.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1601_36x340_2003.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 : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 322 patterns found. (out of a total of 340 sites) . 79 sites without polymorphism (23.24%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 28Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -7041.5767] [Alpha ][ 1.039970] . ( 1 sec) [ -7041.5767] [Topology ] . ( 4 sec) [ -6954.7233] [Topology ] . ( 7 sec) [ -6937.3995] [Topology ] . ( 10 sec) [ -6929.6201] [Topology ] . ( 13 sec) [ -6925.4982] [Topology ] . ( 16 sec) [ -6923.5250] [Topology ] . ( 20 sec) [ -6923.0761] [Topology ] . ( 23 sec) [ -6922.8111] [Topology ] . ( 26 sec) [ -6922.4654] [Topology ] . ( 29 sec) [ -6921.7624] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -6921.4194] [Alpha ][ 1.108338] . ( 54 sec) [ -6921.4194] [Topology ] . ( 57 sec) [ -6921.3642] [Topology ] . ( 60 sec) [ -6921.3434] [Topology ] . ( 63 sec) [ -6921.3336] [Topology ] . ( 66 sec) [ -6921.3286] [Topology ] . ( 69 sec) [ -6921.3259] [Topology ] . ( 72 sec) [ -6921.3244] [Topology ] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -6921.3244] [Alpha ][ 1.107229] . ( 94 sec) [ -6921.3244] [Topology ] . ( 97 sec) [ -6921.3235] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 139 sec) [ -7041.5767] [Alpha ][ 1.039970] . ( 140 sec) [ -7041.4766] [ 1170] [depth= 1] . ( 140 sec) [ -7032.3161] [ 1167] [depth= 1] . ( 142 sec) [ -7032.0406] [ 1171] [depth= 1] . ( 144 sec) [ -7029.4414] [ 1170] [depth= 1] . ( 150 sec) [ -7021.2467] [ 1169] [depth= 1] . ( 151 sec) [ -7020.6891] [ 1169] [depth= 1] . ( 151 sec) [ -7019.0608] [ 1169] [depth= 1] . ( 151 sec) [ -7019.0134] [ 1169] [depth= 1] . ( 152 sec) [ -7014.7294] [ 1168] [depth= 1] . ( 153 sec) [ -7014.0785] [ 1172] [depth= 2] . ( 154 sec) [ -6995.0640] [ 1171] [depth= 3] . ( 154 sec) [ -6989.8121] [ 1169] [depth= 1] . ( 155 sec) [ -6987.0472] [ 1167] [depth= 1] . ( 158 sec) [ -6983.8166] [ 1168] [depth= 2] . ( 159 sec) [ -6982.3027] [ 1166] [depth= 1] . ( 166 sec) [ -6975.1448] [ 1163] [depth= 1] . ( 169 sec) [ -6973.3467] [ 1163] [depth= 1] . ( 172 sec) [ -6969.0660] [ 1162] [depth= 1] . ( 172 sec) [ -6965.6660] [ 1162] [depth= 2] . ( 173 sec) [ -6963.6494] [ 1162] [depth= 1] . ( 182 sec) [ -6963.3661] [ 1162] [depth= 1] . ( 182 sec) [ -6957.2622] [ 1159] [depth= 2] . ( 194 sec) [ -6953.8349] [ 1158] [depth= 1] . ( 194 sec) [ -6951.2446] [ 1157] [depth= 1] . ( 196 sec) [ -6951.1408] [ 1157] [depth= 1] . ( 205 sec) [ -6920.4360] [Branch lengths ] . ( 205 sec) [ -6920.1948] [Alpha ][ 1.117385] . ( 207 sec) [ -6918.7101] [ 1154] [depth= 1] . ( 210 sec) [ -6917.2558] [ 1155] [depth= 4] . ( 235 sec) [ -6916.4072] [ 1155] [depth= 1] . ( 288 sec) [ -6912.9641] [Branch lengths ] . ( 288 sec) [ -6912.9639] [Alpha ][ 1.115145] . ( 373 sec) [ -6912.5176] [Branch lengths ] . ( 373 sec) [ -6912.5176] [Topology ] . ( 377 sec) [ -6912.4635] [Topology ] . ( 380 sec) [ -6912.4413] [Topology ] . ( 383 sec) [ -6912.4295] [Topology ] . ( 386 sec) [ -6912.4229] [Topology ] . ( 389 sec) [ -6912.4193] [Topology ] . ( 393 sec) [ -6912.4171] [Topology ] . ( 393 sec) [ -6912.4114] [Alpha ][ 1.102780] . ( 393 sec) [ -6912.4114] [Topology ] . ( 397 sec) [ -6912.4094] [Topology ] . ( 400 sec) [ -6912.4083] [Topology ] . ( 403 sec) [ -6912.4077] [Topology ] . ( 403 sec) [ -6912.4077] [Alpha ][ 1.101636] . ( 404 sec) [ -6912.4077] [Topology ] . ( 407 sec) [ -6912.4073] [Topology ] . ( 407 sec) [ -6912.4073] [Alpha ][ 1.101636] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6921.323469 . Log likelihood obtained after SPR moves : -6912.407324 . Log likelihood of the current tree: -6912.407324. . Printing the most likely tree in file 'proteic_M1601_36x340_2003.phy_phyml_tree.txt'... . Time used 0h7m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 422.84user 0.00system 7:09.66elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps