [ 3916] [depth= 8] . ( 53 sec) [ -22332.0341] [ 3872] [depth= 1] . ( 54 sec) [ -22139.4894] [ 3843] [depth= 4] . ( 55 sec) [ -22078.0323] [ 3843] [depth= 1] . ( 56 sec) [ -22043.6491] [ 3834] [depth= 1] . ( 58 sec) [ -21984.3619] [ 3800] [depth= 1] . ( 58 sec) [ -21945.4806] [ 3794] [depth= 1] . ( 59 sec) [ -21907.5111] [ 3788] [depth= 1] . ( 60 sec) [ -21896.5462] [ 3786] [depth= 1] . ( 64 sec) [ -21542.3719] [Branch lengths ] . ( 64 sec) [ -21542.3568] [Alpha ][ 0.504812] . ( 67 sec) [ -21542.0477] [ 3789] [depth= 1] . ( 68 sec) [ -21536.7191] [ 3786] [depth= 1] . ( 70 sec) [ -21522.2890] [ 3780] [depth= 1] . ( 71 sec) [ -21509.9162] [ 3769] [depth= 3] . ( 72 sec) [ -21361.3283] [ 3726] [depth= 3] . ( 73 sec) [ -21319.0832] [ 3715] [depth= 2] . ( 75 sec) [ -21272.4188] [ 3683] [depth= 5] . ( 77 sec) [ -21269.3055] [ 3681] [depth= 1] . ( 79 sec) [ -21265.9817] [ 3679] [depth= 1] . ( 82 sec) [ -21244.2529] [ 3671] [depth= 1] . ( 86 sec) [ -21240.7970] [ 3675] [depth= 1] . ( 88 sec) [ -21229.0239] [ 3671] [depth= 1] . ( 89 sec) [ -21228.5005] [ 3671] [depth= 1] . ( 90 sec) [ -21227.8239] [ 3674] [depth= 1] . ( 92 sec) [ -21215.6372] [ 3670] [depth= 1] . ( 93 sec) [ -21215.1548] [ 3668] [depth= 1] . ( 93 sec) [ -21197.8300] [ 3665] [depth= 2] . ( 94 sec) [ -21194.0313] [ 3667] [depth= 1] . ( 98 sec) [ -21192.6192] [ 3668] [depth= 1] . ( 104 sec) [ -21190.3138] [ 3666] [depth= 1] . ( 106 sec) [ -21190.1815] [ 3665] [depth= 1] . ( 116 sec) [ -21166.1429] [Branch lengths ] . ( 117 sec) [ -21165.9744] [Alpha ][ 0.517816] . ( 167 sec) [ -21164.4763] [Branch lengths ] . ( 168 sec) [ -21164.4763] [Topology ] . ( 173 sec) [ -21164.2988] [Topology ] . ( 178 sec) [ -21164.2289] [Topology ] . ( 184 sec) [ -21164.1911] [Topology ] . ( 189 sec) [ -21164.1701] [Topology ] . ( 194 sec) [ -21164.1583] [Topology ] . ( 200 sec) [ -21164.1517] [Topology ] . ( 200 sec) [ -21164.1423] [Alpha ][ 0.520987] . ( 201 sec) [ -21164.1423] [Topology ] . ( 206 sec) [ -21164.1379] [Topology ] . ( 211 sec) [ -21164.1355] [Topology ] . ( 217 sec) [ -21164.1341] [Topology ] . ( 222 sec) [ -21164.1333] [Topology ] . ( 223 sec) [ -21164.1333] [Alpha ][ 0.520987] . ( 223 sec) [ -21164.1333] [Topology ] . ( 228 sec) [ -21164.1329] [Topology ] . ( 229 sec) [ -21164.1329] [Alpha ][ 0.520987] . Checking for NNIs, optimizing five branches... . ( 273 sec) [ -21163.4742] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -21163.474232. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -34444.5679] [Alpha ][ 0.500960] . ( 3 sec) [ -34312.9983] [ 5872] [depth= 8] . ( 4 sec) [ -33949.7727] [ 5788] [depth= 7] . ( 4 sec) [ -33932.8707] [ 5780] [depth= 2] . ( 5 sec) [ -33556.8570] [ 5710] [depth= 7] . ( 6 sec) [ -32883.2378] [ 5657] [depth= 6] . ( 7 sec) [ -32689.7061] [ 5618] [depth= 5] . ( 7 sec) [ -32602.1865] [ 5609] [depth= 1] . ( 8 sec) [ -31809.7664] [ 5524] [depth= 10] . ( 8 sec) [ -31599.3895] [ 5547] [depth= 1] . ( 9 sec) [ -31351.6573] [ 5447] [depth= 10] . ( 10 sec) [ -30771.8430] [ 5300] [depth= 8] . ( 11 sec) [ -29784.1717] [ 5181] [depth= 6] . ( 12 sec) [ -29201.5612] [ 5138] [depth= 5] . ( 13 sec) [ -28872.8959] [ 5087] [depth= 11] . ( 13 sec) [ -28858.2647] [ 5097] [depth= 1] . ( 14 sec) [ -28828.3790] [ 5087] [depth= 1] . ( 15 sec) [ -28134.6342] [ 5046] [depth= 7] . ( 16 sec) [ -28068.9569] [ 5032] [depth= 5] . ( 17 sec) [ -28064.7162] [ 5028] [depth= 1] . ( 18 sec) [ -27900.8440] [ 4968] [depth= 2] . ( 19 sec) [ -27689.4986] [ 4965] [depth= 1] . ( 19 sec) [ -27564.9530] [ 4963] [depth= 2] . ( 20 sec) [ -27478.6520] [ 4935] [depth= 3] . ( 21 sec) [ -26971.7500] [ 4850] [depth= 10] . ( 22 sec) [ -26846.0275] [ 4825] [depth= 8] . ( 22 sec) [ -26824.9973] [ 4821] [depth= 2] . ( 23 sec) [ -26807.6753] [ 4815] [depth= 1] . ( 25 sec) [ -26734.6418] [ 4768] [depth= 8] . ( 25 sec) [ -26733.0570] [ 4774] [depth= 1] . ( 26 sec) [ -26219.4619] [ 4674] [depth= 8] . ( 27 sec) [ -25901.4178] [ 4656] [depth= 6] . ( 27 sec) [ -25460.0499] [ 4608] [depth= 3] . ( 28 sec) [ -25452.5835] [ 4611] [depth= 1] . ( 29 sec) [ -25203.0879] [ 4551] [depth= 7] . ( 30 sec) [ -25166.1520] [ 4534] [depth= 1] . ( 30 sec) [ -25160.8874] [ 4528] [depth= 3] . ( 31 sec) [ -24695.0545] [ 4401] [depth= 4] . ( 32 sec) [ -24610.9731] [ 4397] [depth= 1] . ( 33 sec) [ -24114.9871] [ 4261] [depth= 5] . ( 34 sec) [ -23931.1305] [ 4230] [depth= 3] . ( 35 sec) [ -23877.6385] [ 4221] [depth= 1] . ( 35 sec) [ -23866.1850] [ 4242] [depth= 8] . ( 36 sec) [ -23789.6771] [ 4215] [depth= 1] . ( 37 sec) [ -23649.1158] [ 4194] [depth= 1] . ( 37 sec) [ -23635.0286] [ 4194] [depth= 1] . ( 38 sec) [ -23154.1034] [ 4049] [depth= 7] . ( 40 sec) [ -23098.4923] [ 4027] [depth= 1] . ( 41 sec) [ -22924.2923] [ 3994] [depth= 1] . ( 42 sec) [ -22887.4663] [ 3992] [depth= 1] . ( 43 sec) [ -22880.7071] [ 3989] [depth= 1] . ( 45 sec) [ -22608.1234] [ 3895] [depth= 2] . ( 45 sec) [ -22594.4039] [ 3891] [depth= 1] . ( 48 sec) [ -22442.6296] [ 3881] [depth= 1] . ( 48 sec) [ -22356.4023] [ 3844] [depth= 1] . ( 49 sec) [ -22298.7728] [ 3836] [depth= 1] . ( 50 sec) [ -22181.6967] [ 3808] [depth= 1] . ( 51 sec) [ -22084.7858] [ 3807] [depth= 4] . ( 51 sec) [ -22067.2867] [ 3806] [depth= 1] . ( 53 sec) [ -22051.5670] [ 3799] [depth= 1] . ( 54 sec) [ -21838.5512] [ 3749] [depth= 1] . ( 55 sec) [ -21823.7100] [ 3754] [depth= 1] . ( 57 sec) [ -21734.7185] [ 3736] [depth= 1] . ( 57 sec) [ -21673.5290] [ 3742] [depth= 1] . ( 58 sec) [ -21666.7744] [ 3761] [depth= 1] . ( 60 sec) [ -21664.9029] [ 3764] [depth= 1] . ( 62 sec) [ -21651.9071] [ 3761] [depth= 1] . ( 64 sec) [ -21448.3565] [Branch lengths ] . ( 65 sec) [ -21448.3090] [Alpha ][ 0.507951] . ( 67 sec) [ -21447.5818] [ 3761] [depth= 1] . ( 69 sec) [ -21265.3834] [ 3693] [depth= 2] . ( 70 sec) [ -21259.1330] [ 3686] [depth= 1] . ( 72 sec) [ -21254.7809] [ 3683] [depth= 1] . ( 77 sec) [ -21248.1764] [ 3680] [depth= 1] . ( 78 sec) [ -21220.6998] [ 3667] [depth= 2] . ( 80 sec) [ -21202.1036] [ 3663] [depth= 1] . ( 89 sec) [ -21197.9414] [ 3663] [depth= 1] . ( 98 sec) [ -21197.1570] [ 3660] [depth= 1] . ( 114 sec) [ -21165.7062] [Branch lengths ] . ( 115 sec) [ -21165.5895] [Alpha ][ 0.518733] . ( 163 sec) [ -21163.8194] [Branch lengths ] . ( 163 sec) [ -21163.8194] [Topology ] . ( 169 sec) [ -21163.6076] [Topology ] . ( 174 sec) [ -21163.5328] [Topology ] . ( 179 sec) [ -21163.4940] [Topology ] . ( 184 sec) [ -21163.4732] [Topology ] . ( 190 sec) [ -21163.4618] [Topology ] . ( 195 sec) [ -21163.4555] [Topology ] . ( 196 sec) [ -21163.4455] [Alpha ][ 0.522014] . ( 196 sec) [ -21163.4455] [Topology ] . ( 201 sec) [ -21163.4413] [Topology ] . ( 207 sec) [ -21163.4390] [Topology ] . ( 212 sec) [ -21163.4378] [Topology ] . ( 217 sec) [ -21163.4371] [Topology ] . ( 218 sec) [ -21163.4371] [Alpha ][ 0.522014] . ( 218 sec) [ -21163.4371] [Topology ] . ( 224 sec) [ -21163.4367] [Topology ] . ( 224 sec) [ -21163.4367] [Alpha ][ 0.522014] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -21163.436709. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -36817.7885] [Alpha ][ 0.500960] . ( 3 sec) [ -36496.4598] [ 6166] [depth= 2] . ( 4 sec) [ -36211.0562] [ 6125] [depth= 10] . ( 4 sec) [ -35351.7816] [ 6058] [depth= 1] . ( 5 sec) [ -34752.0339] [ 5948] [depth= 7] . ( 6 sec) [ -34608.1273] [ 5926] [depth= 2] . ( 6 sec) [ -34157.3117] [ 5869] [depth= 6] . ( 7 sec) [ -33904.2241] [ 5859] [depth= 4] . ( 8 sec) [ -33854.9514] [ 5843] [depth= 1] . ( 8 sec) [ -33485.8235] [ 5764] [depth= 8] . ( 9 sec) [ -33397.8609] [ 5745] [depth= 2] . ( 10 sec) [ -33231.5544] [ 5731] [depth= 6] . ( 10 sec) [ -33099.7450] [ 5691] [depth= 3] . ( 11 sec) [ -33080.8749] [ 5689] [depth= 2] . ( 12 sec) [ -32618.9644] [ 5664] [depth= 8] . ( 12 sec) [ -32170.5888] [ 5644] [depth= 1] . ( 13 sec) [ -31977.2628] [ 5590] [depth= 9] . ( 14 sec) [ -31760.0056] [ 5574] [depth= 1] . ( 14 sec) [ -31400.8625] [ 5513] [depth= 3] . ( 16 sec) [ -30957.4961] [ 5436] [depth= 8] . ( 16 sec) [ -30851.0236] [ 5423] [depth= 4] . ( 17 sec) [ -30789.7848] [ 5400] [depth= 1] . ( 18 sec) [ -30408.5265] [ 5338] [depth= 9] . ( 18 sec) [ -30272.5544] [ 5324] [depth= 6] . ( 19 sec) [ -29962.3246] [ 5223] [depth= 7] . ( 20 sec) [ -29852.8148] [ 5209] [depth= 2] . ( 21 sec) [ -29562.7917] [ 5094] [depth= 2] . ( 21 sec) [ -29530.9507] [ 5088] [depth= 1] . ( 22 sec) [ -28942.1446] [ 5101] [depth= 1] . ( 23 sec) [ -28593.9256] [ 5005] [depth= 6] . ( 23 sec) [ -27924.7097] [ 4869] [depth= 9] . ( 24 sec) [ -27624.7684] [ 4848] [depth= 2] . ( 25 sec) [ -26598.8959] [ 4701] [depth= 5] . ( 26 sec) [ -26522.4497] [ 4695] [depth= 1] . ( 27 sec) [ -26433.0209] [ 4669] [depth= 4] . ( 27 sec) [ -26088.9914] [ 4659] [depth= 2] . ( 28 sec) [ -25858.8544] [ 4574] [depth= 6] . ( 29 sec) [ -25533.8951] [ 4512] [depth= 1] . ( 30 sec) [ -25140.1160] [ 4478] [depth= 3] . ( 31 sec) [ -24761.6978] [ 4348] [depth= 6] . ( 32 sec) [ -24729.4986] [ 4351] [depth= 2] . ( 33 sec) [ -24264.6634] [ 4265] [depth= 4] . ( 34 sec) [ -24186.7822] [ 4245] [depth= 15] . ( 35 sec) [ -23252.5377] [ 4106] [depth= 16] . ( 35 sec) [ -23019.0697] [ 4047] [depth= 8] . ( 36 sec) [ -22934.4619] [ 4065] [depth= 1] . ( 37 sec) [ -22733.2370] [ 4074] [depth= 4] . ( 37 sec) [ -22715.7662] [ 4057] [depth= 1] . ( 38 sec) [ -22672.5702] [ 4046] [depth= 7] . ( 39 sec) [ -22625.1275] [ 4037] [depth= 1] . ( 40 sec) [ -22589.1952] [ 4040] [depth= 5] . ( 41 sec) [ -22456.2927] [ 4008] [depth= 7] . ( 43 sec) [ -22344.9334] [ 3986] [depth= 1] . ( 43 sec) [ -22327.5598] [ 3976] [depth= 1] . ( 44 sec) [ -22085.4161] [ 3919] [depth= 11] . ( 45 sec) [ -22070.8674] [ 3915] [depth= 1] . ( 46 sec) [ -21991.1506] [ 3884] [depth= 1] . ( 46 sec) [ -21832.3243] [ 3821] [depth= 3] . ( 47 sec) [ -21816.9018] [ 3812] [depth= 1] . ( 50 sec) [ -21797.1834] [ 3808] [depth= 1] . ( 52 sec) [ -21782.8238] [ 3818] [depth= 4] . ( 53 sec) [ -21779.0602] [ 3819] [depth= 1] . ( 54 sec) [ -21765.5479] [ 3816] [depth= 1] . ( 55 sec) [ -21763.2336] [ 3817] [depth= 1] . ( 57 sec) [ -21757.5191] [ 3822] [depth= 1] . ( 58 sec) [ -21680.1241] [ 3805] [depth= 2] . ( 59 sec) [ -21662.6549] [ 3797] [depth= 1] . ( 60 sec) [ -21619.0576] [ 3775] [depth= 3] . ( 61 sec) [ -21614.8048] [ 3779] [depth= 1] . ( 64 sec) [ -21425.5390] [Branch lengths ] . ( 65 sec) [ -21425.5371] [Alpha ][ 0.499495] . ( 66 sec) [ -21420.7341] [ 3775] [depth= 1] . ( 68 sec) [ -21420.5168] [ 3775] [depth= 1] . ( 68 sec) [ -21400.7560] [ 3768] [depth= 2] . ( 71 sec) [ -21382.0213] [ 3759] [depth= 2] . ( 72 sec) [ -21378.6223] [ 3759] [depth= 1] . ( 74 sec) [ -21370.7929] [ 3754] [depth= 1] . ( 74 sec) [ -21364.3257] [ 3751] [depth= 1] . ( 77 sec) [ -21253.2147] [ 3682] [depth= 5] . ( 79 sec) [ -21238.3104] [ 3676] [depth= 1] . ( 80 sec) [ -21237.6728] [ 3680] [depth= 1] . ( 82 sec) [ -21237.3606] [ 3676] [depth= 1] . ( 84 sec) [ -21236.6991] [ 3674] [depth= 1] . ( 87 sec) [ -21235.9260] [ 3675] [depth= 1] . ( 91 sec) [ -21192.1236] [ 3660] [depth= 2] . ( 117 sec) [ -21166.4909] [Branch lengths ] . ( 118 sec) [ -21166.1551] [Alpha ][ 0.517944] . ( 167 sec) [ -21163.8568] [Branch lengths ] . ( 167 sec) [ -21163.8568] [Topology ] . ( 172 sec) [ -21163.6231] [Topology ] . ( 178 sec) [ -21163.5424] [Topology ] . ( 183 sec) [ -21163.5016] [Topology ] . ( 188 sec) [ -21163.4798] [Topology ] . ( 193 sec) [ -21163.4680] [Topology ] . ( 199 sec) [ -21163.4615] [Topology ] . ( 200 sec) [ -21163.4462] [Alpha ][ 0.522021] . ( 200 sec) [ -21163.4462] [Topology ] . ( 205 sec) [ -21163.4416] [Topology ] . ( 211 sec) [ -21163.4392] [Topology ] . ( 216 sec) [ -21163.4379] [Topology ] . ( 221 sec) [ -21163.4372] [Topology ] . ( 222 sec) [ -21163.4372] [Alpha ][ 0.522021] . ( 222 sec) [ -21163.4372] [Topology ] . ( 228 sec) [ -21163.4367] [Topology ] . ( 228 sec) [ -21163.4367] [Alpha ][ 0.522021] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -21163.436738. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -35648.8113] [Alpha ][ 0.500960] . ( 3 sec) [ -35344.3362] [ 6108] [depth= 12] . ( 4 sec) [ -35232.6336] [ 6084] [depth= 1] . ( 5 sec) [ -35019.0799] [ 6063] [depth= 6] . ( 5 sec) [ -34920.8869] [ 6023] [depth= 1] . ( 6 sec) [ -34642.3570] [ 6002] [depth= 4] . ( 7 sec) [ -34496.4637] [ 6018] [depth= 1] . ( 7 sec) [ -33793.7204] [ 6003] [depth= 4] . ( 8 sec) [ -33336.7106] [ 5920] [depth= 2] . ( 9 sec) [ -33054.8230] [ 5896] [depth= 4] . ( 9 sec) [ -32854.6692] [ 5864] [depth= 1] . ( 10 sec) [ -32753.1202] [ 5849] [depth= 5] . ( 11 sec) [ -32482.8372] [ 5795] [depth= 4] . ( 11 sec) [ -32322.1870] [ 5773] [depth= 3] . ( 12 sec) [ -32070.2931] [ 5762] [depth= 3] . ( 13 sec) [ -31294.0591] [ 5751] [depth= 6] . ( 13 sec) [ -31012.4720] [ 5681] [depth= 7] . ( 14 sec) [ -30862.9539] [ 5658] [depth= 7] . ( 15 sec) [ -30726.5142] [ 5636] [depth= 11] . ( 15 sec) [ -30578.9310] [ 5636] [depth= 5] . ( 16 sec) [ -30189.6522] [ 5524] [depth= 4] . ( 17 sec) [ -30069.5961] [ 5496] [depth= 2] . ( 18 sec) [ -29854.1350] [ 5435] [depth= 2] . ( 18 sec) [ -29459.5729] [ 5307] [depth= 5] . ( 19 sec) [ -29236.5213] [ 5247] [depth= 15] . ( 20 sec) [ -28915.7119] [ 5156] [depth= 2] . ( 20 sec) [ -28819.8251] [ 5148] [depth= 1] . ( 21 sec) [ -28498.0857] [ 5059] [depth= 4] . ( 22 sec) [ -28113.1176] [ 4985] [depth= 3] . ( 23 sec) [ -27816.7933] [ 4921] [depth= 8] . ( 23 sec) [ -27729.1487] [ 4900] [depth= 1] . ( 24 sec) [ -27496.5943] [ 4865] [depth= 11] . ( 25 sec) [ -26990.9807] [ 4736] [depth= 12] . ( 26 sec) [ -26935.0445] [ 4733] [depth= 2] . ( 27 sec) [ -26727.6404] [ 4680] [depth= 5] . ( 28 sec) [ -26586.4509] [ 4651] [depth= 6] . ( 28 sec) [ -26549.7721] [ 4646] [depth= 1] . ( 29 sec) [ -26549.3207] [ 4649] [depth= 1] . ( 30 sec) [ -26535.0506] [ 4641] [depth= 1] . ( 31 sec) [ -26530.7659] [ 4637] [depth= 1] . ( 32 sec) [ -26369.2106] [ 4589] [depth= 5] . ( 33 sec) [ -26340.6492] [ 4593] [depth= 1] . ( 34 sec) [ -26231.9078] [ 4540] [depth= 8] . ( 35 sec) [ -26134.8273] [ 4508] [depth= 1] . ( 36 sec) [ -25621.9669] [ 4466] [depth= 3] . ( 37 sec) [ -25371.5439] [ 4419] [depth= 1] . ( 38 sec) [ -25346.4999] [ 4402] [depth= 2] . ( 39 sec) [ -25338.9579] [ 4398] [depth= 1] . ( 40 sec) [ -24947.1401] [ 4333] [depth= 5] . ( 41 sec) [ -24566.4433] [ 4232] [depth= 1] . ( 41 sec) [ -24548.9644] [ 4226] [depth= 1] . ( 42 sec) [ -24449.2881] [ 4221] [depth= 6] . ( 43 sec) [ -24380.9677] [ 4194] [depth= 4] . ( 44 sec) [ -24266.0210] [ 4168] [depth= 1] . ( 44 sec) [ -24202.3612] [ 4157] [depth= 4] . ( 45 sec) [ -24188.6730] [ 4170] [depth= 10] . ( 47 sec) [ -24052.6702] [ 4140] [depth= 1] . ( 48 sec) [ -23924.2916] [ 4084] [depth= 7] . ( 49 sec) [ -23889.1911] [ 4071] [depth= 1] . ( 50 sec) [ -23809.9528] [ 4073] [depth= 1] . ( 51 sec) [ -23591.0423] [ 3997] [depth= 1] . ( 51 sec) [ -23590.3568] [ 3999] [depth= 1] . ( 52 sec) [ -22765.1342] [ 3863] [depth= 2] . ( 53 sec) [ -22764.0390] [ 3861] [depth= 1] . ( 54 sec) [ -22477.7797] [ 3807] [depth= 4] . ( 55 sec) [ -22359.0126] [ 3789] [depth= 2] . ( 56 sec) [ -22324.4091] [ 3794] [depth= 1] . ( 57 sec) [ -22258.0398] [ 3789] [depth= 5] . ( 59 sec) [ -22181.1993] [ 3766] [depth= 1] . ( 60 sec) [ -22041.0281] [ 3792] [depth= 1] . ( 61 sec) [ -22036.4006] [ 3798] [depth= 1] . ( 62 sec) [ -22007.2296] [ 3783] [depth= 1] . ( 63 sec) [ -21947.8653] [ 3771] [depth= 2] . ( 65 sec) [ -21946.9228] [ 3769] [depth= 1] . ( 67 sec) [ -21574.6924] [Branch lengths ] . ( 68 sec) [ -21574.6136] [Alpha ][ 0.510036] . ( 70 sec) [ -21574.1799] [ 3771] [depth= 1] . ( 71 sec) [ -21518.6422] [ 3750] [depth= 1] . ( 73 sec) [ -21518.3123] [ 3750] [depth= 1] . ( 74 sec) [ -21395.6347] [ 3716] [depth= 1] . ( 74 sec) [ -21393.9275] [ 3715] [depth= 1] . ( 76 sec) [ -21362.5862] [ 3704] [depth= 1] . ( 77 sec) [ -21360.7694] [ 3698] [depth= 1] . ( 78 sec) [ -21354.8934] [ 3698] [depth= 1] . ( 78 sec) [ -21342.1895] [ 3692] [depth= 2] . ( 79 sec) [ -21322.8248] [ 3684] [depth= 2] . ( 80 sec) [ -21318.1815] [ 3682] [depth= 1] . ( 82 sec) [ -21316.8790] [ 3688] [depth= 1] . ( 87 sec) [ -21311.2654] [ 3684] [depth= 1] . ( 88 sec) [ -21302.2812] [ 3680] [depth= 2] . ( 94 sec) [ -21281.3670] [ 3680] [depth= 1] . ( 98 sec) [ -21268.9464] [ 3678] [depth= 1] . ( 99 sec) [ -21268.1285] [ 3677] [depth= 1] . ( 100 sec) [ -21265.5584] [ 3675] [depth= 1] . ( 102 sec) [ -21251.9141] [ 3673] [depth= 1] . ( 104 sec) [ -21219.2626] [ 3660] [depth= 1] . ( 120 sec) [ -21172.0283] [Branch lengths ] . ( 121 sec) [ -21171.9806] [Alpha ][ 0.517236] . ( 170 sec) [ -21163.9786] [Branch lengths ] . ( 170 sec) [ -21163.9786] [Topology ] . ( 175 sec) [ -21163.5553] [Topology ] . ( 181 sec) [ -21163.4949] [Topology ] . ( 186 sec) [ -21163.4751] [Topology ] . ( 191 sec) [ -21163.4671] [Topology ] . ( 197 sec) [ -21163.4635] [Topology ] . ( 202 sec) [ -21163.4616] [Topology ] . ( 203 sec) [ -21163.4396] [Alpha ][ 0.522136] . ( 203 sec) [ -21163.4396] [Topology ] . ( 208 sec) [ -21163.4379] [Topology ] . ( 214 sec) [ -21163.4372] [Topology ] . ( 214 sec) [ -21163.4372] [Alpha ][ 0.522136] . ( 215 sec) [ -21163.4372] [Topology ] . ( 220 sec) [ -21163.4367] [Topology ] . ( 221 sec) [ -21163.4367] [Alpha ][ 0.522136] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -21163.436727. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -21417.6215] [Alpha ][ 0.500960] . ( 3 sec) [ -21417.6215] [Topology ] . ( 8 sec) [ -21227.1384] [Topology ] . ( 13 sec) [ -21194.3140] [Topology ] . ( 18 sec) [ -21178.6341] [Topology ] . ( 23 sec) [ -21171.3173] [Topology ] . ( 28 sec) [ -21167.7367] [Topology ] . ( 34 sec) [ -21165.9194] [Topology ] . ( 39 sec) [ -21164.9681] [Topology ] . ( 44 sec) [ -21164.4654] [Topology ] . ( 49 sec) [ -21164.1966] [Topology ] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -21163.8223] [Alpha ][ 0.520309] . ( 95 sec) [ -21163.8223] [Topology ] . ( 100 sec) [ -21163.6457] [Topology ] . ( 105 sec) [ -21163.5527] [Topology ] . ( 111 sec) [ -21163.5018] [Topology ] . ( 116 sec) [ -21163.4739] [Topology ] . ( 121 sec) [ -21163.4586] [Topology ] . ( 126 sec) [ -21163.4502] [Topology ] . Checking for NNIs, optimizing five branches... . ( 171 sec) [ -21163.4475] [Alpha ][ 0.521963] . ( 172 sec) [ -21163.4475] [Topology ] . ( 177 sec) [ -21163.4425] [Topology ] . ( 182 sec) [ -21163.4397] [Topology ] . ( 187 sec) [ -21163.4382] [Topology ] . ( 193 sec) [ -21163.4373] [Topology ] . Checking for NNIs, optimizing five branches... . ( 238 sec) [ -21163.4373] [Alpha ][ 0.521963] . ( 238 sec) [ -21163.4373] [Topology ] . ( 243 sec) [ -21163.4368] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 333 sec) [ -21417.6215] [Alpha ][ 0.500960] . ( 341 sec) [ -21416.4601] [ 3664] [depth= 1] . ( 343 sec) [ -21410.5283] [ 3661] [depth= 1] . ( 344 sec) [ -21406.6173] [ 3663] [depth= 1] . ( 345 sec) [ -21404.2374] [ 3664] [depth= 1] . ( 346 sec) [ -21401.2712] [ 3661] [depth= 1] . ( 352 sec) [ -21378.0439] [ 3666] [depth= 2] . ( 352 sec) [ -21377.2197] [ 3662] [depth= 2] . ( 353 sec) [ -21363.2171] [ 3661] [depth= 1] . ( 354 sec) [ -21361.9633] [ 3662] [depth= 1] . ( 356 sec) [ -21352.5151] [ 3661] [depth= 1] . ( 366 sec) [ -21351.3660] [ 3665] [depth= 1] . ( 367 sec) [ -21338.3273] [ 3661] [depth= 1] . ( 373 sec) [ -21336.2810] [ 3665] [depth= 1] . ( 374 sec) [ -21327.3395] [ 3661] [depth= 1] . ( 375 sec) [ -21321.8468] [ 3663] [depth= 1] . ( 377 sec) [ -21320.6861] [ 3661] [depth= 1] . ( 379 sec) [ -21318.9662] [ 3667] [depth= 1] . ( 380 sec) [ -21307.7239] [ 3661] [depth= 1] . ( 381 sec) [ -21305.7494] [ 3662] [depth= 1] . ( 383 sec) [ -21305.6432] [ 3661] [depth= 1] . ( 384 sec) [ -21305.1675] [ 3662] [depth= 1] . ( 386 sec) [ -21192.5756] [Branch lengths ] . ( 387 sec) [ -21192.5555] [Alpha ][ 0.505582] . ( 393 sec) [ -21189.2474] [ 3659] [depth= 1] . ( 427 sec) [ -21187.3106] [ 3660] [depth= 1] . ( 437 sec) [ -21167.7756] [Branch lengths ] . ( 438 sec) [ -21167.6534] [Alpha ][ 0.516613] . ( 486 sec) [ -21164.1315] [Branch lengths ] . ( 487 sec) [ -21164.1315] [Topology ] . ( 492 sec) [ -21163.7522] [Topology ] . ( 497 sec) [ -21163.6168] [Topology ] . ( 503 sec) [ -21163.5478] [Topology ] . ( 508 sec) [ -21163.5108] [Topology ] . ( 513 sec) [ -21163.4906] [Topology ] . ( 519 sec) [ -21163.4795] [Topology ] . ( 519 sec) [ -21163.4532] [Alpha ][ 0.521977] . ( 520 sec) [ -21163.4532] [Topology ] . ( 525 sec) [ -21163.4454] [Topology ] . ( 530 sec) [ -21163.4414] [Topology ] . ( 536 sec) [ -21163.4391] [Topology ] . ( 541 sec) [ -21163.4378] [Topology ] . ( 546 sec) [ -21163.4371] [Topology ] . ( 547 sec) [ -21163.4371] [Alpha ][ 0.521977] . ( 548 sec) [ -21163.4371] [Topology ] . ( 553 sec) [ -21163.4367] [Topology ] . ( 554 sec) [ -21163.4367] [Alpha ][ 0.521977] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -21163.436847 . Log likelihood obtained after SPR moves : -21163.436730 . Log likelihood of the current tree: -21163.436730. . Printing the most likely tree in file 'proteic_M2477_39x888_2005.phy_phyml_tree.txt'... . Best log likelihood : -21163.436709 . Time used 0h10m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2061.89user 0.00system 34:55.67elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps