.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data96.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... . 437 patterns found. (out of a total of 500 sites) . 57 sites without polymorphism (11.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9376.938197 . ( 0 sec) [ -9375.7050] [GTR parameters ] . ( 1 sec) [ -9374.9931] [Alpha ][ 1.100032] . ( 1 sec) [ -9374.9931] [Topology ] . ( 2 sec) [ -9323.1811] [Topology ] . ( 3 sec) [ -9311.1208] [Topology ] . ( 3 sec) [ -9308.4117] [Topology ] . ( 4 sec) [ -9307.4202] [Topology ] . ( 5 sec) [ -9306.9793] [Topology ] . ( 6 sec) [ -9306.7594] [Topology ] . ( 7 sec) [ -9306.6429] [Topology ] . ( 7 sec) [ -9306.5784] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9306.578440 . ( 15 sec) [ -9306.5318] [GTR parameters ] . ( 15 sec) [ -9306.5244] [Alpha ][ 1.089431] . ( 15 sec) [ -9306.5244] [Topology ] . ( 16 sec) [ -9306.4867] [Topology ] . ( 17 sec) [ -9306.4652] [Topology ] . ( 17 sec) [ -9306.4527] [Topology ] . ( 18 sec) [ -9306.4453] [Topology ] . ( 19 sec) [ -9306.4408] [Topology ] . ( 20 sec) [ -9306.4381] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -9306.4353] [Topology ] . Before opt ts/t=1.000000 LK=-9306.435340 . ( 33 sec) [ -9306.4353] [GTR parameters ] . ( 33 sec) [ -9306.4352] [Alpha ][ 1.087965] . ( 33 sec) [ -9306.4352] [Topology ] . ( 35 sec) [ -9306.4345] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 54 sec) [ -9375.7050] [GTR parameters ] . ( 54 sec) [ -9374.9931] [Alpha ][ 1.100032] . ( 55 sec) [ -9372.9122] [ 2070] [depth= 1] . ( 55 sec) [ -9372.4222] [ 2065] [depth= 1] . ( 55 sec) [ -9371.4415] [ 2066] [depth= 1] . ( 56 sec) [ -9369.5389] [ 2071] [depth= 1] . ( 57 sec) [ -9354.6843] [ 2068] [depth= 2] . ( 57 sec) [ -9351.5360] [ 2070] [depth= 2] . ( 57 sec) [ -9351.5043] [ 2067] [depth= 1] . ( 57 sec) [ -9351.0220] [ 2071] [depth= 1] . ( 57 sec) [ -9350.9645] [ 2070] [depth= 1] . ( 58 sec) [ -9349.9678] [ 2070] [depth= 1] . ( 58 sec) [ -9349.7910] [ 2070] [depth= 1] . ( 59 sec) [ -9349.2850] [ 2078] [depth= 1] . ( 59 sec) [ -9348.5086] [ 2075] [depth= 2] . ( 59 sec) [ -9347.1889] [ 2074] [depth= 1] . ( 59 sec) [ -9346.6661] [ 2077] [depth= 2] . ( 59 sec) [ -9346.0125] [ 2078] [depth= 1] . ( 60 sec) [ -9344.4429] [ 2079] [depth= 1] . ( 60 sec) [ -9344.3534] [ 2078] [depth= 1] . ( 61 sec) [ -9312.8308] [Branch lengths ] . ( 62 sec) [ -9312.7562] [GTR parameters ] . ( 62 sec) [ -9312.7544] [Alpha ][ 1.094700] . ( 62 sec) [ -9312.4864] [ 2079] [depth= 1] . ( 63 sec) [ -9312.4599] [ 2083] [depth= 1] . ( 64 sec) [ -9310.9360] [ 2083] [depth= 1] . ( 65 sec) [ -9309.8602] [ 2082] [depth= 2] . ( 69 sec) [ -9306.9829] [Branch lengths ] . ( 69 sec) [ -9306.9694] [GTR parameters ] . ( 70 sec) [ -9306.9663] [Alpha ][ 1.087741] . ( 76 sec) [ -9306.8305] [Branch lengths ] . ( 83 sec) [ -9306.5693] [ 2077] [depth= 1] . ( 106 sec) [ -9306.4422] [Branch lengths ] . ( 107 sec) [ -9306.4403] [GTR parameters ] . ( 107 sec) [ -9306.4403] [Alpha ][ 1.086654] . ( 107 sec) [ -9306.4403] [Topology ] . ( 108 sec) [ -9306.4355] [Topology ] . ( 109 sec) [ -9306.4347] [Topology ] . ( 109 sec) [ -9306.4347] [GTR parameters ] . ( 110 sec) [ -9306.4347] [Alpha ][ 1.086654] . ( 110 sec) [ -9306.4347] [Topology ] . ( 111 sec) [ -9306.4344] [Topology ] . ( 111 sec) [ -9306.4344] [GTR parameters ] . ( 111 sec) [ -9306.4344] [Alpha ][ 1.086654] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9306.434540 . Log likelihood obtained after SPR moves : -9306.434387 . Log likelihood of the current tree: -9306.434387. . Printing the most likely tree in file 'data96.phy_phyml_tree.txt'... . Time used 0h2m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo