.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data60.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... . 433 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . 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=-10281.311378 . ( 1 sec) [ -10277.3620] [GTR parameters ] . ( 1 sec) [ -10274.9238] [Alpha ][ 0.855959] . ( 1 sec) [ -10274.9238] [Topology ] . ( 2 sec) [ -10222.0737] [Topology ] . ( 3 sec) [ -10212.7676] [Topology ] . ( 3 sec) [ -10210.2910] [Topology ] . ( 4 sec) [ -10209.4383] [Topology ] . ( 5 sec) [ -10207.8763] [Topology ] . ( 6 sec) [ -10207.4713] [Topology ] . ( 7 sec) [ -10207.3341] [Topology ] . ( 8 sec) [ -10207.2782] [Topology ] . ( 8 sec) [ -10207.2521] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10207.238852 . ( 16 sec) [ -10207.0932] [GTR parameters ] . ( 16 sec) [ -10206.4617] [Alpha ][ 0.923249] . ( 16 sec) [ -10206.4617] [Topology ] . ( 17 sec) [ -10206.3940] [Topology ] . ( 18 sec) [ -10206.3682] [Topology ] . ( 18 sec) [ -10206.3549] [Topology ] . ( 19 sec) [ -10206.3476] [Topology ] . ( 20 sec) [ -10206.3434] [Topology ] . ( 21 sec) [ -10206.3409] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10206.340874 . ( 27 sec) [ -10206.3406] [GTR parameters ] . ( 27 sec) [ -10206.3340] [Alpha ][ 0.930562] . ( 27 sec) [ -10206.3340] [Topology ] . ( 28 sec) [ -10206.3313] [Topology ] . ( 29 sec) [ -10206.3297] [Topology ] . ( 30 sec) [ -10206.3286] [Topology ] . ( 30 sec) [ -10206.3277] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10206.327739 . ( 37 sec) [ -10206.3277] [GTR parameters ] . ( 37 sec) [ -10206.3276] [Alpha ][ 0.931492] . ( 37 sec) [ -10206.3276] [Topology ] . ( 38 sec) [ -10206.3268] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -10277.3620] [GTR parameters ] . ( 50 sec) [ -10274.9238] [Alpha ][ 0.855959] . ( 51 sec) [ -10274.0662] [ 2348] [depth= 1] . ( 51 sec) [ -10274.0461] [ 2350] [depth= 1] . ( 51 sec) [ -10272.6954] [ 2348] [depth= 1] . ( 52 sec) [ -10270.5677] [ 2356] [depth= 1] . ( 52 sec) [ -10267.6329] [ 2354] [depth= 1] . ( 52 sec) [ -10264.2339] [ 2356] [depth= 1] . ( 52 sec) [ -10261.1650] [ 2353] [depth= 1] . ( 52 sec) [ -10259.5955] [ 2356] [depth= 1] . ( 52 sec) [ -10258.2228] [ 2356] [depth= 1] . ( 52 sec) [ -10256.3671] [ 2354] [depth= 1] . ( 52 sec) [ -10254.3763] [ 2354] [depth= 1] . ( 52 sec) [ -10254.2504] [ 2354] [depth= 1] . ( 53 sec) [ -10254.0115] [ 2356] [depth= 1] . ( 53 sec) [ -10251.7321] [ 2356] [depth= 1] . ( 53 sec) [ -10247.9251] [ 2359] [depth= 2] . ( 53 sec) [ -10246.0282] [ 2359] [depth= 1] . ( 53 sec) [ -10244.8946] [ 2358] [depth= 1] . ( 53 sec) [ -10244.8108] [ 2354] [depth= 1] . ( 53 sec) [ -10243.9033] [ 2352] [depth= 1] . ( 53 sec) [ -10243.1984] [ 2354] [depth= 1] . ( 54 sec) [ -10215.1069] [Branch lengths ] . ( 54 sec) [ -10214.9407] [GTR parameters ] . ( 54 sec) [ -10214.5210] [Alpha ][ 0.910939] . ( 55 sec) [ -10211.7919] [ 2348] [depth= 1] . ( 56 sec) [ -10210.8529] [ 2348] [depth= 1] . ( 56 sec) [ -10210.8183] [ 2345] [depth= 1] . ( 56 sec) [ -10210.7596] [ 2342] [depth= 1] . ( 56 sec) [ -10210.6871] [ 2345] [depth= 1] . ( 56 sec) [ -10210.4042] [ 2343] [depth= 1] . ( 57 sec) [ -10207.0507] [Branch lengths ] . ( 58 sec) [ -10207.0468] [GTR parameters ] . ( 58 sec) [ -10207.0257] [Alpha ][ 0.923926] . ( 61 sec) [ -10206.7973] [Branch lengths ] . ( 71 sec) [ -10206.6904] [ 2343] [depth= 1] . ( 82 sec) [ -10206.6087] [Branch lengths ] . ( 83 sec) [ -10206.6078] [GTR parameters ] . ( 83 sec) [ -10206.6029] [Alpha ][ 0.930192] . ( 83 sec) [ -10206.6029] [Topology ] . ( 83 sec) [ -10206.5956] [Topology ] . ( 84 sec) [ -10206.5931] [Topology ] . ( 85 sec) [ -10206.5916] [Topology ] . ( 86 sec) [ -10206.5906] [Topology ] . ( 87 sec) [ -10206.5897] [Topology ] . ( 87 sec) [ -10206.5897] [GTR parameters ] . ( 87 sec) [ -10206.5895] [Alpha ][ 0.931308] . ( 87 sec) [ -10206.5895] [Topology ] . ( 88 sec) [ -10206.5887] [Topology ] . ( 88 sec) [ -10206.5887] [GTR parameters ] . ( 88 sec) [ -10206.5887] [Alpha ][ 0.931308] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -10206.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10206.326827 . Log likelihood obtained after SPR moves : -10206.329453 . Log likelihood of the current tree: -10206.326827. . Printing the most likely tree in file 'data60.phy_phyml_tree.txt'... . Time used 0h1m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo