.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1768_31x228_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... . 60 patterns found. (out of a total of 228 sites) . 185 sites without polymorphism (81.14%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1930.1849] [Alpha ][ 0.500960] . ( 1 sec) [ -1811.8446] [ 69] [depth= 6] . ( 1 sec) [ -1355.0484] [ 68] [depth= 2] . ( 1 sec) [ -1350.3913] [ 67] [depth= 1] . ( 1 sec) [ -1320.1070] [ 67] [depth= 3] . ( 1 sec) [ -1319.8354] [ 67] [depth= 2] . ( 1 sec) [ -1318.7322] [ 67] [depth= 1] . ( 1 sec) [ -1314.2884] [ 67] [depth= 5] . ( 1 sec) [ -1311.9767] [ 67] [depth= 7] . ( 1 sec) [ -1311.7837] [ 67] [depth= 6] . ( 1 sec) [ -1286.2702] [ 67] [depth= 4] . ( 1 sec) [ -1278.5828] [ 67] [depth= 1] . ( 2 sec) [ -1262.8529] [ 67] [depth= 2] . ( 2 sec) [ -1249.7709] [ 66] [depth= 10] . ( 2 sec) [ -1247.2595] [ 65] [depth= 4] . ( 2 sec) [ -1237.1538] [ 65] [depth= 1] . ( 2 sec) [ -1200.4925] [ 65] [depth= 3] . ( 2 sec) [ -1199.9837] [ 64] [depth= 1] . ( 2 sec) [ -1199.2033] [ 64] [depth= 2] . ( 2 sec) [ -1198.9624] [ 64] [depth= 7] . ( 2 sec) [ -1188.7676] [ 62] [depth= 10] . ( 2 sec) [ -1180.8455] [ 61] [depth= 4] . ( 2 sec) [ -1169.8731] [ 60] [depth= 4] . ( 2 sec) [ -1169.6429] [ 60] [depth= 1] . ( 3 sec) [ -1167.8769] [ 60] [depth= 2] . ( 3 sec) [ -1166.7602] [ 60] [depth= 2] . ( 3 sec) [ -1161.5271] [ 60] [depth= 3] . ( 3 sec) [ -1161.4983] [ 60] [depth= 2] . ( 3 sec) [ -1161.3875] [ 60] [depth= 17] . ( 3 sec) [ -1158.2729] [ 59] [depth= 3] . ( 4 sec) [ -1157.1401] [ 59] [depth= 11] . ( 4 sec) [ -1141.6843] [ 59] [depth= 9] . ( 4 sec) [ -1119.2186] [ 59] [depth= 3] . ( 4 sec) [ -1111.0995] [ 59] [depth= 3] . ( 4 sec) [ -1110.2390] [ 59] [depth= 11] . ( 4 sec) [ -1107.3855] [ 59] [depth= 16] . ( 5 sec) [ -1106.7543] [ 59] [depth= 7] . ( 7 sec) [ -1104.5717] [ 59] [depth= 4] . ( 7 sec) [ -1099.7162] [ 59] [depth= 5] . ( 7 sec) [ -1096.1716] [ 57] [depth= 4] . ( 7 sec) [ -1091.1233] [ 57] [depth= 7] . ( 7 sec) [ -1084.9094] [ 57] [depth= 3] . ( 8 sec) [ -1084.8790] [ 57] [depth= 2] . ( 8 sec) [ -1078.4745] [ 56] [depth= 6] . ( 8 sec) [ -1078.1557] [ 56] [depth= 4] . ( 11 sec) [ -1077.6088] [ 56] [depth= 2] . ( 14 sec) [ -1077.5228] [ 56] [depth= 2] . ( 14 sec) [ -1077.4851] [ 56] [depth= 3] . ( 14 sec) [ -1068.5617] [ 55] [depth= 7] . ( 15 sec) [ -1068.5049] [ 55] [depth= 3] . ( 15 sec) [ -1062.5704] [ 54] [depth= 6] . ( 15 sec) [ -1062.5362] [ 54] [depth= 1] . ( 20 sec) [ -1062.0280] [ 54] [depth= 2] . ( 20 sec) [ -1061.9684] [ 54] [depth= 2] . ( 38 sec) [ -1058.6378] [ 53] [depth= 5] . ( 38 sec) [ -1058.5808] [Branch lengths ] . ( 38 sec) [ -1058.5423] [Alpha ][ 0.593773] . ( 58 sec) [ -1058.4856] [ 53] [depth= 2] . ( 75 sec) [ -1052.8887] [ 52] [depth= 5] . ( 114 sec) [ -1052.8067] [ 52] [depth= 6] . ( 127 sec) [ -1052.7000] [ 52] [depth= 2] . ( 168 sec) [ -1052.6883] [ 52] [depth= 1] . ( 168 sec) [ -1052.6169] [Branch lengths ] . ( 169 sec) [ -1052.5900] [Alpha ][ 0.691039] . ( 318 sec) [ -1052.5836] [Branch lengths ] . ( 318 sec) [ -1052.5836] [Topology ] . ( 319 sec) [ -1052.5832] [Topology ] . ( 319 sec) [ -1052.5832] [Alpha ][ 0.692119] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.583221. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1501.2665] [Alpha ][ 0.500960] . ( 0 sec) [ -1412.1782] [ 63] [depth= 7] . ( 0 sec) [ -1357.5175] [ 61] [depth= 8] . ( 0 sec) [ -1319.4165] [ 59] [depth= 3] . ( 0 sec) [ -1318.5260] [ 59] [depth= 2] . ( 0 sec) [ -1318.4509] [ 59] [depth= 4] . ( 0 sec) [ -1301.9151] [ 59] [depth= 4] . ( 1 sec) [ -1286.0939] [ 59] [depth= 3] . ( 1 sec) [ -1275.9625] [ 59] [depth= 1] . ( 1 sec) [ -1273.1899] [ 59] [depth= 3] . ( 1 sec) [ -1250.9772] [ 59] [depth= 2] . ( 1 sec) [ -1226.5956] [ 59] [depth= 6] . ( 1 sec) [ -1195.7935] [ 59] [depth= 1] . ( 1 sec) [ -1141.9042] [ 59] [depth= 3] . ( 1 sec) [ -1137.0467] [ 59] [depth= 2] . ( 2 sec) [ -1136.5907] [ 59] [depth= 1] . ( 2 sec) [ -1126.1955] [ 59] [depth= 7] . ( 2 sec) [ -1121.1218] [ 58] [depth= 7] . ( 3 sec) [ -1120.8011] [ 58] [depth= 2] . ( 3 sec) [ -1119.4097] [ 58] [depth= 5] . ( 3 sec) [ -1105.4213] [ 58] [depth= 1] . ( 4 sec) [ -1105.3990] [ 58] [depth= 6] . ( 4 sec) [ -1100.8527] [ 57] [depth= 7] . ( 5 sec) [ -1099.8792] [ 57] [depth= 5] . ( 6 sec) [ -1098.9064] [ 57] [depth= 3] . ( 6 sec) [ -1097.9195] [ 57] [depth= 1] . ( 22 sec) [ -1097.5266] [ 57] [depth= 2] . ( 22 sec) [ -1097.4961] [ 57] [depth= 2] . ( 22 sec) [ -1097.4733] [ 57] [depth= 2] . ( 29 sec) [ -1092.3505] [ 56] [depth= 7] . ( 31 sec) [ -1089.6799] [ 56] [depth= 3] . ( 53 sec) [ -1087.3803] [ 56] [depth= 8] . ( 58 sec) [ -1072.7060] [ 55] [depth= 2] . ( 58 sec) [ -1070.7573] [ 55] [depth= 3] . ( 58 sec) [ -1069.9638] [ 55] [depth= 2] . ( 61 sec) [ -1065.2218] [ 54] [depth= 11] . ( 61 sec) [ -1065.0364] [ 54] [depth= 2] . ( 69 sec) [ -1054.0011] [ 52] [depth= 10] . ( 75 sec) [ -1053.0272] [Branch lengths ] . ( 75 sec) [ -1052.9005] [Alpha ][ 0.689410] . ( 156 sec) [ -1052.5347] [ 52] [depth= 3] . ( 230 sec) [ -1052.5315] [Branch lengths ] . ( 230 sec) [ -1052.5315] [Alpha ][ 0.692309] . ( 230 sec) [ -1052.5315] [Topology ] . ( 230 sec) [ -1052.5314] [Topology ] . ( 230 sec) [ -1052.5314] [Alpha ][ 0.692309] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.531386. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1629.0660] [Alpha ][ 0.500960] . ( 0 sec) [ -1447.8819] [ 68] [depth= 10] . ( 0 sec) [ -1300.6315] [ 66] [depth= 6] . ( 0 sec) [ -1290.2202] [ 65] [depth= 2] . ( 0 sec) [ -1263.8847] [ 65] [depth= 2] . ( 0 sec) [ -1245.2419] [ 64] [depth= 1] . ( 0 sec) [ -1232.7696] [ 63] [depth= 3] . ( 0 sec) [ -1216.1979] [ 62] [depth= 5] . ( 0 sec) [ -1215.7700] [ 62] [depth= 1] . ( 1 sec) [ -1200.9863] [ 63] [depth= 1] . ( 1 sec) [ -1199.2458] [ 63] [depth= 3] . ( 1 sec) [ -1197.5744] [ 63] [depth= 1] . ( 1 sec) [ -1184.2352] [ 61] [depth= 6] . ( 1 sec) [ -1169.7115] [ 61] [depth= 1] . ( 1 sec) [ -1148.1873] [ 60] [depth= 5] . ( 1 sec) [ -1133.2756] [ 58] [depth= 7] . ( 1 sec) [ -1132.8716] [ 57] [depth= 3] . ( 1 sec) [ -1132.7107] [ 57] [depth= 2] . ( 2 sec) [ -1131.8817] [ 57] [depth= 6] . ( 2 sec) [ -1127.2120] [ 57] [depth= 4] . ( 2 sec) [ -1115.6831] [ 56] [depth= 5] . ( 2 sec) [ -1115.4238] [ 56] [depth= 3] . ( 3 sec) [ -1114.7332] [ 57] [depth= 5] . ( 3 sec) [ -1093.1520] [ 56] [depth= 3] . ( 3 sec) [ -1092.9691] [ 56] [depth= 2] . ( 3 sec) [ -1092.0133] [ 56] [depth= 2] . ( 3 sec) [ -1091.0644] [ 56] [depth= 2] . ( 3 sec) [ -1090.6147] [ 56] [depth= 2] . ( 3 sec) [ -1090.6012] [ 56] [depth= 4] . ( 4 sec) [ -1088.2530] [ 56] [depth= 5] . ( 4 sec) [ -1088.0864] [ 56] [depth= 5] . ( 5 sec) [ -1086.2030] [ 56] [depth= 6] . ( 5 sec) [ -1086.1773] [ 56] [depth= 1] . ( 5 sec) [ -1085.7384] [ 56] [depth= 1] . ( 7 sec) [ -1085.7036] [ 57] [depth= 6] . ( 8 sec) [ -1082.5268] [ 56] [depth= 5] . ( 8 sec) [ -1082.5133] [ 56] [depth= 2] . ( 11 sec) [ -1077.4122] [ 55] [depth= 2] . ( 11 sec) [ -1076.3376] [ 55] [depth= 1] . ( 11 sec) [ -1076.1866] [ 55] [depth= 1] . ( 36 sec) [ -1068.5756] [ 55] [depth= 7] . ( 36 sec) [ -1068.5102] [ 54] [depth= 2] . ( 36 sec) [ -1065.3813] [ 54] [depth= 1] . ( 36 sec) [ -1065.3380] [ 54] [depth= 1] . ( 39 sec) [ -1065.3274] [ 54] [depth= 2] . ( 43 sec) [ -1065.2679] [ 54] [depth= 6] . ( 45 sec) [ -1057.9810] [ 53] [depth= 6] . ( 59 sec) [ -1053.2492] [ 52] [depth= 5] . ( 70 sec) [ -1053.0401] [Branch lengths ] . ( 70 sec) [ -1052.9132] [Alpha ][ 0.689663] . ( 176 sec) [ -1052.8543] [ 52] [depth= 3] . ( 190 sec) [ -1052.6537] [ 52] [depth= 7] . ( 198 sec) [ -1052.5981] [ 52] [depth= 1] . ( 212 sec) [ -1052.5836] [Branch lengths ] . ( 212 sec) [ -1052.5835] [Alpha ][ 0.692097] . ( 212 sec) [ -1052.5835] [Topology ] . ( 213 sec) [ -1052.5834] [Topology ] . ( 213 sec) [ -1052.5834] [Alpha ][ 0.692097] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.583399. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1657.1715] [Alpha ][ 0.500960] . ( 0 sec) [ -1544.0927] [ 71] [depth= 6] . ( 0 sec) [ -1524.6247] [ 69] [depth= 7] . ( 0 sec) [ -1523.5280] [ 69] [depth= 2] . ( 0 sec) [ -1523.4577] [ 69] [depth= 1] . ( 0 sec) [ -1521.8508] [ 68] [depth= 3] . ( 1 sec) [ -1505.3677] [ 68] [depth= 2] . ( 1 sec) [ -1479.3811] [ 68] [depth= 6] . ( 1 sec) [ -1479.2073] [ 68] [depth= 3] . ( 1 sec) [ -1471.3393] [ 68] [depth= 1] . ( 1 sec) [ -1442.9851] [ 68] [depth= 5] . ( 1 sec) [ -1426.4383] [ 68] [depth= 5] . ( 1 sec) [ -1410.4485] [ 68] [depth= 5] . ( 1 sec) [ -1409.8862] [ 68] [depth= 1] . ( 1 sec) [ -1409.4768] [ 68] [depth= 8] . ( 2 sec) [ -1395.8455] [ 68] [depth= 5] . ( 2 sec) [ -1360.7453] [ 68] [depth= 7] . ( 2 sec) [ -1341.3792] [ 65] [depth= 9] . ( 2 sec) [ -1330.7128] [ 63] [depth= 5] . ( 2 sec) [ -1319.6769] [ 62] [depth= 12] . ( 2 sec) [ -1318.5886] [ 62] [depth= 3] . ( 2 sec) [ -1309.3592] [ 62] [depth= 8] . ( 2 sec) [ -1305.5317] [ 61] [depth= 7] . ( 3 sec) [ -1126.5927] [ 61] [depth= 3] . ( 3 sec) [ -1114.3905] [ 59] [depth= 8] . ( 3 sec) [ -1110.9268] [ 58] [depth= 9] . ( 3 sec) [ -1107.5628] [ 56] [depth= 7] . ( 3 sec) [ -1106.4925] [ 56] [depth= 6] . ( 4 sec) [ -1105.6017] [ 56] [depth= 7] . ( 4 sec) [ -1105.5743] [ 56] [depth= 11] . ( 5 sec) [ -1104.6712] [ 56] [depth= 4] . ( 5 sec) [ -1100.6513] [ 56] [depth= 1] . ( 9 sec) [ -1094.9996] [ 56] [depth= 6] . ( 9 sec) [ -1092.9925] [ 56] [depth= 5] . ( 10 sec) [ -1081.1074] [ 56] [depth= 6] . ( 12 sec) [ -1079.7156] [ 56] [depth= 2] . ( 12 sec) [ -1079.7051] [ 56] [depth= 7] . ( 14 sec) [ -1074.8409] [ 55] [depth= 12] . ( 22 sec) [ -1073.0744] [ 54] [depth= 10] . ( 23 sec) [ -1072.7935] [ 54] [depth= 6] . ( 25 sec) [ -1072.7108] [ 54] [depth= 1] . ( 50 sec) [ -1071.6893] [ 54] [depth= 18] . ( 51 sec) [ -1070.1797] [ 54] [depth= 12] . ( 51 sec) [ -1070.0890] [ 54] [depth= 11] . ( 51 sec) [ -1069.1068] [ 54] [depth= 3] . ( 52 sec) [ -1068.8670] [ 54] [depth= 2] . ( 57 sec) [ -1068.2288] [Branch lengths ] . ( 57 sec) [ -1068.2278] [Alpha ][ 0.513625] . ( 57 sec) [ -1065.9913] [ 55] [depth= 3] . ( 58 sec) [ -1059.3798] [ 54] [depth= 9] . ( 58 sec) [ -1056.7850] [ 53] [depth= 1] . ( 58 sec) [ -1056.7292] [ 53] [depth= 1] . ( 58 sec) [ -1056.6728] [ 53] [depth= 4] . ( 135 sec) [ -1056.5588] [ 53] [depth= 3] . ( 149 sec) [ -1053.6559] [ 52] [depth= 6] . ( 170 sec) [ -1053.2878] [ 52] [depth= 7] . ( 173 sec) [ -1052.8573] [ 52] [depth= 1] . ( 179 sec) [ -1052.8352] [ 52] [depth= 1] . ( 184 sec) [ -1052.7582] [Branch lengths ] . ( 184 sec) [ -1052.6512] [Alpha ][ 0.689813] . ( 191 sec) [ -1052.5584] [ 52] [depth= 1] . ( 326 sec) [ -1052.5322] [Branch lengths ] . ( 326 sec) [ -1052.5322] [Alpha ][ 0.692373] . ( 326 sec) [ -1052.5322] [Topology ] . ( 326 sec) [ -1052.5319] [Topology ] . ( 326 sec) [ -1052.5319] [Alpha ][ 0.692373] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.531942. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1753.7917] [Alpha ][ 0.500960] . ( 1 sec) [ -1633.2473] [ 70] [depth= 6] . ( 1 sec) [ -1587.7618] [ 68] [depth= 6] . ( 1 sec) [ -1584.6511] [ 68] [depth= 1] . ( 1 sec) [ -1583.3644] [ 67] [depth= 3] . ( 1 sec) [ -1582.8867] [ 67] [depth= 2] . ( 1 sec) [ -1572.2729] [ 66] [depth= 3] . ( 1 sec) [ -1549.5314] [ 65] [depth= 7] . ( 1 sec) [ -1547.3191] [ 65] [depth= 2] . ( 1 sec) [ -1547.2640] [ 65] [depth= 1] . ( 1 sec) [ -1540.3658] [ 65] [depth= 7] . ( 1 sec) [ -1362.6744] [ 64] [depth= 2] . ( 1 sec) [ -1360.6746] [ 64] [depth= 1] . ( 2 sec) [ -1355.2812] [ 64] [depth= 12] . ( 2 sec) [ -1349.6121] [ 64] [depth= 8] . ( 2 sec) [ -1342.9206] [ 63] [depth= 5] . ( 2 sec) [ -1342.6640] [ 63] [depth= 1] . ( 2 sec) [ -1338.1059] [ 63] [depth= 10] . ( 2 sec) [ -1337.4675] [ 63] [depth= 9] . ( 2 sec) [ -1317.3907] [ 63] [depth= 10] . ( 2 sec) [ -1316.9209] [ 63] [depth= 8] . ( 3 sec) [ -1316.1082] [ 67] [depth= 1] . ( 3 sec) [ -1254.7297] [ 66] [depth= 11] . ( 3 sec) [ -1219.5007] [ 68] [depth= 9] . ( 3 sec) [ -1219.2393] [ 68] [depth= 8] . ( 3 sec) [ -1219.1784] [ 68] [depth= 1] . ( 4 sec) [ -1217.8716] [ 68] [depth= 10] . ( 4 sec) [ -1217.1532] [ 68] [depth= 2] . ( 4 sec) [ -1217.0281] [ 68] [depth= 1] . ( 6 sec) [ -1216.8373] [ 69] [depth= 3] . ( 6 sec) [ -1216.7299] [ 68] [depth= 3] . ( 7 sec) [ -1216.7093] [ 68] [depth= 5] . ( 7 sec) [ -1215.7750] [ 68] [depth= 1] . ( 7 sec) [ -1215.7509] [ 68] [depth= 8] . ( 7 sec) [ -1214.2908] [ 68] [depth= 2] . ( 7 sec) [ -1213.1286] [ 68] [depth= 11] . ( 7 sec) [ -1196.1881] [ 68] [depth= 12] . ( 8 sec) [ -1196.1631] [ 68] [depth= 1] . ( 9 sec) [ -1190.2113] [ 69] [depth= 11] . ( 9 sec) [ -1185.6926] [ 68] [depth= 6] . ( 10 sec) [ -1168.5558] [ 68] [depth= 10] . ( 10 sec) [ -1153.0881] [ 68] [depth= 1] . ( 13 sec) [ -1152.6331] [ 68] [depth= 6] . ( 13 sec) [ -1133.0938] [ 65] [depth= 7] . ( 13 sec) [ -1125.5019] [ 64] [depth= 5] . ( 18 sec) [ -1112.7263] [ 62] [depth= 3] . ( 18 sec) [ -1110.8551] [ 62] [depth= 2] . ( 19 sec) [ -1110.7445] [ 62] [depth= 1] . ( 19 sec) [ -1110.3777] [ 62] [depth= 4] . ( 19 sec) [ -1110.0864] [ 62] [depth= 3] . ( 19 sec) [ -1107.2927] [ 62] [depth= 12] . ( 20 sec) [ -1104.9412] [ 61] [depth= 10] . ( 23 sec) [ -1104.8764] [ 61] [depth= 1] . ( 23 sec) [ -1104.8411] [ 61] [depth= 1] . ( 34 sec) [ -1100.0641] [ 60] [depth= 3] . ( 34 sec) [ -1095.2003] [ 59] [depth= 7] . ( 34 sec) [ -1095.1901] [ 59] [depth= 10] . ( 35 sec) [ -1095.1573] [ 59] [depth= 1] . ( 35 sec) [ -1094.9931] [ 59] [depth= 1] . ( 35 sec) [ -1094.9028] [ 59] [depth= 1] . ( 48 sec) [ -1094.6945] [Branch lengths ] . ( 48 sec) [ -1094.2989] [Alpha ][ 0.321172] . ( 48 sec) [ -1064.0840] [ 54] [depth= 1] . ( 48 sec) [ -1063.7342] [ 54] [depth= 3] . ( 49 sec) [ -1063.7155] [ 54] [depth= 3] . ( 67 sec) [ -1063.6886] [ 54] [depth= 4] . ( 70 sec) [ -1063.6632] [ 54] [depth= 2] . ( 112 sec) [ -1058.5363] [ 53] [depth= 3] . ( 114 sec) [ -1058.4213] [ 53] [depth= 1] . ( 120 sec) [ -1058.3757] [ 53] [depth= 1] . ( 139 sec) [ -1053.8621] [ 52] [depth= 13] . ( 142 sec) [ -1053.7561] [ 52] [depth= 7] . ( 155 sec) [ -1053.6987] [ 52] [depth= 2] . ( 160 sec) [ -1053.4892] [ 52] [depth= 1] . ( 185 sec) [ -1053.4012] [Branch lengths ] . ( 186 sec) [ -1052.5947] [Alpha ][ 0.641223] . ( 331 sec) [ -1052.5897] [Branch lengths ] . ( 331 sec) [ -1052.5897] [Topology ] . ( 331 sec) [ -1052.5897] [Topology ] . ( 331 sec) [ -1052.5832] [Alpha ][ 0.691478] . ( 331 sec) [ -1052.5832] [Topology ] . ( 332 sec) [ -1052.5832] [Topology ] . ( 332 sec) [ -1052.5832] [Alpha ][ 0.692169] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.583162. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1053.9951] [Alpha ][ 0.697638] . ( 0 sec) [ -1053.9951] [Topology ] . ( 0 sec) [ -1052.8861] [Topology ] . ( 1 sec) [ -1052.6774] [Topology ] . ( 1 sec) [ -1052.6053] [Topology ] . ( 2 sec) [ -1052.5698] [Topology ] . ( 2 sec) [ -1052.5565] [Topology ] . ( 2 sec) [ -1052.5493] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5 sec) [ -1052.5493] [Alpha ][ 0.692747] . ( 5 sec) [ -1052.5493] [Topology ] . ( 5 sec) [ -1052.5438] [Topology ] . ( 6 sec) [ -1052.5383] [Topology ] . ( 6 sec) [ -1052.5340] [Topology ] . ( 6 sec) [ -1052.5323] [Topology ] . ( 7 sec) [ -1052.5317] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -1052.5317] [Alpha ][ 0.692747] . ( 9 sec) [ -1052.5317] [Topology ] . ( 10 sec) [ -1052.5316] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 15 sec) [ -1053.9951] [Alpha ][ 0.697638] . ( 22 sec) [ -1053.8029] [ 52] [depth= 2] . ( 22 sec) [ -1053.4564] [ 52] [depth= 2] . ( 22 sec) [ -1053.3694] [ 52] [depth= 1] . ( 23 sec) [ -1053.2922] [ 52] [depth= 1] . ( 26 sec) [ -1053.2816] [ 52] [depth= 1] . ( 27 sec) [ -1053.2563] [ 52] [depth= 1] . ( 33 sec) [ -1052.9696] [ 52] [depth= 1] . ( 36 sec) [ -1052.9497] [ 52] [depth= 1] . ( 40 sec) [ -1052.7540] [ 52] [depth= 1] . ( 43 sec) [ -1052.7138] [ 52] [depth= 3] . ( 53 sec) [ -1052.6304] [ 52] [depth= 1] . ( 53 sec) [ -1052.6020] [ 52] [depth= 1] . ( 101 sec) [ -1052.5319] [Branch lengths ] . ( 101 sec) [ -1052.5318] [Alpha ][ 0.692829] . ( 241 sec) [ -1052.5310] [Branch lengths ] . ( 241 sec) [ -1052.5310] [Topology ] . ( 241 sec) [ -1052.5310] [Topology ] . ( 241 sec) [ -1052.5310] [Alpha ][ 0.692136] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1052.531551 . Log likelihood obtained after SPR moves : -1052.530968 . Log likelihood of the current tree: -1052.530968. . Printing the most likely tree in file 'proteic_M1768_31x228_2004.phy_phyml_tree.txt'... . Best log likelihood : -1052.530968 . Time used 0h4m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1677.36user 0.00system 28:00.39elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps