.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data99.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... . 435 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=-9344.513092 . ( 0 sec) [ -9340.2121] [GTR parameters ] . ( 0 sec) [ -9340.0840] [Alpha ][ 0.961734] . ( 0 sec) [ -9340.0840] [Topology ] . ( 2 sec) [ -9287.2686] [Topology ] . ( 2 sec) [ -9278.1083] [Topology ] . ( 3 sec) [ -9274.7836] [Topology ] . ( 4 sec) [ -9273.3477] [Topology ] . ( 5 sec) [ -9272.6564] [Topology ] . ( 6 sec) [ -9272.3013] [Topology ] . ( 7 sec) [ -9272.1066] [Topology ] . ( 8 sec) [ -9271.9490] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9271.949043 . ( 17 sec) [ -9271.7805] [GTR parameters ] . ( 17 sec) [ -9271.6934] [Alpha ][ 0.991117] . ( 17 sec) [ -9271.6934] [Topology ] . ( 19 sec) [ -9271.2852] [Topology ] . ( 20 sec) [ -9270.4779] [Topology ] . ( 21 sec) [ -9270.1417] [Topology ] . ( 22 sec) [ -9270.0517] [Topology ] . ( 23 sec) [ -9270.0278] [Topology ] . ( 24 sec) [ -9270.0205] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.020474 . ( 36 sec) [ -9270.0170] [GTR parameters ] . ( 36 sec) [ -9270.0164] [Alpha ][ 0.993723] . ( 36 sec) [ -9270.0164] [Topology ] . ( 38 sec) [ -9270.0135] [Topology ] . ( 39 sec) [ -9270.0123] [Topology ] . ( 40 sec) [ -9270.0117] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.011651 . ( 51 sec) [ -9270.0117] [GTR parameters ] . ( 51 sec) [ -9270.0117] [Alpha ][ 0.993723] . ( 51 sec) [ -9270.0117] [Topology ] . ( 52 sec) [ -9270.0113] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 74 sec) [ -9340.2121] [GTR parameters ] . ( 74 sec) [ -9340.0840] [Alpha ][ 0.961734] . ( 74 sec) [ -9338.6513] [ 2106] [depth= 1] . ( 74 sec) [ -9338.3221] [ 2106] [depth= 1] . ( 75 sec) [ -9335.2727] [ 2110] [depth= 1] . ( 75 sec) [ -9335.2017] [ 2106] [depth= 1] . ( 75 sec) [ -9332.7874] [ 2110] [depth= 1] . ( 75 sec) [ -9329.7893] [ 2105] [depth= 2] . ( 76 sec) [ -9329.4975] [ 2105] [depth= 1] . ( 76 sec) [ -9328.4316] [ 2102] [depth= 2] . ( 76 sec) [ -9327.9485] [ 2114] [depth= 1] . ( 76 sec) [ -9326.2099] [ 2102] [depth= 1] . ( 76 sec) [ -9324.5767] [ 2107] [depth= 1] . ( 76 sec) [ -9324.1124] [ 2106] [depth= 1] . ( 76 sec) [ -9323.9033] [ 2107] [depth= 1] . ( 76 sec) [ -9322.4336] [ 2102] [depth= 1] . ( 77 sec) [ -9322.3497] [ 2101] [depth= 1] . ( 77 sec) [ -9320.8473] [ 2102] [depth= 1] . ( 77 sec) [ -9320.2342] [ 2105] [depth= 1] . ( 77 sec) [ -9319.3029] [ 2102] [depth= 1] . ( 78 sec) [ -9318.3908] [ 2104] [depth= 1] . ( 78 sec) [ -9318.1942] [ 2108] [depth= 1] . ( 78 sec) [ -9275.2031] [Branch lengths ] . ( 78 sec) [ -9275.0740] [GTR parameters ] . ( 78 sec) [ -9274.9916] [Alpha ][ 0.990784] . ( 79 sec) [ -9274.9632] [ 2108] [depth= 1] . ( 79 sec) [ -9274.9292] [ 2113] [depth= 1] . ( 80 sec) [ -9274.2702] [ 2112] [depth= 1] . ( 80 sec) [ -9274.1537] [ 2108] [depth= 1] . ( 82 sec) [ -9271.2878] [Branch lengths ] . ( 82 sec) [ -9271.2832] [GTR parameters ] . ( 82 sec) [ -9271.2822] [Alpha ][ 0.994088] . ( 83 sec) [ -9270.9026] [ 2108] [depth= 1] . ( 83 sec) [ -9270.8766] [ 2107] [depth= 1] . ( 86 sec) [ -9270.4357] [Branch lengths ] . ( 86 sec) [ -9270.4339] [GTR parameters ] . ( 86 sec) [ -9270.4338] [Alpha ][ 0.993094] . ( 91 sec) [ -9270.4200] [ 2108] [depth= 1] . ( 92 sec) [ -9270.4041] [ 2107] [depth= 1] . ( 110 sec) [ -9270.3085] [Branch lengths ] . ( 111 sec) [ -9270.3081] [GTR parameters ] . ( 111 sec) [ -9270.3081] [Alpha ][ 0.993094] . ( 111 sec) [ -9270.3081] [Topology ] . ( 112 sec) [ -9270.2939] [Topology ] . ( 113 sec) [ -9270.2882] [Topology ] . ( 114 sec) [ -9270.2852] [Topology ] . ( 115 sec) [ -9270.2836] [Topology ] . ( 116 sec) [ -9270.2827] [Topology ] . ( 116 sec) [ -9270.2825] [GTR parameters ] . ( 116 sec) [ -9270.2825] [Alpha ][ 0.993094] . ( 116 sec) [ -9270.2825] [Topology ] . ( 117 sec) [ -9270.2820] [Topology ] . ( 118 sec) [ -9270.2820] [GTR parameters ] . ( 118 sec) [ -9270.2820] [Alpha ][ 0.993094] . Checking for NNIs, optimizing five branches... . ( 127 sec) [ -9270.2818] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9270.011349 . Log likelihood obtained after SPR moves : -9270.281846 . Log likelihood of the current tree: -9270.011349. . Printing the most likely tree in file 'data99.phy_phyml_tree.txt'... . Time used 0h2m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo