.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data100.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... . 450 patterns found. (out of a total of 500 sites) . 47 sites without polymorphism (9.40%). . 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=-10614.462202 . ( 1 sec) [ -10610.1657] [GTR parameters ] . ( 1 sec) [ -10610.1656] [Alpha ][ 1.001154] . ( 1 sec) [ -10610.1656] [Topology ] . ( 2 sec) [ -10531.3624] [Topology ] . ( 3 sec) [ -10511.2075] [Topology ] . ( 4 sec) [ -10505.1369] [Topology ] . ( 5 sec) [ -10502.3616] [Topology ] . ( 6 sec) [ -10500.9767] [Topology ] . ( 8 sec) [ -10500.2834] [Topology ] . ( 9 sec) [ -10499.9077] [Topology ] . ( 11 sec) [ -10499.6992] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10499.699178 . ( 19 sec) [ -10499.3949] [GTR parameters ] . ( 19 sec) [ -10499.3214] [Alpha ][ 0.975377] . ( 19 sec) [ -10499.3214] [Topology ] . ( 20 sec) [ -10499.1740] [Topology ] . ( 21 sec) [ -10499.0934] [Topology ] . ( 22 sec) [ -10499.0472] [Topology ] . ( 22 sec) [ -10499.0204] [Topology ] . ( 23 sec) [ -10499.0049] [Topology ] . ( 24 sec) [ -10498.9959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.995947 . ( 31 sec) [ -10498.9941] [GTR parameters ] . ( 31 sec) [ -10498.9900] [Alpha ][ 0.969090] . ( 31 sec) [ -10498.9900] [Topology ] . ( 32 sec) [ -10498.9835] [Topology ] . ( 33 sec) [ -10498.9798] [Topology ] . ( 34 sec) [ -10498.9777] [Topology ] . ( 35 sec) [ -10498.9765] [Topology ] . ( 36 sec) [ -10498.9757] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.975740 . ( 45 sec) [ -10498.9757] [GTR parameters ] . ( 45 sec) [ -10498.9755] [Alpha ][ 0.967885] . ( 45 sec) [ -10498.9755] [Topology ] . ( 46 sec) [ -10498.9750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 64 sec) [ -10610.1657] [GTR parameters ] . ( 65 sec) [ -10610.1656] [Alpha ][ 1.001154] . ( 65 sec) [ -10608.0965] [ 2507] [depth= 1] . ( 65 sec) [ -10607.2250] [ 2507] [depth= 1] . ( 65 sec) [ -10606.9712] [ 2507] [depth= 1] . ( 65 sec) [ -10606.9582] [ 2507] [depth= 1] . ( 66 sec) [ -10601.5769] [ 2508] [depth= 1] . ( 67 sec) [ -10597.1747] [ 2513] [depth= 1] . ( 67 sec) [ -10595.2247] [ 2508] [depth= 1] . ( 67 sec) [ -10591.5719] [ 2510] [depth= 1] . ( 67 sec) [ -10591.3353] [ 2515] [depth= 1] . ( 67 sec) [ -10589.1863] [ 2529] [depth= 1] . ( 67 sec) [ -10587.6234] [ 2532] [depth= 1] . ( 67 sec) [ -10587.0615] [ 2529] [depth= 1] . ( 67 sec) [ -10584.0384] [ 2525] [depth= 1] . ( 67 sec) [ -10582.3196] [ 2528] [depth= 1] . ( 68 sec) [ -10579.6436] [ 2525] [depth= 1] . ( 68 sec) [ -10569.8342] [ 2525] [depth= 1] . ( 68 sec) [ -10569.0272] [ 2525] [depth= 1] . ( 68 sec) [ -10563.4355] [ 2525] [depth= 1] . ( 68 sec) [ -10562.6789] [ 2524] [depth= 1] . ( 69 sec) [ -10558.0434] [ 2536] [depth= 1] . ( 70 sec) [ -10557.6969] [ 2535] [depth= 1] . ( 71 sec) [ -10512.1811] [Branch lengths ] . ( 71 sec) [ -10511.9068] [GTR parameters ] . ( 72 sec) [ -10511.8032] [Alpha ][ 0.970150] . ( 73 sec) [ -10510.4104] [ 2523] [depth= 1] . ( 73 sec) [ -10506.7544] [ 2505] [depth= 1] . ( 74 sec) [ -10506.6295] [ 2508] [depth= 1] . ( 74 sec) [ -10506.5790] [ 2505] [depth= 1] . ( 74 sec) [ -10506.5582] [ 2508] [depth= 1] . ( 75 sec) [ -10506.0693] [ 2505] [depth= 1] . ( 77 sec) [ -10500.4665] [Branch lengths ] . ( 78 sec) [ -10500.4513] [GTR parameters ] . ( 78 sec) [ -10500.4513] [Alpha ][ 0.971121] . ( 83 sec) [ -10499.8005] [Branch lengths ] . ( 112 sec) [ -10499.7411] [Branch lengths ] . ( 112 sec) [ -10499.7411] [Topology ] . ( 113 sec) [ -10499.2211] [Topology ] . ( 114 sec) [ -10499.1183] [Topology ] . ( 114 sec) [ -10499.0997] [Topology ] . ( 115 sec) [ -10499.0948] [Topology ] . ( 116 sec) [ -10499.0933] [Topology ] . ( 118 sec) [ -10499.0928] [Topology ] . ( 118 sec) [ -10499.0889] [GTR parameters ] . ( 118 sec) [ -10499.0869] [Alpha ][ 0.966770] . ( 118 sec) [ -10499.0869] [Topology ] . ( 119 sec) [ -10499.0866] [Topology ] . ( 119 sec) [ -10499.0865] [GTR parameters ] . ( 119 sec) [ -10499.0865] [Alpha ][ 0.966770] . Checking for NNIs, optimizing five branches... . ( 129 sec) [ -10499.0857] [Topology ] . Checking for NNIs, optimizing five branches... . ( 138 sec) [ -10499.0856] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10498.975038 . Log likelihood obtained after SPR moves : -10499.085559 . Log likelihood of the current tree: -10498.975038. . Printing the most likely tree in file 'data100.phy_phyml_tree.txt'... . Time used 0h2m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo