.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data73.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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... . 372 patterns found. (out of a total of 500 sites) . 117 sites without polymorphism (23.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6901.023459 . ( 0 sec) [ -6897.4830] [GTR parameters ] . ( 1 sec) [ -6896.2294] [Alpha ][ 0.867784] . ( 1 sec) [ -6896.2294] [Topology ] . ( 1 sec) [ -6854.9826] [Topology ] . ( 2 sec) [ -6848.5129] [Topology ] . ( 3 sec) [ -6847.5405] [Topology ] . ( 4 sec) [ -6847.1551] [Topology ] . ( 5 sec) [ -6846.9790] [Topology ] . ( 5 sec) [ -6846.8982] [Topology ] . ( 6 sec) [ -6846.8629] [Topology ] . ( 7 sec) [ -6846.8473] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.847277 . ( 12 sec) [ -6846.7912] [GTR parameters ] . ( 12 sec) [ -6846.6948] [Alpha ][ 0.900748] . ( 12 sec) [ -6846.6948] [Topology ] . ( 13 sec) [ -6846.6778] [Topology ] . ( 14 sec) [ -6846.6709] [Topology ] . ( 15 sec) [ -6846.6678] [Topology ] . ( 15 sec) [ -6846.6664] [Topology ] . ( 16 sec) [ -6846.6657] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.665678 . ( 22 sec) [ -6846.6656] [GTR parameters ] . ( 22 sec) [ -6846.6648] [Alpha ][ 0.903758] . ( 22 sec) [ -6846.6648] [Topology ] . ( 23 sec) [ -6846.6644] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6846.664389 . ( 31 sec) [ -6846.6644] [GTR parameters ] . ( 31 sec) [ -6846.6644] [Alpha ][ 0.903758] . ( 31 sec) [ -6846.6644] [Topology ] . ( 32 sec) [ -6846.6642] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -6897.4830] [GTR parameters ] . ( 45 sec) [ -6896.2294] [Alpha ][ 0.867784] . ( 46 sec) [ -6895.8096] [ 1375] [depth= 1] . ( 46 sec) [ -6895.2942] [ 1373] [depth= 1] . ( 46 sec) [ -6893.1697] [ 1373] [depth= 1] . ( 46 sec) [ -6891.8901] [ 1373] [depth= 1] . ( 46 sec) [ -6879.6208] [ 1372] [depth= 2] . ( 47 sec) [ -6878.5843] [ 1371] [depth= 1] . ( 47 sec) [ -6876.3357] [ 1372] [depth= 1] . ( 47 sec) [ -6876.0006] [ 1375] [depth= 1] . ( 48 sec) [ -6875.0245] [ 1376] [depth= 1] . ( 48 sec) [ -6874.4301] [ 1376] [depth= 1] . ( 48 sec) [ -6874.3400] [ 1376] [depth= 1] . ( 49 sec) [ -6874.1483] [ 1379] [depth= 1] . ( 49 sec) [ -6865.8024] [ 1383] [depth= 4] . ( 49 sec) [ -6862.2962] [ 1381] [depth= 2] . ( 49 sec) [ -6860.6229] [ 1382] [depth= 1] . ( 49 sec) [ -6860.1004] [ 1382] [depth= 1] . ( 49 sec) [ -6856.8223] [ 1386] [depth= 1] . ( 50 sec) [ -6856.4520] [ 1382] [depth= 1] . ( 51 sec) [ -6846.0383] [Branch lengths ] . ( 51 sec) [ -6845.9586] [GTR parameters ] . ( 52 sec) [ -6845.8781] [Alpha ][ 0.898235] . ( 52 sec) [ -6843.0671] [ 1379] [depth= 1] . ( 52 sec) [ -6842.4326] [ 1383] [depth= 1] . ( 53 sec) [ -6842.2954] [ 1378] [depth= 1] . ( 55 sec) [ -6842.1386] [ 1378] [depth= 1] . ( 56 sec) [ -6840.5218] [Branch lengths ] . ( 57 sec) [ -6840.5076] [GTR parameters ] . ( 57 sec) [ -6840.5014] [Alpha ][ 0.906999] . ( 63 sec) [ -6840.3669] [Branch lengths ] . ( 87 sec) [ -6840.3516] [Branch lengths ] . ( 87 sec) [ -6840.3516] [Topology ] . ( 88 sec) [ -6840.3505] [Topology ] . ( 89 sec) [ -6840.3502] [Topology ] . ( 89 sec) [ -6840.3500] [GTR parameters ] . ( 89 sec) [ -6840.3489] [Alpha ][ 0.910664] . ( 89 sec) [ -6840.3489] [Topology ] . ( 91 sec) [ -6840.3487] [Topology ] . ( 91 sec) [ -6840.3486] [GTR parameters ] . ( 91 sec) [ -6840.3486] [Alpha ][ 0.910664] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6846.664201 . Log likelihood obtained after SPR moves : -6840.348627 . Log likelihood of the current tree: -6840.348627. . Printing the most likely tree in file 'data73.phy_phyml_tree.txt'... . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo