.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2304_31x429_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 . 35 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 305 patterns found. (out of a total of 429 sites) . 122 sites without polymorphism (28.44%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9332.1542] [Alpha ][ 0.500960] . ( 1 sec) [ -9099.6020] [ 1231] [depth= 6] . ( 2 sec) [ -8923.2217] [ 1221] [depth= 5] . ( 2 sec) [ -8906.3920] [ 1242] [depth= 1] . ( 2 sec) [ -8612.8314] [ 1209] [depth= 4] . ( 3 sec) [ -8468.6401] [ 1173] [depth= 2] . ( 3 sec) [ -8320.7456] [ 1161] [depth= 4] . ( 3 sec) [ -8310.7710] [ 1160] [depth= 2] . ( 3 sec) [ -8309.3079] [ 1160] [depth= 1] . ( 4 sec) [ -8228.4853] [ 1160] [depth= 1] . ( 4 sec) [ -8225.9866] [ 1160] [depth= 2] . ( 4 sec) [ -8200.6903] [ 1160] [depth= 5] . ( 5 sec) [ -8199.4005] [ 1160] [depth= 2] . ( 5 sec) [ -8174.6706] [ 1158] [depth= 3] . ( 5 sec) [ -8136.7789] [ 1155] [depth= 7] . ( 5 sec) [ -8134.2141] [ 1155] [depth= 2] . ( 6 sec) [ -8128.9368] [ 1153] [depth= 3] . ( 6 sec) [ -7756.6359] [ 1108] [depth= 6] . ( 6 sec) [ -7370.7944] [ 1099] [depth= 2] . ( 7 sec) [ -7232.9407] [ 1058] [depth= 1] . ( 7 sec) [ -6912.6531] [ 1001] [depth= 1] . ( 7 sec) [ -6799.7653] [ 980] [depth= 1] . ( 8 sec) [ -6744.7050] [ 973] [depth= 12] . ( 8 sec) [ -6741.9885] [ 973] [depth= 1] . ( 9 sec) [ -6725.4036] [ 963] [depth= 5] . ( 9 sec) [ -6715.9706] [ 963] [depth= 6] . ( 10 sec) [ -6527.3985] [ 930] [depth= 7] . ( 10 sec) [ -6476.1785] [ 926] [depth= 6] . ( 10 sec) [ -6475.8760] [ 926] [depth= 1] . ( 11 sec) [ -6474.7892] [ 926] [depth= 5] . ( 11 sec) [ -6396.6415] [ 919] [depth= 3] . ( 11 sec) [ -6355.0179] [ 918] [depth= 1] . ( 11 sec) [ -6311.4393] [ 906] [depth= 6] . ( 12 sec) [ -6307.4061] [ 904] [depth= 1] . ( 12 sec) [ -6244.6256] [ 892] [depth= 3] . ( 12 sec) [ -6223.7967] [ 890] [depth= 2] . ( 13 sec) [ -6193.5377] [ 883] [depth= 6] . ( 13 sec) [ -6104.1490] [ 887] [depth= 1] . ( 13 sec) [ -6096.7370] [ 882] [depth= 1] . ( 14 sec) [ -6077.7658] [ 878] [depth= 4] . ( 14 sec) [ -6019.7761] [ 875] [depth= 2] . ( 14 sec) [ -6004.7510] [ 873] [depth= 2] . ( 15 sec) [ -5960.0459] [ 868] [depth= 2] . ( 15 sec) [ -5954.4273] [ 867] [depth= 1] . ( 16 sec) [ -5942.7090] [ 851] [depth= 2] . ( 16 sec) [ -5938.7156] [ 852] [depth= 2] . ( 18 sec) [ -5938.3158] [ 852] [depth= 1] . ( 19 sec) [ -5904.7445] [ 843] [depth= 2] . ( 20 sec) [ -5897.3445] [ 842] [depth= 10] . ( 21 sec) [ -5888.3955] [ 840] [depth= 6] . ( 21 sec) [ -5872.4620] [ 836] [depth= 4] . ( 21 sec) [ -5838.9767] [ 828] [depth= 2] . ( 21 sec) [ -5822.0928] [ 825] [depth= 1] . ( 22 sec) [ -5821.7711] [ 825] [depth= 1] . ( 22 sec) [ -5821.6020] [ 825] [depth= 1] . ( 26 sec) [ -5821.2617] [ 825] [depth= 1] . ( 26 sec) [ -5815.9690] [ 825] [depth= 1] . ( 29 sec) [ -5815.7611] [ 825] [depth= 1] . ( 30 sec) [ -5809.1828] [ 825] [depth= 1] . ( 33 sec) [ -5792.1316] [ 830] [depth= 1] . ( 33 sec) [ -5773.4675] [ 825] [depth= 1] . ( 33 sec) [ -5738.0356] [ 815] [depth= 1] . ( 34 sec) [ -5680.7886] [Branch lengths ] . ( 35 sec) [ -5668.0675] [Alpha ][ 0.847390] . ( 39 sec) [ -5668.0202] [ 815] [depth= 2] . ( 40 sec) [ -5666.5407] [ 816] [depth= 1] . ( 44 sec) [ -5601.9096] [ 808] [depth= 1] . ( 44 sec) [ -5601.8882] [ 808] [depth= 2] . ( 45 sec) [ -5598.4421] [ 818] [depth= 2] . ( 63 sec) [ -5583.2878] [ 809] [depth= 1] . ( 64 sec) [ -5583.2443] [ 811] [depth= 1] . ( 64 sec) [ -5578.6297] [ 810] [depth= 1] . ( 65 sec) [ -5574.5112] [ 811] [depth= 1] . ( 70 sec) [ -5574.4977] [ 811] [depth= 1] . ( 70 sec) [ -5574.3226] [ 809] [depth= 1] . ( 70 sec) [ -5571.2055] [ 795] [depth= 1] . ( 71 sec) [ -5571.0765] [ 795] [depth= 1] . ( 77 sec) [ -5571.0008] [ 794] [depth= 1] . ( 84 sec) [ -5570.9817] [ 794] [depth= 1] . ( 101 sec) [ -5510.6718] [Branch lengths ] . ( 102 sec) [ -5509.7384] [Alpha ][ 0.989007] . ( 112 sec) [ -5509.1984] [ 795] [depth= 1] . ( 151 sec) [ -5509.1699] [ 795] [depth= 1] . ( 164 sec) [ -5509.1595] [ 795] [depth= 2] . ( 181 sec) [ -5506.1085] [Branch lengths ] . ( 181 sec) [ -5506.0825] [Alpha ][ 1.015341] . ( 265 sec) [ -5506.0417] [Branch lengths ] . ( 265 sec) [ -5506.0417] [Topology ] . ( 267 sec) [ -5506.0412] [Topology ] . ( 268 sec) [ -5506.0411] [Alpha ][ 1.016712] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5506.041087. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9808.7707] [Alpha ][ 0.500960] . ( 1 sec) [ -9614.7883] [ 1265] [depth= 4] . ( 1 sec) [ -9217.6080] [ 1262] [depth= 6] . ( 1 sec) [ -9137.8358] [ 1260] [depth= 1] . ( 2 sec) [ -9023.3241] [ 1240] [depth= 1] . ( 2 sec) [ -8972.0182] [ 1228] [depth= 7] . ( 2 sec) [ -8930.5210] [ 1215] [depth= 2] . ( 3 sec) [ -8901.5343] [ 1206] [depth= 5] . ( 3 sec) [ -8750.2252] [ 1184] [depth= 7] . ( 4 sec) [ -8629.4698] [ 1160] [depth= 1] . ( 4 sec) [ -8585.9031] [ 1159] [depth= 6] . ( 4 sec) [ -8553.6624] [ 1160] [depth= 1] . ( 5 sec) [ -8437.9458] [ 1133] [depth= 13] . ( 5 sec) [ -7981.0141] [ 1131] [depth= 3] . ( 5 sec) [ -7905.5572] [ 1122] [depth= 2] . ( 6 sec) [ -7861.8770] [ 1119] [depth= 1] . ( 6 sec) [ -7861.7516] [ 1119] [depth= 1] . ( 6 sec) [ -7443.4922] [ 1119] [depth= 2] . ( 7 sec) [ -7434.0010] [ 1115] [depth= 3] . ( 7 sec) [ -7422.9014] [ 1114] [depth= 2] . ( 7 sec) [ -7415.0332] [ 1108] [depth= 1] . ( 7 sec) [ -7397.2709] [ 1106] [depth= 1] . ( 8 sec) [ -7345.5159] [ 1093] [depth= 3] . ( 8 sec) [ -7188.8047] [ 1093] [depth= 1] . ( 8 sec) [ -7161.8873] [ 1088] [depth= 1] . ( 9 sec) [ -7051.5511] [ 1085] [depth= 8] . ( 9 sec) [ -7035.2067] [ 1078] [depth= 10] . ( 9 sec) [ -6665.9684] [ 1004] [depth= 1] . ( 9 sec) [ -6663.3981] [ 1008] [depth= 1] . ( 10 sec) [ -6625.2672] [ 1007] [depth= 2] . ( 10 sec) [ -6619.4938] [ 1003] [depth= 1] . ( 10 sec) [ -6609.6653] [ 1003] [depth= 2] . ( 11 sec) [ -6605.8854] [ 1002] [depth= 1] . ( 11 sec) [ -6593.0234] [ 1002] [depth= 1] . ( 12 sec) [ -6579.2816] [ 1001] [depth= 1] . ( 12 sec) [ -6577.7872] [ 1001] [depth= 1] . ( 12 sec) [ -6526.2386] [ 992] [depth= 4] . ( 13 sec) [ -6525.0250] [ 992] [depth= 1] . ( 13 sec) [ -6449.1573] [ 996] [depth= 2] . ( 13 sec) [ -6374.0819] [ 963] [depth= 7] . ( 14 sec) [ -6318.3395] [ 966] [depth= 9] . ( 14 sec) [ -6312.6984] [ 966] [depth= 3] . ( 14 sec) [ -6299.8653] [ 965] [depth= 3] . ( 15 sec) [ -6294.5327] [ 964] [depth= 2] . ( 15 sec) [ -6290.1712] [ 966] [depth= 2] . ( 16 sec) [ -6096.8035] [ 908] [depth= 1] . ( 16 sec) [ -5997.4122] [ 878] [depth= 4] . ( 17 sec) [ -5997.3190] [ 880] [depth= 1] . ( 17 sec) [ -5992.3720] [ 880] [depth= 4] . ( 18 sec) [ -5986.8857] [ 878] [depth= 1] . ( 18 sec) [ -5984.8842] [ 877] [depth= 2] . ( 18 sec) [ -5980.3993] [ 876] [depth= 1] . ( 19 sec) [ -5979.6982] [ 876] [depth= 1] . ( 19 sec) [ -5978.1395] [ 876] [depth= 1] . ( 19 sec) [ -5964.4598] [ 876] [depth= 3] . ( 20 sec) [ -5928.6194] [ 876] [depth= 6] . ( 20 sec) [ -5927.9101] [ 877] [depth= 1] . ( 21 sec) [ -5915.5730] [ 875] [depth= 4] . ( 21 sec) [ -5883.0326] [ 872] [depth= 6] . ( 21 sec) [ -5847.0913] [ 868] [depth= 2] . ( 22 sec) [ -5832.3908] [ 858] [depth= 1] . ( 22 sec) [ -5831.1075] [ 858] [depth= 2] . ( 22 sec) [ -5830.2004] [ 858] [depth= 1] . ( 23 sec) [ -5829.6733] [ 858] [depth= 1] . ( 23 sec) [ -5828.6695] [ 858] [depth= 1] . ( 24 sec) [ -5827.6249] [ 859] [depth= 2] . ( 24 sec) [ -5825.1144] [ 859] [depth= 1] . ( 24 sec) [ -5823.2957] [ 858] [depth= 5] . ( 25 sec) [ -5818.6357] [ 857] [depth= 2] . ( 25 sec) [ -5799.8671] [ 856] [depth= 1] . ( 26 sec) [ -5724.5510] [Branch lengths ] . ( 26 sec) [ -5712.3684] [Alpha ][ 0.809759] . ( 28 sec) [ -5711.1203] [ 854] [depth= 4] . ( 28 sec) [ -5676.9409] [ 847] [depth= 7] . ( 29 sec) [ -5583.1770] [ 825] [depth= 6] . ( 29 sec) [ -5575.9900] [ 826] [depth= 1] . ( 30 sec) [ -5575.8729] [ 826] [depth= 1] . ( 30 sec) [ -5550.9505] [ 816] [depth= 3] . ( 30 sec) [ -5550.8260] [ 816] [depth= 1] . ( 31 sec) [ -5546.3581] [ 816] [depth= 1] . ( 31 sec) [ -5545.3510] [ 816] [depth= 1] . ( 32 sec) [ -5534.6949] [ 795] [depth= 3] . ( 36 sec) [ -5534.4542] [ 795] [depth= 2] . ( 37 sec) [ -5533.9305] [ 795] [depth= 1] . ( 38 sec) [ -5533.8917] [ 795] [depth= 2] . ( 48 sec) [ -5530.7126] [ 796] [depth= 1] . ( 49 sec) [ -5529.4556] [ 797] [depth= 1] . ( 51 sec) [ -5521.5866] [ 796] [depth= 1] . ( 75 sec) [ -5521.5112] [ 796] [depth= 1] . ( 93 sec) [ -5514.3866] [Branch lengths ] . ( 93 sec) [ -5512.6936] [Alpha ][ 0.994291] . ( 97 sec) [ -5508.0762] [ 795] [depth= 1] . ( 176 sec) [ -5506.1856] [Branch lengths ] . ( 177 sec) [ -5506.1685] [Alpha ][ 1.015411] . ( 260 sec) [ -5506.0542] [Branch lengths ] . ( 260 sec) [ -5506.0542] [Topology ] . ( 262 sec) [ -5506.0447] [Topology ] . ( 265 sec) [ -5506.0423] [Topology ] . ( 267 sec) [ -5506.0415] [Topology ] . ( 267 sec) [ -5506.0414] [Alpha ][ 1.016836] . ( 267 sec) [ -5506.0414] [Topology ] . ( 270 sec) [ -5506.0411] [Topology ] . ( 270 sec) [ -5506.0411] [Alpha ][ 1.016836] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5506.041144. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9259.1582] [Alpha ][ 0.500960] . ( 1 sec) [ -9004.7075] [ 1220] [depth= 7] . ( 2 sec) [ -8931.9413] [ 1207] [depth= 6] . ( 2 sec) [ -8854.6391] [ 1207] [depth= 1] . ( 2 sec) [ -8715.6945] [ 1207] [depth= 2] . ( 2 sec) [ -8647.2987] [ 1182] [depth= 2] . ( 3 sec) [ -8645.3926] [ 1182] [depth= 1] . ( 3 sec) [ -8628.9087] [ 1180] [depth= 3] . ( 3 sec) [ -8583.0682] [ 1180] [depth= 2] . ( 4 sec) [ -8543.3978] [ 1173] [depth= 1] . ( 4 sec) [ -8440.5590] [ 1168] [depth= 3] . ( 4 sec) [ -8000.7227] [ 1172] [depth= 1] . ( 4 sec) [ -7901.8987] [ 1161] [depth= 4] . ( 5 sec) [ -7828.8358] [ 1147] [depth= 2] . ( 5 sec) [ -7806.7207] [ 1146] [depth= 1] . ( 5 sec) [ -7777.5164] [ 1145] [depth= 3] . ( 6 sec) [ -7716.1133] [ 1134] [depth= 8] . ( 6 sec) [ -7630.0905] [ 1130] [depth= 8] . ( 6 sec) [ -7548.4679] [ 1132] [depth= 2] . ( 7 sec) [ -7541.3380] [ 1125] [depth= 3] . ( 7 sec) [ -7493.0878] [ 1121] [depth= 1] . ( 7 sec) [ -7456.3736] [ 1114] [depth= 6] . ( 7 sec) [ -7447.3804] [ 1112] [depth= 5] . ( 8 sec) [ -7396.6902] [ 1102] [depth= 2] . ( 8 sec) [ -7340.2852] [ 1096] [depth= 5] . ( 9 sec) [ -7336.6955] [ 1098] [depth= 2] . ( 9 sec) [ -7322.3267] [ 1094] [depth= 1] . ( 9 sec) [ -7313.9182] [ 1092] [depth= 1] . ( 10 sec) [ -7313.6650] [ 1093] [depth= 2] . ( 10 sec) [ -7300.7604] [ 1090] [depth= 2] . ( 11 sec) [ -7278.0877] [ 1085] [depth= 12] . ( 11 sec) [ -7236.8751] [ 1078] [depth= 9] . ( 11 sec) [ -7232.6037] [ 1078] [depth= 1] . ( 12 sec) [ -7221.8378] [ 1078] [depth= 1] . ( 12 sec) [ -7213.8239] [ 1078] [depth= 6] . ( 13 sec) [ -7199.6238] [ 1079] [depth= 1] . ( 13 sec) [ -7156.3308] [ 1077] [depth= 8] . ( 13 sec) [ -6587.6461] [ 1061] [depth= 9] . ( 14 sec) [ -6578.3210] [ 1061] [depth= 1] . ( 14 sec) [ -6577.5805] [ 1061] [depth= 1] . ( 15 sec) [ -6573.7995] [ 1060] [depth= 2] . ( 15 sec) [ -6565.5366] [ 1059] [depth= 7] . ( 17 sec) [ -6565.0795] [ 1058] [depth= 2] . ( 17 sec) [ -6506.3935] [ 1041] [depth= 6] . ( 18 sec) [ -6492.6069] [ 1039] [depth= 1] . ( 18 sec) [ -6486.0449] [ 1038] [depth= 5] . ( 18 sec) [ -6485.6206] [ 1037] [depth= 1] . ( 19 sec) [ -6417.8481] [ 1021] [depth= 2] . ( 19 sec) [ -6413.8837] [ 1021] [depth= 1] . ( 19 sec) [ -6260.3128] [ 948] [depth= 6] . ( 22 sec) [ -6251.8992] [ 951] [depth= 4] . ( 22 sec) [ -6251.7159] [ 952] [depth= 2] . ( 23 sec) [ -6219.2690] [ 943] [depth= 3] . ( 23 sec) [ -6189.6175] [ 914] [depth= 7] . ( 23 sec) [ -5929.1681] [ 871] [depth= 1] . ( 24 sec) [ -5918.1816] [ 870] [depth= 2] . ( 24 sec) [ -5804.9004] [ 835] [depth= 10] . ( 25 sec) [ -5804.1646] [ 835] [depth= 1] . ( 26 sec) [ -5786.4263] [ 832] [depth= 3] . ( 27 sec) [ -5768.5863] [ 824] [depth= 3] . ( 27 sec) [ -5762.2583] [ 828] [depth= 1] . ( 27 sec) [ -5748.7019] [ 827] [depth= 12] . ( 28 sec) [ -5745.7688] [ 827] [depth= 1] . ( 28 sec) [ -5745.2647] [ 827] [depth= 1] . ( 28 sec) [ -5731.8896] [ 825] [depth= 1] . ( 32 sec) [ -5722.8246] [ 824] [depth= 1] . ( 33 sec) [ -5722.6349] [ 824] [depth= 1] . ( 34 sec) [ -5682.6916] [Branch lengths ] . ( 34 sec) [ -5666.5173] [Alpha ][ 0.894075] . ( 43 sec) [ -5664.6450] [ 824] [depth= 1] . ( 52 sec) [ -5664.6341] [ 826] [depth= 2] . ( 54 sec) [ -5663.9962] [ 826] [depth= 1] . ( 54 sec) [ -5661.9020] [ 821] [depth= 1] . ( 55 sec) [ -5661.4877] [ 819] [depth= 2] . ( 57 sec) [ -5661.4773] [ 819] [depth= 1] . ( 60 sec) [ -5660.8629] [ 819] [depth= 1] . ( 63 sec) [ -5660.8361] [ 819] [depth= 2] . ( 65 sec) [ -5660.7106] [ 819] [depth= 2] . ( 69 sec) [ -5660.6256] [ 820] [depth= 1] . ( 72 sec) [ -5655.1492] [ 819] [depth= 1] . ( 75 sec) [ -5655.0942] [ 819] [depth= 2] . ( 76 sec) [ -5589.5193] [ 808] [depth= 5] . ( 76 sec) [ -5576.7958] [ 802] [depth= 2] . ( 80 sec) [ -5554.1594] [ 794] [depth= 5] . ( 85 sec) [ -5552.0159] [ 794] [depth= 1] . ( 86 sec) [ -5551.9557] [ 794] [depth= 2] . ( 86 sec) [ -5550.6680] [ 795] [depth= 1] . ( 96 sec) [ -5550.6314] [ 795] [depth= 1] . ( 102 sec) [ -5535.0714] [Branch lengths ] . ( 102 sec) [ -5534.6052] [Alpha ][ 0.996905] . ( 121 sec) [ -5533.3830] [ 795] [depth= 1] . ( 185 sec) [ -5511.5296] [Branch lengths ] . ( 186 sec) [ -5511.5133] [Alpha ][ 1.017501] . ( 269 sec) [ -5506.3851] [Branch lengths ] . ( 269 sec) [ -5506.3851] [Topology ] . ( 271 sec) [ -5506.1179] [Topology ] . ( 273 sec) [ -5506.0650] [Topology ] . ( 276 sec) [ -5506.0492] [Topology ] . ( 278 sec) [ -5506.0439] [Topology ] . ( 281 sec) [ -5506.0421] [Topology ] . ( 283 sec) [ -5506.0414] [Topology ] . ( 283 sec) [ -5506.0414] [Alpha ][ 1.017501] . ( 283 sec) [ -5506.0414] [Topology ] . ( 286 sec) [ -5506.0411] [Topology ] . ( 286 sec) [ -5506.0411] [Alpha ][ 1.017501] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5506.041121. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9725.0956] [Alpha ][ 0.500960] . ( 1 sec) [ -8851.5974] [ 1273] [depth= 9] . ( 1 sec) [ -8795.8647] [ 1269] [depth= 5] . ( 2 sec) [ -8546.0937] [ 1262] [depth= 6] . ( 2 sec) [ -8538.2446] [ 1247] [depth= 1] . ( 2 sec) [ -8508.2374] [ 1246] [depth= 7] . ( 3 sec) [ -8419.8718] [ 1233] [depth= 7] . ( 3 sec) [ -8297.2520] [ 1210] [depth= 1] . ( 3 sec) [ -8194.5606] [ 1205] [depth= 3] . ( 4 sec) [ -8149.1168] [ 1205] [depth= 2] . ( 4 sec) [ -8117.6331] [ 1204] [depth= 9] . ( 4 sec) [ -8071.7147] [ 1185] [depth= 2] . ( 5 sec) [ -7980.9308] [ 1169] [depth= 7] . ( 5 sec) [ -7966.9359] [ 1169] [depth= 1] . ( 5 sec) [ -7903.2379] [ 1163] [depth= 5] . ( 6 sec) [ -7901.8307] [ 1163] [depth= 2] . ( 6 sec) [ -7732.1065] [ 1145] [depth= 2] . ( 6 sec) [ -7628.2264] [ 1136] [depth= 7] . ( 7 sec) [ -7625.7446] [ 1136] [depth= 2] . ( 7 sec) [ -7622.3681] [ 1134] [depth= 4] . ( 7 sec) [ -7462.8078] [ 1135] [depth= 1] . ( 8 sec) [ -7144.5381] [ 1134] [depth= 13] . ( 8 sec) [ -7103.5143] [ 1133] [depth= 11] . ( 8 sec) [ -6903.5382] [ 1114] [depth= 10] . ( 9 sec) [ -6863.4121] [ 1101] [depth= 2] . ( 9 sec) [ -6855.8428] [ 1099] [depth= 1] . ( 9 sec) [ -6782.5285] [ 1084] [depth= 10] . ( 9 sec) [ -6765.1105] [ 1079] [depth= 5] . ( 10 sec) [ -6757.3552] [ 1077] [depth= 1] . ( 10 sec) [ -6738.6950] [ 1073] [depth= 3] . ( 10 sec) [ -6730.6268] [ 1073] [depth= 1] . ( 11 sec) [ -6716.5284] [ 1072] [depth= 5] . ( 11 sec) [ -6576.8752] [ 1051] [depth= 3] . ( 11 sec) [ -6573.4965] [ 1049] [depth= 1] . ( 12 sec) [ -6516.8100] [ 1031] [depth= 4] . ( 12 sec) [ -6362.5970] [ 959] [depth= 6] . ( 12 sec) [ -6328.8310] [ 952] [depth= 1] . ( 13 sec) [ -6327.0022] [ 952] [depth= 3] . ( 13 sec) [ -6305.2199] [ 958] [depth= 4] . ( 14 sec) [ -6291.4815] [ 954] [depth= 3] . ( 14 sec) [ -6290.2197] [ 951] [depth= 1] . ( 15 sec) [ -6140.1979] [ 952] [depth= 3] . ( 16 sec) [ -6131.6103] [ 949] [depth= 1] . ( 16 sec) [ -6128.1681] [ 945] [depth= 2] . ( 20 sec) [ -6098.9254] [ 933] [depth= 2] . ( 20 sec) [ -6053.4700] [ 927] [depth= 2] . ( 20 sec) [ -6050.9376] [ 927] [depth= 2] . ( 21 sec) [ -6041.0510] [ 927] [depth= 1] . ( 21 sec) [ -6029.2498] [ 926] [depth= 6] . ( 21 sec) [ -5823.0929] [ 858] [depth= 2] . ( 22 sec) [ -5746.6679] [ 845] [depth= 1] . ( 22 sec) [ -5742.9589] [ 842] [depth= 1] . ( 22 sec) [ -5725.3240] [ 834] [depth= 1] . ( 23 sec) [ -5711.9829] [ 816] [depth= 2] . ( 23 sec) [ -5711.0046] [ 817] [depth= 4] . ( 25 sec) [ -5693.0524] [ 814] [depth= 4] . ( 25 sec) [ -5693.0120] [ 814] [depth= 3] . ( 25 sec) [ -5684.3204] [ 815] [depth= 1] . ( 26 sec) [ -5684.0961] [ 815] [depth= 3] . ( 26 sec) [ -5683.9739] [ 815] [depth= 1] . ( 28 sec) [ -5677.2128] [ 814] [depth= 1] . ( 28 sec) [ -5677.1696] [ 814] [depth= 1] . ( 28 sec) [ -5676.8955] [ 814] [depth= 1] . ( 29 sec) [ -5675.6586] [ 814] [depth= 1] . ( 29 sec) [ -5672.6206] [ 817] [depth= 1] . ( 30 sec) [ -5671.4510] [ 817] [depth= 3] . ( 31 sec) [ -5618.2025] [Branch lengths ] . ( 31 sec) [ -5600.8616] [Alpha ][ 0.902148] . ( 33 sec) [ -5593.3654] [ 812] [depth= 1] . ( 34 sec) [ -5542.5159] [ 799] [depth= 6] . ( 41 sec) [ -5541.8531] [ 799] [depth= 1] . ( 43 sec) [ -5535.3679] [ 798] [depth= 1] . ( 51 sec) [ -5521.4845] [ 797] [depth= 2] . ( 58 sec) [ -5519.8559] [ 797] [depth= 2] . ( 61 sec) [ -5518.5076] [ 797] [depth= 1] . ( 65 sec) [ -5517.3420] [ 796] [depth= 1] . ( 89 sec) [ -5517.3309] [ 796] [depth= 2] . ( 99 sec) [ -5517.2542] [ 795] [depth= 2] . ( 103 sec) [ -5508.8804] [Branch lengths ] . ( 103 sec) [ -5508.4217] [Alpha ][ 1.004542] . ( 104 sec) [ -5507.3213] [ 795] [depth= 1] . ( 114 sec) [ -5507.2796] [ 795] [depth= 1] . ( 185 sec) [ -5506.1363] [Branch lengths ] . ( 186 sec) [ -5506.1317] [Alpha ][ 1.016056] . ( 269 sec) [ -5506.0496] [Branch lengths ] . ( 269 sec) [ -5506.0496] [Topology ] . ( 271 sec) [ -5506.0439] [Topology ] . ( 274 sec) [ -5506.0422] [Topology ] . ( 276 sec) [ -5506.0415] [Topology ] . ( 276 sec) [ -5506.0415] [Alpha ][ 1.017072] . ( 276 sec) [ -5506.0415] [Topology ] . ( 279 sec) [ -5506.0412] [Topology ] . ( 279 sec) [ -5506.0412] [Alpha ][ 1.017072] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5506.041191. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9713.1916] [Alpha ][ 0.500960] . ( 1 sec) [ -9547.3063] [ 1258] [depth= 2] . ( 2 sec) [ -9519.1571] [ 1250] [depth= 6] . ( 2 sec) [ -9311.0553] [ 1249] [depth= 2] . ( 2 sec) [ -9261.0035] [ 1248] [depth= 8] . ( 2 sec) [ -9256.8100] [ 1247] [depth= 3] . ( 3 sec) [ -9131.3970] [ 1246] [depth= 12] . ( 3 sec) [ -9052.6141] [ 1234] [depth= 2] . ( 3 sec) [ -8937.6025] [ 1234] [depth= 1] . ( 4 sec) [ -8909.5914] [ 1223] [depth= 9] . ( 4 sec) [ -8836.2991] [ 1219] [depth= 4] . ( 4 sec) [ -8802.0393] [ 1216] [depth= 6] . ( 4 sec) [ -8207.5400] [ 1214] [depth= 7] . ( 5 sec) [ -7706.3606] [ 1133] [depth= 6] . ( 5 sec) [ -7461.2252] [ 1114] [depth= 3] . ( 5 sec) [ -7423.8952] [ 1110] [depth= 5] . ( 6 sec) [ -7381.9876] [ 1105] [depth= 2] . ( 6 sec) [ -7348.6699] [ 1102] [depth= 4] . ( 6 sec) [ -7234.8726] [ 1073] [depth= 10] . ( 7 sec) [ -7217.6641] [ 1072] [depth= 10] . ( 7 sec) [ -7216.3664] [ 1072] [depth= 2] . ( 8 sec) [ -7195.5814] [ 1072] [depth= 1] . ( 11 sec) [ -7157.7828] [ 1077] [depth= 7] . ( 11 sec) [ -7053.4618] [ 1057] [depth= 6] . ( 11 sec) [ -6908.4143] [ 1026] [depth= 3] . ( 12 sec) [ -6838.3307] [ 1021] [depth= 8] . ( 12 sec) [ -6745.7069] [ 1002] [depth= 1] . ( 13 sec) [ -6523.4797] [ 1005] [depth= 11] . ( 13 sec) [ -6445.9496] [ 989] [depth= 9] . ( 13 sec) [ -6166.9402] [ 927] [depth= 6] . ( 14 sec) [ -6127.6505] [ 922] [depth= 1] . ( 14 sec) [ -6087.6945] [ 912] [depth= 4] . ( 14 sec) [ -6021.9834] [ 898] [depth= 1] . ( 16 sec) [ -5980.8918] [ 889] [depth= 1] . ( 17 sec) [ -5882.3813] [ 870] [depth= 1] . ( 17 sec) [ -5865.7730] [ 869] [depth= 1] . ( 17 sec) [ -5855.7309] [ 869] [depth= 3] . ( 18 sec) [ -5851.2015] [ 868] [depth= 1] . ( 18 sec) [ -5849.5000] [ 868] [depth= 2] . ( 18 sec) [ -5848.8029] [ 868] [depth= 2] . ( 19 sec) [ -5804.0992] [ 854] [depth= 8] . ( 19 sec) [ -5800.0104] [ 853] [depth= 3] . ( 20 sec) [ -5799.9939] [ 853] [depth= 3] . ( 20 sec) [ -5789.5201] [ 852] [depth= 3] . ( 20 sec) [ -5783.5991] [ 851] [depth= 1] . ( 21 sec) [ -5783.3046] [ 851] [depth= 1] . ( 21 sec) [ -5699.0655] [ 832] [depth= 1] . ( 21 sec) [ -5683.0299] [ 811] [depth= 7] . ( 21 sec) [ -5680.2719] [ 810] [depth= 4] . ( 22 sec) [ -5678.6415] [ 810] [depth= 1] . ( 22 sec) [ -5677.9330] [ 810] [depth= 1] . ( 23 sec) [ -5675.8103] [ 812] [depth= 2] . ( 26 sec) [ -5672.7185] [ 812] [depth= 1] . ( 27 sec) [ -5655.5604] [ 804] [depth= 1] . ( 28 sec) [ -5653.3761] [ 805] [depth= 1] . ( 28 sec) [ -5652.5467] [ 803] [depth= 2] . ( 28 sec) [ -5629.0739] [ 802] [depth= 1] . ( 29 sec) [ -5608.8301] [ 799] [depth= 1] . ( 29 sec) [ -5606.9394] [ 799] [depth= 1] . ( 30 sec) [ -5601.8266] [ 798] [depth= 1] . ( 30 sec) [ -5582.5276] [ 796] [depth= 3] . ( 30 sec) [ -5582.0632] [ 796] [depth= 1] . ( 31 sec) [ -5536.8407] [Branch lengths ] . ( 32 sec) [ -5516.6910] [Alpha ][ 0.977231] . ( 33 sec) [ -5516.6785] [ 796] [depth= 1] . ( 34 sec) [ -5516.6620] [ 796] [depth= 1] . ( 37 sec) [ -5514.2516] [ 796] [depth= 1] . ( 37 sec) [ -5514.0881] [ 796] [depth= 1] . ( 38 sec) [ -5514.0493] [ 795] [depth= 1] . ( 38 sec) [ -5513.9545] [ 795] [depth= 2] . ( 56 sec) [ -5513.8948] [ 795] [depth= 1] . ( 56 sec) [ -5512.0971] [ 795] [depth= 1] . ( 57 sec) [ -5510.6675] [ 795] [depth= 1] . ( 62 sec) [ -5510.6326] [ 795] [depth= 1] . ( 67 sec) [ -5510.5625] [ 795] [depth= 2] . ( 97 sec) [ -5510.5281] [ 795] [depth= 1] . ( 99 sec) [ -5506.4199] [Branch lengths ] . ( 100 sec) [ -5506.3768] [Alpha ][ 1.010788] . ( 182 sec) [ -5506.0636] [Branch lengths ] . ( 182 sec) [ -5506.0636] [Topology ] . ( 184 sec) [ -5506.0489] [Topology ] . ( 187 sec) [ -5506.0448] [Topology ] . ( 189 sec) [ -5506.0433] [Topology ] . ( 191 sec) [ -5506.0426] [Topology ] . ( 192 sec) [ -5506.0413] [Alpha ][ 1.016894] . ( 192 sec) [ -5506.0413] [Topology ] . ( 194 sec) [ -5506.0410] [Topology ] . ( 195 sec) [ -5506.0410] [Alpha ][ 1.016894] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5506.041044. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -5525.2178] [Alpha ][ 1.019870] . ( 0 sec) [ -5525.2178] [Topology ] . ( 3 sec) [ -5509.1416] [Topology ] . ( 6 sec) [ -5506.8771] [Topology ] . ( 8 sec) [ -5506.3210] [Topology ] . ( 11 sec) [ -5506.1448] [Topology ] . ( 13 sec) [ -5506.0815] [Topology ] . ( 16 sec) [ -5506.0573] [Topology ] . ( 18 sec) [ -5506.0478] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -5506.0474] [Alpha ][ 1.016286] . ( 33 sec) [ -5506.0474] [Topology ] . ( 36 sec) [ -5506.0435] [Topology ] . ( 38 sec) [ -5506.0420] [Topology ] . ( 41 sec) [ -5506.0414] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -5506.0414] [Alpha ][ 1.017303] . ( 56 sec) [ -5506.0414] [Topology ] . ( 58 sec) [ -5506.0411] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 89 sec) [ -5525.2178] [Alpha ][ 1.019870] . ( 90 sec) [ -5523.7723] [ 799] [depth= 1] . ( 91 sec) [ -5518.4228] [ 794] [depth= 1] . ( 93 sec) [ -5517.8227] [ 795] [depth= 1] . ( 95 sec) [ -5517.6086] [ 794] [depth= 1] . ( 96 sec) [ -5517.0146] [ 794] [depth= 1] . ( 96 sec) [ -5516.7583] [ 794] [depth= 1] . ( 97 sec) [ -5514.9515] [ 794] [depth= 1] . ( 105 sec) [ -5514.9117] [ 794] [depth= 1] . ( 108 sec) [ -5514.7584] [ 794] [depth= 1] . ( 140 sec) [ -5514.1524] [ 794] [depth= 1] . ( 141 sec) [ -5513.7654] [ 794] [depth= 1] . ( 143 sec) [ -5513.6489] [ 794] [depth= 2] . ( 145 sec) [ -5513.5736] [ 794] [depth= 1] . ( 150 sec) [ -5513.3028] [ 794] [depth= 1] . ( 151 sec) [ -5512.9288] [ 794] [depth= 1] . ( 152 sec) [ -5512.9169] [ 794] [depth= 2] . ( 153 sec) [ -5507.5579] [Branch lengths ] . ( 154 sec) [ -5507.5577] [Alpha ][ 1.017255] . ( 158 sec) [ -5506.6049] [ 795] [depth= 1] . ( 236 sec) [ -5506.0668] [Branch lengths ] . ( 237 sec) [ -5506.0668] [Alpha ][ 1.018272] . ( 320 sec) [ -5506.0415] [Branch lengths ] . ( 320 sec) [ -5506.0415] [Topology ] . ( 323 sec) [ -5506.0411] [Topology ] . ( 323 sec) [ -5506.0410] [Alpha ][ 1.016884] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5506.041091 . Log likelihood obtained after SPR moves : -5506.041042 . Log likelihood of the current tree: -5506.041042. . Printing the most likely tree in file 'proteic_M2304_31x429_2005.phy_phyml_tree.txt'... . Best log likelihood : -5506.041042 . Time used 0h5m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1708.09user 0.00system 28:37.28elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps