.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2480_40x430_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 : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 399 patterns found. (out of a total of 430 sites) . 44 sites without polymorphism (10.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -24093.8919] [Alpha ][ 0.744037] . ( 2 sec) [ -24093.8919] [Topology ] . ( 5 sec) [ -23933.0303] [Topology ] . ( 8 sec) [ -23905.5947] [Topology ] . ( 11 sec) [ -23897.0873] [Topology ] . ( 15 sec) [ -23894.6999] [Topology ] . ( 18 sec) [ -23894.1137] [Topology ] . ( 22 sec) [ -23894.4239] [Topology ] . Moving backward . ( 22 sec) [ -23888.7339] [Topology ] . ( 25 sec) [ -23885.8511] [Topology ] . ( 29 sec) [ -23883.4821] [Topology ] . ( 32 sec) [ -23875.2197] [Alpha ][ 0.893113] . ( 33 sec) [ -23875.2197] [Topology ] . ( 36 sec) [ -23872.7801] [Topology ] . ( 39 sec) [ -23871.6161] [Topology ] . ( 43 sec) [ -23871.4433] [Topology ] . ( 46 sec) [ -23871.3851] [Topology ] . ( 49 sec) [ -23871.3595] [Topology ] . ( 53 sec) [ -23871.3470] [Topology ] . ( 56 sec) [ -23871.3406] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -23871.3012] [Alpha ][ 0.906587] . ( 84 sec) [ -23871.3012] [Topology ] . ( 87 sec) [ -23871.2910] [Topology ] . ( 90 sec) [ -23871.2860] [Topology ] . ( 94 sec) [ -23871.2835] [Topology ] . ( 97 sec) [ -23871.2821] [Topology ] . ( 100 sec) [ -23871.2814] [Topology ] . Checking for NNIs, optimizing five branches... . ( 128 sec) [ -23871.2804] [Alpha ][ 0.908766] . ( 128 sec) [ -23871.2804] [Topology ] . ( 131 sec) [ -23871.2797] [Topology ] . Checking for NNIs, optimizing five branches... . ( 159 sec) [ -23871.2797] [Alpha ][ 0.908766] . ( 159 sec) [ -23871.2797] [Topology ] . ( 162 sec) [ -23871.2794] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 217 sec) [ -24093.8919] [Alpha ][ 0.744037] . ( 222 sec) [ -24093.1300] [ 5023] [depth= 1] . ( 223 sec) [ -24074.3469] [ 5017] [depth= 1] . ( 227 sec) [ -24074.2184] [ 5018] [depth= 1] . ( 228 sec) [ -24070.3588] [ 5017] [depth= 1] . ( 228 sec) [ -24070.3081] [ 5010] [depth= 1] . ( 229 sec) [ -24059.4258] [ 5017] [depth= 1] . ( 229 sec) [ -24053.8688] [ 5012] [depth= 1] . ( 230 sec) [ -24053.8338] [ 5016] [depth= 1] . ( 231 sec) [ -24044.7092] [ 5012] [depth= 1] . ( 231 sec) [ -24041.4949] [ 5006] [depth= 1] . ( 232 sec) [ -24038.2194] [ 5009] [depth= 1] . ( 232 sec) [ -24037.4616] [ 5006] [depth= 1] . ( 234 sec) [ -24034.8911] [ 5009] [depth= 1] . ( 235 sec) [ -24028.1894] [ 5009] [depth= 2] . ( 236 sec) [ -24027.4720] [ 5011] [depth= 1] . ( 236 sec) [ -24017.8850] [ 5013] [depth= 1] . ( 238 sec) [ -24015.8225] [ 5013] [depth= 1] . ( 239 sec) [ -24010.0331] [ 5012] [depth= 1] . ( 239 sec) [ -23998.2863] [ 5011] [depth= 1] . ( 240 sec) [ -23993.8977] [ 5005] [depth= 3] . ( 240 sec) [ -23993.4091] [ 5007] [depth= 1] . ( 243 sec) [ -23991.7665] [ 5006] [depth= 1] . ( 243 sec) [ -23982.2916] [ 5007] [depth= 1] . ( 244 sec) [ -23978.7872] [ 5007] [depth= 1] . ( 244 sec) [ -23973.4050] [ 5007] [depth= 1] . ( 245 sec) [ -23966.9241] [ 5005] [depth= 1] . ( 245 sec) [ -23964.7344] [ 5007] [depth= 1] . ( 252 sec) [ -23963.0203] [ 5010] [depth= 1] . ( 253 sec) [ -23961.9891] [ 5007] [depth= 1] . ( 257 sec) [ -23892.1227] [Branch lengths ] . ( 257 sec) [ -23887.7439] [Alpha ][ 0.870589] . ( 274 sec) [ -23886.1656] [ 5007] [depth= 1] . ( 306 sec) [ -23880.5868] [Branch lengths ] . ( 307 sec) [ -23880.4813] [Alpha ][ 0.892537] . ( 353 sec) [ -23879.5816] [Branch lengths ] . ( 353 sec) [ -23879.5816] [Topology ] . ( 357 sec) [ -23878.0499] [Topology ] . ( 361 sec) [ -23877.7849] [Topology ] . ( 364 sec) [ -23877.7482] [Topology ] . ( 369 sec) [ -23877.7360] [Topology ] . ( 372 sec) [ -23877.7307] [Topology ] . ( 376 sec) [ -23877.7281] [Topology ] . ( 379 sec) [ -23877.7268] [Topology ] . ( 380 sec) [ -23877.6630] [Alpha ][ 0.909862] . ( 380 sec) [ -23877.6630] [Topology ] . ( 383 sec) [ -23877.6554] [Topology ] . ( 386 sec) [ -23877.6520] [Topology ] . ( 390 sec) [ -23877.6503] [Topology ] . ( 393 sec) [ -23877.6494] [Topology ] . ( 394 sec) [ -23877.6487] [Alpha ][ 0.911614] . ( 394 sec) [ -23877.6487] [Topology ] . ( 397 sec) [ -23877.6480] [Topology ] . ( 398 sec) [ -23877.6480] [Alpha ][ 0.911614] . Checking for NNIs, optimizing five branches... . ( 428 sec) [ -23877.3394] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -23871.279362 . Log likelihood obtained after SPR moves : -23877.339434 . Log likelihood of the current tree: -23871.279362. . Printing the most likely tree in file 'proteic_M2480_40x430_2005.phy_phyml_tree.txt'... . Time used 0h7m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 439.12user 0.00system 7:38.71elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps