.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1812_34x176_2004.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... . 173 patterns found. (out of a total of 176 sites) . 16 sites without polymorphism (9.09%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9262.5117] [Alpha ][ 0.500960] . ( 2 sec) [ -9177.2687] [ 1628] [depth= 1] . ( 2 sec) [ -9025.9346] [ 1611] [depth= 6] . ( 2 sec) [ -8958.7210] [ 1609] [depth= 2] . ( 3 sec) [ -8896.5466] [ 1597] [depth= 4] . ( 3 sec) [ -8719.9803] [ 1585] [depth= 5] . ( 3 sec) [ -8695.7827] [ 1581] [depth= 1] . ( 3 sec) [ -7972.3859] [ 1526] [depth= 5] . ( 3 sec) [ -7968.1911] [ 1530] [depth= 1] . ( 4 sec) [ -7916.7567] [ 1524] [depth= 2] . ( 4 sec) [ -7895.5047] [ 1520] [depth= 1] . ( 5 sec) [ -7832.2243] [ 1492] [depth= 4] . ( 5 sec) [ -7814.9785] [ 1486] [depth= 1] . ( 5 sec) [ -7607.2141] [ 1484] [depth= 1] . ( 5 sec) [ -7471.3279] [ 1464] [depth= 3] . ( 5 sec) [ -7441.1546] [ 1461] [depth= 4] . ( 6 sec) [ -7353.1439] [ 1442] [depth= 4] . ( 6 sec) [ -7287.9286] [ 1425] [depth= 7] . ( 6 sec) [ -7268.5887] [ 1424] [depth= 1] . ( 6 sec) [ -7237.0174] [ 1396] [depth= 10] . ( 7 sec) [ -7201.2719] [ 1399] [depth= 4] . ( 7 sec) [ -7141.0701] [ 1396] [depth= 2] . ( 7 sec) [ -7027.0670] [ 1376] [depth= 7] . ( 7 sec) [ -6975.9758] [ 1365] [depth= 2] . ( 7 sec) [ -6966.5789] [ 1362] [depth= 7] . ( 8 sec) [ -6943.4220] [ 1360] [depth= 4] . ( 8 sec) [ -6774.9428] [ 1324] [depth= 9] . ( 8 sec) [ -6661.6722] [ 1299] [depth= 1] . ( 8 sec) [ -6617.1004] [ 1295] [depth= 5] . ( 9 sec) [ -6616.5371] [ 1295] [depth= 1] . ( 9 sec) [ -6599.5885] [ 1292] [depth= 1] . ( 9 sec) [ -6508.0861] [ 1283] [depth= 3] . ( 9 sec) [ -6444.7823] [ 1263] [depth= 1] . ( 10 sec) [ -6422.5483] [ 1240] [depth= 1] . ( 10 sec) [ -6397.3621] [ 1240] [depth= 1] . ( 10 sec) [ -6359.1006] [ 1238] [depth= 2] . ( 11 sec) [ -6315.1268] [ 1228] [depth= 1] . ( 11 sec) [ -6287.0255] [ 1212] [depth= 1] . ( 11 sec) [ -6206.9634] [ 1202] [depth= 6] . ( 11 sec) [ -6141.8761] [ 1182] [depth= 1] . ( 11 sec) [ -6088.7347] [ 1172] [depth= 1] . ( 12 sec) [ -6048.6674] [ 1164] [depth= 3] . ( 12 sec) [ -6021.2246] [ 1153] [depth= 1] . ( 12 sec) [ -6007.3825] [ 1152] [depth= 1] . ( 12 sec) [ -5936.2526] [ 1129] [depth= 4] . ( 13 sec) [ -5913.7612] [ 1118] [depth= 4] . ( 13 sec) [ -5868.9765] [ 1108] [depth= 1] . ( 13 sec) [ -5804.1273] [ 1086] [depth= 1] . ( 13 sec) [ -5803.7777] [ 1085] [depth= 5] . ( 13 sec) [ -5790.8656] [ 1083] [depth= 1] . ( 14 sec) [ -5772.5342] [ 1078] [depth= 2] . ( 14 sec) [ -5768.1483] [ 1082] [depth= 1] . ( 14 sec) [ -5751.1448] [ 1075] [depth= 1] . ( 14 sec) [ -5726.9198] [ 1062] [depth= 3] . ( 15 sec) [ -5682.0608] [ 1052] [depth= 1] . ( 15 sec) [ -5680.4787] [ 1051] [depth= 1] . ( 15 sec) [ -5667.6816] [ 1051] [depth= 2] . ( 15 sec) [ -5662.0356] [ 1049] [depth= 1] . ( 16 sec) [ -5660.0360] [ 1049] [depth= 1] . ( 17 sec) [ -5630.4350] [ 1047] [depth= 1] . ( 17 sec) [ -5592.1458] [ 1013] [depth= 10] . ( 18 sec) [ -5571.3078] [ 1008] [depth= 1] . ( 20 sec) [ -5544.0554] [ 1011] [depth= 1] . ( 20 sec) [ -5543.5684] [ 1009] [depth= 1] . ( 21 sec) [ -5499.9080] [Branch lengths ] . ( 21 sec) [ -5468.8989] [Alpha ][ 1.000038] . ( 24 sec) [ -5468.8372] [ 1009] [depth= 1] . ( 24 sec) [ -5467.1605] [ 1008] [depth= 1] . ( 26 sec) [ -5463.5254] [ 1005] [depth= 1] . ( 28 sec) [ -5462.1797] [ 1000] [depth= 1] . ( 33 sec) [ -5461.8113] [ 1000] [depth= 1] . ( 33 sec) [ -5461.2281] [ 1004] [depth= 1] . ( 35 sec) [ -5457.8818] [ 1006] [depth= 1] . ( 35 sec) [ -5457.4010] [ 1004] [depth= 1] . ( 38 sec) [ -5457.0152] [ 1003] [depth= 1] . ( 44 sec) [ -5449.4113] [Branch lengths ] . ( 44 sec) [ -5443.8022] [Alpha ][ 1.514074] . ( 51 sec) [ -5443.7501] [ 1004] [depth= 1] . ( 68 sec) [ -5440.2136] [Branch lengths ] . ( 69 sec) [ -5440.1483] [Alpha ][ 1.583760] . ( 93 sec) [ -5436.2495] [Branch lengths ] . ( 93 sec) [ -5436.2495] [Topology ] . ( 95 sec) [ -5435.7445] [Topology ] . ( 96 sec) [ -5435.4015] [Topology ] . ( 97 sec) [ -5435.3204] [Topology ] . ( 99 sec) [ -5435.1605] [Topology ] . ( 100 sec) [ -5434.2619] [Topology ] . ( 102 sec) [ -5430.6586] [Topology ] . ( 103 sec) [ -5423.5255] [Topology ] . ( 103 sec) [ -5423.4986] [Alpha ][ 1.629928] . ( 104 sec) [ -5423.4986] [Topology ] . ( 105 sec) [ -5421.5345] [Topology ] . ( 106 sec) [ -5421.0462] [Topology ] . ( 108 sec) [ -5420.9185] [Topology ] . ( 109 sec) [ -5420.8840] [Topology ] . ( 111 sec) [ -5420.8744] [Topology ] . ( 112 sec) [ -5420.8717] [Topology ] . ( 113 sec) [ -5420.8715] [Alpha ][ 1.625656] . ( 113 sec) [ -5420.8715] [Topology ] . ( 114 sec) [ -5420.8707] [Topology ] . ( 114 sec) [ -5420.8707] [Alpha ][ 1.625656] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -5420.5861] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5420.586115. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9464.0164] [Alpha ][ 0.500960] . ( 0 sec) [ -9353.1607] [ 1768] [depth= 10] . ( 1 sec) [ -9262.9124] [ 1768] [depth= 2] . ( 1 sec) [ -9045.9343] [ 1754] [depth= 1] . ( 1 sec) [ -8970.6585] [ 1751] [depth= 9] . ( 1 sec) [ -8888.9233] [ 1736] [depth= 3] . ( 1 sec) [ -8842.1511] [ 1727] [depth= 2] . ( 2 sec) [ -8805.5443] [ 1713] [depth= 3] . ( 2 sec) [ -8790.1971] [ 1710] [depth= 5] . ( 2 sec) [ -8740.9552] [ 1697] [depth= 6] . ( 2 sec) [ -8732.7980] [ 1693] [depth= 1] . ( 2 sec) [ -8588.3789] [ 1671] [depth= 9] . ( 3 sec) [ -8541.6804] [ 1653] [depth= 7] . ( 3 sec) [ -8479.0058] [ 1651] [depth= 1] . ( 3 sec) [ -8227.3172] [ 1606] [depth= 10] . ( 3 sec) [ -8009.5303] [ 1555] [depth= 9] . ( 3 sec) [ -7962.5761] [ 1529] [depth= 15] . ( 4 sec) [ -7832.1147] [ 1508] [depth= 3] . ( 4 sec) [ -7794.6318] [ 1507] [depth= 4] . ( 4 sec) [ -7732.3635] [ 1494] [depth= 1] . ( 4 sec) [ -7714.5587] [ 1485] [depth= 2] . ( 4 sec) [ -7550.9972] [ 1435] [depth= 4] . ( 5 sec) [ -7533.6198] [ 1409] [depth= 3] . ( 5 sec) [ -7507.4563] [ 1401] [depth= 4] . ( 5 sec) [ -7319.2194] [ 1401] [depth= 6] . ( 5 sec) [ -7256.1189] [ 1372] [depth= 7] . ( 5 sec) [ -7217.1440] [ 1370] [depth= 1] . ( 6 sec) [ -7169.9856] [ 1370] [depth= 4] . ( 6 sec) [ -7019.7372] [ 1347] [depth= 9] . ( 6 sec) [ -6975.7028] [ 1344] [depth= 1] . ( 6 sec) [ -6970.1628] [ 1344] [depth= 1] . ( 7 sec) [ -6929.6578] [ 1338] [depth= 1] . ( 7 sec) [ -6852.9697] [ 1331] [depth= 2] . ( 7 sec) [ -6819.1452] [ 1319] [depth= 2] . ( 7 sec) [ -6622.1300] [ 1310] [depth= 1] . ( 8 sec) [ -6471.8100] [ 1264] [depth= 6] . ( 8 sec) [ -6461.4868] [ 1263] [depth= 1] . ( 8 sec) [ -6389.0366] [ 1245] [depth= 3] . ( 8 sec) [ -6338.1520] [ 1236] [depth= 7] . ( 9 sec) [ -6227.4647] [ 1221] [depth= 6] . ( 9 sec) [ -6217.4096] [ 1221] [depth= 1] . ( 9 sec) [ -6202.1996] [ 1210] [depth= 2] . ( 9 sec) [ -6158.1368] [ 1198] [depth= 2] . ( 9 sec) [ -5968.8202] [ 1148] [depth= 5] . ( 10 sec) [ -5966.4956] [ 1147] [depth= 1] . ( 10 sec) [ -5961.1012] [ 1146] [depth= 5] . ( 11 sec) [ -5911.1528] [ 1133] [depth= 3] . ( 11 sec) [ -5893.9114] [ 1135] [depth= 1] . ( 11 sec) [ -5887.7857] [ 1133] [depth= 1] . ( 11 sec) [ -5887.1010] [ 1131] [depth= 6] . ( 12 sec) [ -5876.4288] [ 1119] [depth= 2] . ( 12 sec) [ -5862.3406] [ 1118] [depth= 2] . ( 13 sec) [ -5785.9165] [ 1091] [depth= 9] . ( 13 sec) [ -5703.6476] [ 1068] [depth= 4] . ( 13 sec) [ -5673.1369] [ 1051] [depth= 3] . ( 14 sec) [ -5670.6766] [ 1051] [depth= 1] . ( 14 sec) [ -5664.5029] [ 1048] [depth= 1] . ( 14 sec) [ -5663.3543] [ 1048] [depth= 1] . ( 15 sec) [ -5584.3117] [ 1021] [depth= 2] . ( 15 sec) [ -5559.4843] [ 1021] [depth= 1] . ( 15 sec) [ -5556.2833] [ 1022] [depth= 2] . ( 16 sec) [ -5553.7265] [ 1023] [depth= 2] . ( 17 sec) [ -5546.7594] [ 1023] [depth= 1] . ( 17 sec) [ -5507.1170] [Branch lengths ] . ( 18 sec) [ -5482.7863] [Alpha ][ 1.000296] . ( 18 sec) [ -5481.2782] [ 1022] [depth= 2] . ( 19 sec) [ -5481.2052] [ 1022] [depth= 1] . ( 19 sec) [ -5480.8247] [ 1022] [depth= 1] . ( 20 sec) [ -5478.2484] [ 1020] [depth= 1] . ( 22 sec) [ -5474.2213] [ 1016] [depth= 1] . ( 22 sec) [ -5474.0810] [ 1018] [depth= 1] . ( 24 sec) [ -5472.0622] [ 1016] [depth= 3] . ( 25 sec) [ -5469.7532] [ 1017] [depth= 1] . ( 35 sec) [ -5469.0496] [ 1014] [depth= 1] . ( 36 sec) [ -5467.6844] [ 1014] [depth= 1] . ( 37 sec) [ -5467.2483] [ 1018] [depth= 1] . ( 37 sec) [ -5448.4370] [ 1009] [depth= 1] . ( 39 sec) [ -5447.2301] [ 1006] [depth= 1] . ( 39 sec) [ -5447.1898] [ 1005] [depth= 1] . ( 42 sec) [ -5446.1001] [ 1006] [depth= 1] . ( 42 sec) [ -5433.3181] [Branch lengths ] . ( 43 sec) [ -5428.0998] [Alpha ][ 1.501835] . ( 51 sec) [ -5426.6770] [ 1006] [depth= 5] . ( 69 sec) [ -5422.1194] [Branch lengths ] . ( 69 sec) [ -5422.0177] [Alpha ][ 1.590022] . ( 97 sec) [ -5421.0295] [Branch lengths ] . ( 97 sec) [ -5421.0295] [Topology ] . ( 99 sec) [ -5420.9371] [Topology ] . ( 100 sec) [ -5420.9094] [Topology ] . ( 101 sec) [ -5420.8969] [Topology ] . ( 103 sec) [ -5420.8911] [Topology ] . ( 104 sec) [ -5420.8883] [Topology ] . ( 106 sec) [ -5420.8870] [Topology ] . ( 106 sec) [ -5420.8725] [Alpha ][ 1.623578] . ( 106 sec) [ -5420.8725] [Topology ] . ( 108 sec) [ -5420.8713] [Topology ] . ( 109 sec) [ -5420.8709] [Topology ] . ( 109 sec) [ -5420.8708] [Alpha ][ 1.625204] . ( 109 sec) [ -5420.8708] [Topology ] . ( 111 sec) [ -5420.8706] [Topology ] . ( 111 sec) [ -5420.8706] [Alpha ][ 1.625204] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -5420.5865] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5420.586526. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9685.3778] [Alpha ][ 0.500960] . ( 1 sec) [ -9594.3361] [ 1758] [depth= 1] . ( 1 sec) [ -9547.4788] [ 1739] [depth= 5] . ( 1 sec) [ -9264.3432] [ 1708] [depth= 4] . ( 2 sec) [ -9230.0642] [ 1710] [depth= 3] . ( 2 sec) [ -9182.6118] [ 1695] [depth= 5] . ( 2 sec) [ -9096.2500] [ 1694] [depth= 1] . ( 2 sec) [ -9028.2420] [ 1691] [depth= 1] . ( 2 sec) [ -8908.3089] [ 1655] [depth= 8] . ( 3 sec) [ -8850.5231] [ 1640] [depth= 5] . ( 3 sec) [ -8823.2954] [ 1641] [depth= 4] . ( 3 sec) [ -8743.2088] [ 1630] [depth= 10] . ( 3 sec) [ -8601.9483] [ 1603] [depth= 9] . ( 4 sec) [ -8578.9909] [ 1598] [depth= 3] . ( 4 sec) [ -8530.5276] [ 1597] [depth= 3] . ( 4 sec) [ -8499.7004] [ 1572] [depth= 4] . ( 4 sec) [ -8307.8674] [ 1572] [depth= 1] . ( 4 sec) [ -8087.9409] [ 1520] [depth= 7] . ( 5 sec) [ -7751.8494] [ 1465] [depth= 7] . ( 5 sec) [ -7712.1077] [ 1463] [depth= 1] . ( 5 sec) [ -7613.9923] [ 1441] [depth= 11] . ( 5 sec) [ -7583.4144] [ 1439] [depth= 8] . ( 5 sec) [ -7514.0758] [ 1439] [depth= 1] . ( 6 sec) [ -7470.6560] [ 1428] [depth= 10] . ( 6 sec) [ -7317.6565] [ 1402] [depth= 12] . ( 6 sec) [ -7249.3699] [ 1366] [depth= 4] . ( 6 sec) [ -7207.2089] [ 1364] [depth= 1] . ( 6 sec) [ -7153.9242] [ 1352] [depth= 10] . ( 7 sec) [ -7040.3435] [ 1334] [depth= 1] . ( 7 sec) [ -6938.6079] [ 1315] [depth= 2] . ( 7 sec) [ -6936.0647] [ 1311] [depth= 5] . ( 7 sec) [ -6907.1214] [ 1303] [depth= 3] . ( 8 sec) [ -6803.5965] [ 1275] [depth= 10] . ( 8 sec) [ -6789.9165] [ 1274] [depth= 3] . ( 8 sec) [ -6680.8594] [ 1261] [depth= 5] . ( 9 sec) [ -6678.8028] [ 1260] [depth= 1] . ( 9 sec) [ -6670.3211] [ 1259] [depth= 1] . ( 9 sec) [ -6662.4199] [ 1260] [depth= 2] . ( 10 sec) [ -6609.4536] [ 1239] [depth= 10] . ( 10 sec) [ -6603.5112] [ 1237] [depth= 2] . ( 10 sec) [ -6595.9958] [ 1236] [depth= 1] . ( 11 sec) [ -6594.3813] [ 1244] [depth= 1] . ( 11 sec) [ -6564.9319] [ 1236] [depth= 1] . ( 12 sec) [ -6454.1681] [ 1211] [depth= 8] . ( 12 sec) [ -6450.5754] [ 1213] [depth= 1] . ( 12 sec) [ -6336.9046] [ 1196] [depth= 1] . ( 13 sec) [ -6237.0787] [ 1173] [depth= 3] . ( 13 sec) [ -6228.3483] [ 1169] [depth= 2] . ( 13 sec) [ -6198.0737] [ 1168] [depth= 1] . ( 13 sec) [ -6145.6385] [ 1153] [depth= 5] . ( 14 sec) [ -6118.5142] [ 1166] [depth= 1] . ( 14 sec) [ -6035.3849] [ 1141] [depth= 2] . ( 14 sec) [ -5982.6940] [ 1135] [depth= 4] . ( 14 sec) [ -5972.9910] [ 1130] [depth= 4] . ( 14 sec) [ -5951.2575] [ 1111] [depth= 2] . ( 15 sec) [ -5949.9379] [ 1113] [depth= 2] . ( 15 sec) [ -5803.3845] [ 1078] [depth= 4] . ( 15 sec) [ -5800.5033] [ 1076] [depth= 1] . ( 15 sec) [ -5766.2530] [ 1067] [depth= 2] . ( 16 sec) [ -5741.0596] [ 1075] [depth= 1] . ( 16 sec) [ -5722.9398] [ 1084] [depth= 1] . ( 16 sec) [ -5683.0818] [ 1078] [depth= 1] . ( 16 sec) [ -5679.1341] [ 1077] [depth= 1] . ( 17 sec) [ -5673.3513] [ 1076] [depth= 1] . ( 18 sec) [ -5659.7799] [ 1073] [depth= 1] . ( 18 sec) [ -5613.2305] [ 1049] [depth= 6] . ( 18 sec) [ -5541.3746] [Branch lengths ] . ( 19 sec) [ -5506.1579] [Alpha ][ 1.000316] . ( 19 sec) [ -5504.1379] [ 1049] [depth= 1] . ( 20 sec) [ -5494.5880] [ 1045] [depth= 1] . ( 20 sec) [ -5485.7797] [ 1019] [depth= 5] . ( 22 sec) [ -5484.9940] [ 1018] [depth= 1] . ( 25 sec) [ -5480.3037] [ 1020] [depth= 1] . ( 25 sec) [ -5480.2856] [ 1020] [depth= 1] . ( 25 sec) [ -5476.4652] [ 1018] [depth= 1] . ( 32 sec) [ -5465.9852] [ 1008] [depth= 2] . ( 32 sec) [ -5463.5093] [ 1007] [depth= 1] . ( 35 sec) [ -5463.3265] [ 1002] [depth= 1] . ( 35 sec) [ -5462.1225] [ 1006] [depth= 1] . ( 36 sec) [ -5458.0426] [ 1007] [depth= 1] . ( 36 sec) [ -5457.2912] [ 1005] [depth= 1] . ( 36 sec) [ -5457.1902] [ 1007] [depth= 1] . ( 37 sec) [ -5456.6985] [ 1006] [depth= 1] . ( 40 sec) [ -5456.1858] [ 1015] [depth= 1] . ( 42 sec) [ -5447.0693] [Branch lengths ] . ( 42 sec) [ -5440.4801] [Alpha ][ 1.562284] . ( 58 sec) [ -5426.0366] [ 1006] [depth= 1] . ( 69 sec) [ -5424.6094] [Branch lengths ] . ( 69 sec) [ -5424.5887] [Alpha ][ 1.601770] . ( 95 sec) [ -5424.4559] [Branch lengths ] . ( 95 sec) [ -5424.4559] [Topology ] . ( 96 sec) [ -5424.4434] [Topology ] . ( 98 sec) [ -5424.4369] [Topology ] . ( 99 sec) [ -5424.4148] [Topology ] . ( 101 sec) [ -5424.2672] [Topology ] . ( 102 sec) [ -5423.4930] [Topology ] . ( 104 sec) [ -5421.6003] [Topology ] . ( 104 sec) [ -5421.5975] [Alpha ][ 1.617013] . ( 104 sec) [ -5421.5975] [Topology ] . ( 105 sec) [ -5420.8348] [Topology ] . ( 107 sec) [ -5420.6785] [Topology ] . ( 108 sec) [ -5420.6415] [Topology ] . ( 110 sec) [ -5420.6318] [Topology ] . ( 111 sec) [ -5420.6290] [Topology ] . ( 112 sec) [ -5420.6282] [Topology ] . ( 113 sec) [ -5420.6281] [Alpha ][ 1.615240] . ( 113 sec) [ -5420.6281] [Topology ] . ( 114 sec) [ -5420.6279] [Topology ] . ( 114 sec) [ -5420.6279] [Alpha ][ 1.615240] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -5420.5614] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5420.561372. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9106.0508] [Alpha ][ 0.500960] . ( 1 sec) [ -9008.2346] [ 1694] [depth= 7] . ( 1 sec) [ -8820.0827] [ 1663] [depth= 3] . ( 1 sec) [ -8760.5707] [ 1624] [depth= 6] . ( 1 sec) [ -8679.9003] [ 1616] [depth= 1] . ( 1 sec) [ -8652.5074] [ 1615] [depth= 14] . ( 2 sec) [ -8571.2814] [ 1600] [depth= 3] . ( 2 sec) [ -8522.2906] [ 1591] [depth= 5] . ( 2 sec) [ -8400.7118] [ 1568] [depth= 11] . ( 2 sec) [ -8173.3823] [ 1520] [depth= 11] . ( 2 sec) [ -8102.3615] [ 1518] [depth= 1] . ( 3 sec) [ -7861.5335] [ 1494] [depth= 5] . ( 3 sec) [ -7851.0015] [ 1492] [depth= 6] . ( 3 sec) [ -7675.5977] [ 1468] [depth= 1] . ( 3 sec) [ -7588.6633] [ 1450] [depth= 9] . ( 4 sec) [ -7554.1516] [ 1436] [depth= 4] . ( 4 sec) [ -7493.1704] [ 1434] [depth= 1] . ( 4 sec) [ -7338.9069] [ 1422] [depth= 5] . ( 4 sec) [ -7254.9353] [ 1419] [depth= 4] . ( 4 sec) [ -7251.9138] [ 1419] [depth= 1] . ( 5 sec) [ -7248.8538] [ 1418] [depth= 1] . ( 5 sec) [ -7157.7082] [ 1387] [depth= 2] . ( 5 sec) [ -7131.1175] [ 1393] [depth= 6] . ( 5 sec) [ -6984.9983] [ 1357] [depth= 6] . ( 5 sec) [ -6931.4827] [ 1366] [depth= 1] . ( 6 sec) [ -6901.2128] [ 1363] [depth= 7] . ( 6 sec) [ -6853.7132] [ 1352] [depth= 3] . ( 6 sec) [ -6789.6875] [ 1342] [depth= 8] . ( 6 sec) [ -6754.9277] [ 1339] [depth= 3] . ( 7 sec) [ -6715.1267] [ 1337] [depth= 2] . ( 7 sec) [ -6696.5579] [ 1332] [depth= 4] . ( 7 sec) [ -6675.1295] [ 1314] [depth= 2] . ( 7 sec) [ -6671.4355] [ 1314] [depth= 1] . ( 8 sec) [ -6669.9631] [ 1311] [depth= 2] . ( 8 sec) [ -6573.6509] [ 1297] [depth= 2] . ( 8 sec) [ -6500.9005] [ 1281] [depth= 7] . ( 8 sec) [ -6395.3843] [ 1273] [depth= 1] . ( 9 sec) [ -6333.5916] [ 1252] [depth= 9] . ( 9 sec) [ -6329.1079] [ 1250] [depth= 1] . ( 9 sec) [ -6265.8456] [ 1231] [depth= 3] . ( 9 sec) [ -6256.2020] [ 1227] [depth= 1] . ( 9 sec) [ -6255.9118] [ 1225] [depth= 1] . ( 10 sec) [ -6253.9333] [ 1220] [depth= 1] . ( 10 sec) [ -6221.5717] [ 1205] [depth= 6] . ( 11 sec) [ -6180.8794] [ 1196] [depth= 4] . ( 11 sec) [ -6164.5975] [ 1182] [depth= 2] . ( 11 sec) [ -6159.6581] [ 1186] [depth= 2] . ( 11 sec) [ -6137.2849] [ 1180] [depth= 4] . ( 12 sec) [ -6132.2362] [ 1180] [depth= 1] . ( 12 sec) [ -6129.2842] [ 1176] [depth= 2] . ( 12 sec) [ -6122.4151] [ 1172] [depth= 2] . ( 12 sec) [ -6118.4513] [ 1176] [depth= 1] . ( 13 sec) [ -6111.2027] [ 1174] [depth= 4] . ( 13 sec) [ -6075.1138] [ 1151] [depth= 4] . ( 13 sec) [ -5994.6343] [ 1131] [depth= 5] . ( 13 sec) [ -5956.2803] [ 1128] [depth= 1] . ( 14 sec) [ -5948.4441] [ 1126] [depth= 1] . ( 14 sec) [ -5903.5829] [ 1127] [depth= 2] . ( 14 sec) [ -5838.0299] [ 1092] [depth= 12] . ( 14 sec) [ -5828.2369] [ 1088] [depth= 2] . ( 15 sec) [ -5822.1649] [ 1093] [depth= 1] . ( 15 sec) [ -5818.2512] [ 1092] [depth= 1] . ( 15 sec) [ -5804.3067] [ 1103] [depth= 1] . ( 16 sec) [ -5795.0479] [ 1091] [depth= 2] . ( 16 sec) [ -5767.5016] [ 1076] [depth= 6] . ( 17 sec) [ -5712.9702] [ 1064] [depth= 1] . ( 18 sec) [ -5651.1436] [Branch lengths ] . ( 18 sec) [ -5620.0516] [Alpha ][ 1.000029] . ( 18 sec) [ -5616.4674] [ 1062] [depth= 2] . ( 19 sec) [ -5614.0798] [ 1063] [depth= 1] . ( 20 sec) [ -5613.6335] [ 1063] [depth= 2] . ( 22 sec) [ -5529.9872] [ 1043] [depth= 4] . ( 22 sec) [ -5524.4791] [ 1038] [depth= 1] . ( 22 sec) [ -5524.3599] [ 1038] [depth= 2] . ( 22 sec) [ -5522.1157] [ 1036] [depth= 1] . ( 23 sec) [ -5521.9736] [ 1039] [depth= 1] . ( 23 sec) [ -5514.3536] [ 1036] [depth= 1] . ( 24 sec) [ -5513.7335] [ 1038] [depth= 1] . ( 25 sec) [ -5509.2374] [ 1030] [depth= 1] . ( 25 sec) [ -5500.2569] [ 1027] [depth= 1] . ( 29 sec) [ -5498.3227] [ 1024] [depth= 1] . ( 29 sec) [ -5495.2524] [ 1025] [depth= 1] . ( 32 sec) [ -5474.7491] [ 1015] [depth= 1] . ( 34 sec) [ -5474.7276] [ 1014] [depth= 1] . ( 35 sec) [ -5474.4623] [ 1015] [depth= 1] . ( 37 sec) [ -5462.5868] [ 1009] [depth= 1] . ( 38 sec) [ -5459.8073] [ 1006] [depth= 1] . ( 39 sec) [ -5458.9408] [ 1006] [depth= 1] . ( 42 sec) [ -5430.4838] [Branch lengths ] . ( 42 sec) [ -5423.8834] [Alpha ][ 1.573970] . ( 69 sec) [ -5421.2296] [Branch lengths ] . ( 70 sec) [ -5421.2296] [Topology ] . ( 71 sec) [ -5421.0218] [Topology ] . ( 72 sec) [ -5420.9566] [Topology ] . ( 74 sec) [ -5420.9280] [Topology ] . ( 75 sec) [ -5420.9149] [Topology ] . ( 77 sec) [ -5420.9088] [Topology ] . ( 78 sec) [ -5420.9058] [Topology ] . ( 78 sec) [ -5420.8750] [Alpha ][ 1.623367] . ( 79 sec) [ -5420.8750] [Topology ] . ( 80 sec) [ -5420.8723] [Topology ] . ( 81 sec) [ -5420.8714] [Topology ] . ( 82 sec) [ -5420.8713] [Alpha ][ 1.625053] . ( 82 sec) [ -5420.8713] [Topology ] . ( 83 sec) [ -5420.8709] [Topology ] . ( 83 sec) [ -5420.8709] [Alpha ][ 1.625053] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -5420.5866] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5420.586640. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9516.3535] [Alpha ][ 0.500960] . ( 1 sec) [ -9269.8352] [ 1720] [depth= 8] . ( 1 sec) [ -9123.3417] [ 1700] [depth= 8] . ( 1 sec) [ -9055.3844] [ 1691] [depth= 10] . ( 1 sec) [ -9022.3823] [ 1687] [depth= 2] . ( 2 sec) [ -8846.2328] [ 1645] [depth= 9] . ( 2 sec) [ -8479.0995] [ 1641] [depth= 1] . ( 2 sec) [ -8454.9543] [ 1634] [depth= 4] . ( 2 sec) [ -8440.3717] [ 1616] [depth= 1] . ( 2 sec) [ -8406.9607] [ 1613] [depth= 6] . ( 2 sec) [ -8338.2838] [ 1613] [depth= 1] . ( 3 sec) [ -8336.8860] [ 1611] [depth= 2] . ( 3 sec) [ -8225.3179] [ 1598] [depth= 5] . ( 3 sec) [ -8170.7458] [ 1591] [depth= 3] . ( 3 sec) [ -8044.8332] [ 1573] [depth= 2] . ( 3 sec) [ -8026.0342] [ 1568] [depth= 2] . ( 4 sec) [ -7797.4031] [ 1531] [depth= 6] . ( 4 sec) [ -7743.6148] [ 1514] [depth= 1] . ( 4 sec) [ -7715.6133] [ 1493] [depth= 5] . ( 4 sec) [ -7639.0541] [ 1482] [depth= 6] . ( 4 sec) [ -7523.1180] [ 1483] [depth= 1] . ( 5 sec) [ -7514.5739] [ 1473] [depth= 1] . ( 5 sec) [ -7504.5330] [ 1474] [depth= 1] . ( 5 sec) [ -7414.5623] [ 1449] [depth= 9] . ( 5 sec) [ -7226.3616] [ 1391] [depth= 3] . ( 5 sec) [ -7186.3039] [ 1361] [depth= 5] . ( 6 sec) [ -7085.9291] [ 1362] [depth= 1] . ( 6 sec) [ -7069.7211] [ 1361] [depth= 1] . ( 6 sec) [ -7049.1891] [ 1356] [depth= 2] . ( 6 sec) [ -7037.0627] [ 1353] [depth= 2] . ( 6 sec) [ -6997.7545] [ 1340] [depth= 2] . ( 7 sec) [ -6901.0362] [ 1324] [depth= 3] . ( 7 sec) [ -6826.2344] [ 1310] [depth= 3] . ( 7 sec) [ -6783.1459] [ 1292] [depth= 8] . ( 7 sec) [ -6764.9378] [ 1301] [depth= 4] . ( 8 sec) [ -6713.8870] [ 1293] [depth= 4] . ( 8 sec) [ -6628.2653] [ 1265] [depth= 2] . ( 8 sec) [ -6530.4576] [ 1252] [depth= 6] . ( 8 sec) [ -6458.2466] [ 1248] [depth= 4] . ( 8 sec) [ -6347.4657] [ 1235] [depth= 10] . ( 9 sec) [ -6333.0616] [ 1227] [depth= 10] . ( 9 sec) [ -6329.5294] [ 1233] [depth= 1] . ( 9 sec) [ -6227.6084] [ 1216] [depth= 8] . ( 9 sec) [ -6222.6763] [ 1213] [depth= 1] . ( 10 sec) [ -6201.9624] [ 1207] [depth= 1] . ( 10 sec) [ -6179.3671] [ 1203] [depth= 1] . ( 10 sec) [ -6177.2724] [ 1204] [depth= 2] . ( 11 sec) [ -6132.9878] [ 1193] [depth= 1] . ( 11 sec) [ -6116.7307] [ 1185] [depth= 1] . ( 11 sec) [ -6101.8944] [ 1188] [depth= 1] . ( 11 sec) [ -6015.8700] [ 1163] [depth= 2] . ( 12 sec) [ -5936.6208] [ 1143] [depth= 9] . ( 12 sec) [ -5903.5076] [ 1112] [depth= 14] . ( 12 sec) [ -5891.5847] [ 1113] [depth= 2] . ( 12 sec) [ -5837.8922] [ 1098] [depth= 2] . ( 12 sec) [ -5788.7563] [ 1083] [depth= 2] . ( 13 sec) [ -5773.7935] [ 1081] [depth= 1] . ( 13 sec) [ -5756.8945] [ 1079] [depth= 1] . ( 13 sec) [ -5755.0538] [ 1067] [depth= 1] . ( 13 sec) [ -5736.1855] [ 1064] [depth= 1] . ( 14 sec) [ -5730.3848] [ 1064] [depth= 1] . ( 14 sec) [ -5716.5828] [ 1062] [depth= 1] . ( 15 sec) [ -5706.4170] [ 1057] [depth= 3] . ( 16 sec) [ -5703.7455] [ 1057] [depth= 2] . ( 16 sec) [ -5699.3465] [ 1056] [depth= 1] . ( 16 sec) [ -5691.3776] [ 1057] [depth= 1] . ( 17 sec) [ -5689.1917] [ 1057] [depth= 1] . ( 17 sec) [ -5654.6924] [ 1053] [depth= 1] . ( 17 sec) [ -5647.6526] [ 1050] [depth= 2] . ( 18 sec) [ -5637.6181] [ 1050] [depth= 1] . ( 18 sec) [ -5587.8649] [Branch lengths ] . ( 19 sec) [ -5557.4270] [Alpha ][ 1.000110] . ( 19 sec) [ -5556.4141] [ 1053] [depth= 3] . ( 20 sec) [ -5555.4423] [ 1047] [depth= 2] . ( 20 sec) [ -5523.0534] [ 1037] [depth= 2] . ( 20 sec) [ -5509.6492] [ 1027] [depth= 4] . ( 21 sec) [ -5509.2403] [ 1027] [depth= 1] . ( 21 sec) [ -5506.5173] [ 1025] [depth= 1] . ( 21 sec) [ -5465.4439] [ 1015] [depth= 2] . ( 22 sec) [ -5459.5741] [ 1013] [depth= 1] . ( 22 sec) [ -5458.6317] [ 1014] [depth= 1] . ( 23 sec) [ -5457.6950] [ 1012] [depth= 1] . ( 26 sec) [ -5455.9630] [ 1013] [depth= 1] . ( 30 sec) [ -5448.5314] [ 1010] [depth= 1] . ( 32 sec) [ -5445.1908] [ 1010] [depth= 2] . ( 35 sec) [ -5445.0317] [ 1009] [depth= 1] . ( 37 sec) [ -5441.6135] [ 1006] [depth= 3] . ( 39 sec) [ -5440.6775] [ 1008] [depth= 1] . ( 42 sec) [ -5429.3285] [Branch lengths ] . ( 42 sec) [ -5423.0347] [Alpha ][ 1.553205] . ( 68 sec) [ -5421.5490] [Branch lengths ] . ( 68 sec) [ -5421.5490] [Topology ] . ( 69 sec) [ -5420.9913] [Topology ] . ( 71 sec) [ -5420.6744] [Topology ] . ( 72 sec) [ -5420.6123] [Topology ] . ( 74 sec) [ -5420.5910] [Topology ] . ( 75 sec) [ -5420.5828] [Topology ] . ( 77 sec) [ -5420.5793] [Topology ] . ( 78 sec) [ -5420.5778] [Topology ] . ( 79 sec) [ -5420.5316] [Alpha ][ 1.612120] . ( 79 sec) [ -5420.5316] [Topology ] . ( 80 sec) [ -5420.5293] [Topology ] . ( 82 sec) [ -5420.5287] [Topology ] . ( 82 sec) [ -5420.5286] [Alpha ][ 1.614337] . ( 82 sec) [ -5420.5286] [Topology ] . ( 83 sec) [ -5420.5283] [Topology ] . ( 84 sec) [ -5420.5283] [Alpha ][ 1.614337] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5420.528276. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -5450.8068] [Alpha ][ 1.505579] . ( 0 sec) [ -5450.8068] [Topology ] . ( 2 sec) [ -5428.0477] [Topology ] . ( 3 sec) [ -5424.1790] [Topology ] . ( 4 sec) [ -5422.1045] [Topology ] . ( 6 sec) [ -5421.4064] [Topology ] . ( 7 sec) [ -5421.1991] [Topology ] . ( 9 sec) [ -5421.1186] [Topology ] . ( 10 sec) [ -5421.0845] [Topology ] . ( 12 sec) [ -5421.0693] [Topology ] . ( 13 sec) [ -5421.0622] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -5420.7479] [Topology ] . ( 24 sec) [ -5420.5957] [Alpha ][ 1.611532] . ( 24 sec) [ -5420.5957] [Topology ] . ( 26 sec) [ -5420.5417] [Topology ] . ( 27 sec) [ -5420.5324] [Topology ] . ( 29 sec) [ -5420.5297] [Topology ] . ( 30 sec) [ -5420.5288] [Topology ] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -5420.5287] [Alpha ][ 1.614399] . ( 41 sec) [ -5420.5287] [Topology ] . ( 42 sec) [ -5420.5283] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 64 sec) [ -5450.8068] [Alpha ][ 1.505579] . ( 70 sec) [ -5450.0189] [ 1012] [depth= 1] . ( 70 sec) [ -5448.9229] [ 1012] [depth= 1] . ( 70 sec) [ -5448.5154] [ 1012] [depth= 1] . ( 71 sec) [ -5448.4366] [ 1008] [depth= 1] . ( 72 sec) [ -5447.8104] [ 1010] [depth= 1] . ( 74 sec) [ -5442.4187] [ 1008] [depth= 1] . ( 79 sec) [ -5442.0670] [ 1009] [depth= 1] . ( 79 sec) [ -5441.3342] [ 1008] [depth= 1] . ( 86 sec) [ -5440.1143] [ 1008] [depth= 1] . ( 87 sec) [ -5438.2939] [ 1005] [depth= 1] . ( 89 sec) [ -5423.1735] [Branch lengths ] . ( 89 sec) [ -5423.0919] [Alpha ][ 1.584207] . ( 96 sec) [ -5422.7747] [ 1006] [depth= 1] . ( 116 sec) [ -5421.0139] [Branch lengths ] . ( 116 sec) [ -5420.9977] [Alpha ][ 1.619858] . ( 144 sec) [ -5420.8880] [Branch lengths ] . ( 144 sec) [ -5420.8880] [Topology ] . ( 146 sec) [ -5420.8765] [Topology ] . ( 147 sec) [ -5420.8733] [Topology ] . ( 149 sec) [ -5420.8719] [Topology ] . ( 150 sec) [ -5420.8713] [Topology ] . ( 150 sec) [ -5420.8709] [Alpha ][ 1.625216] . ( 150 sec) [ -5420.8709] [Topology ] . ( 152 sec) [ -5420.8706] [Topology ] . ( 152 sec) [ -5420.8706] [Alpha ][ 1.625216] . Checking for NNIs, optimizing five branches... . ( 163 sec) [ -5420.5862] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5420.528259 . Log likelihood obtained after SPR moves : -5420.586153 . Log likelihood of the current tree: -5420.528259. . Printing the most likely tree in file 'proteic_M1812_34x176_2004.phy_phyml_tree.txt'... . Best log likelihood : -5420.528259 . Time used 0h2m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 775.88user 0.00system 12:58.87elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps