.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data91.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... . 436 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . 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=-9969.108107 . ( 1 sec) [ -9965.2502] [GTR parameters ] . ( 1 sec) [ -9965.2156] [Alpha ][ 0.980951] . ( 1 sec) [ -9965.2156] [Topology ] . ( 3 sec) [ -9880.6273] [Topology ] . ( 5 sec) [ -9863.6476] [Topology ] . ( 6 sec) [ -9857.7578] [Topology ] . ( 7 sec) [ -9852.1065] [Topology ] . ( 8 sec) [ -9850.2448] [Topology ] . ( 9 sec) [ -9849.4495] [Topology ] . ( 10 sec) [ -9849.0220] [Topology ] . ( 11 sec) [ -9848.7813] [Topology ] . ( 11 sec) [ -9848.6392] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -9848.2987] [Topology ] . Before opt ts/t=1.000000 LK=-9848.298747 . ( 20 sec) [ -9848.1993] [GTR parameters ] . ( 20 sec) [ -9847.9291] [Alpha ][ 0.933397] . ( 20 sec) [ -9847.9291] [Topology ] . ( 21 sec) [ -9847.8717] [Topology ] . ( 23 sec) [ -9847.8482] [Topology ] . ( 24 sec) [ -9847.8347] [Topology ] . ( 26 sec) [ -9847.8264] [Topology ] . ( 27 sec) [ -9847.8212] [Topology ] . ( 29 sec) [ -9847.8178] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.817810 . ( 38 sec) [ -9847.8160] [GTR parameters ] . ( 39 sec) [ -9847.8138] [Alpha ][ 0.929063] . ( 39 sec) [ -9847.8138] [Topology ] . ( 39 sec) [ -9847.8113] [Topology ] . ( 40 sec) [ -9847.8097] [Topology ] . ( 41 sec) [ -9847.8086] [Topology ] . ( 42 sec) [ -9847.8079] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.807881 . ( 51 sec) [ -9847.8078] [GTR parameters ] . ( 51 sec) [ -9847.8078] [Alpha ][ 0.929063] . ( 51 sec) [ -9847.8078] [Topology ] . ( 52 sec) [ -9847.8073] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 73 sec) [ -9965.2502] [GTR parameters ] . ( 73 sec) [ -9965.2156] [Alpha ][ 0.980951] . ( 74 sec) [ -9945.2695] [ 2314] [depth= 1] . ( 74 sec) [ -9939.2778] [ 2310] [depth= 2] . ( 75 sec) [ -9935.7886] [ 2305] [depth= 1] . ( 76 sec) [ -9934.9568] [ 2304] [depth= 1] . ( 76 sec) [ -9932.2891] [ 2306] [depth= 1] . ( 76 sec) [ -9931.7504] [ 2303] [depth= 1] . ( 77 sec) [ -9931.4114] [ 2303] [depth= 1] . ( 77 sec) [ -9930.8885] [ 2303] [depth= 1] . ( 77 sec) [ -9927.3884] [ 2306] [depth= 1] . ( 77 sec) [ -9901.3985] [ 2321] [depth= 4] . ( 78 sec) [ -9900.8488] [ 2331] [depth= 1] . ( 78 sec) [ -9900.3341] [ 2335] [depth= 1] . ( 78 sec) [ -9898.9125] [ 2331] [depth= 1] . ( 79 sec) [ -9855.8572] [Branch lengths ] . ( 79 sec) [ -9855.7844] [GTR parameters ] . ( 80 sec) [ -9855.3795] [Alpha ][ 0.921868] . ( 80 sec) [ -9855.2780] [ 2316] [depth= 1] . ( 80 sec) [ -9855.2484] [ 2331] [depth= 1] . ( 80 sec) [ -9852.9606] [ 2317] [depth= 2] . ( 81 sec) [ -9852.6223] [ 2314] [depth= 1] . ( 82 sec) [ -9852.4283] [ 2317] [depth= 1] . ( 82 sec) [ -9851.9184] [ 2322] [depth= 1] . ( 85 sec) [ -9849.3188] [Branch lengths ] . ( 85 sec) [ -9849.3094] [GTR parameters ] . ( 85 sec) [ -9849.3086] [Alpha ][ 0.924310] . ( 91 sec) [ -9848.8603] [Branch lengths ] . ( 121 sec) [ -9848.7594] [Branch lengths ] . ( 121 sec) [ -9848.7594] [Topology ] . ( 122 sec) [ -9848.7435] [Topology ] . ( 123 sec) [ -9848.7313] [Topology ] . ( 125 sec) [ -9848.7099] [Topology ] . ( 126 sec) [ -9848.6936] [Topology ] . ( 127 sec) [ -9848.6830] [Topology ] . ( 128 sec) [ -9848.6758] [Topology ] . ( 129 sec) [ -9848.6706] [Topology ] . ( 131 sec) [ -9848.6668] [Topology ] . ( 132 sec) [ -9848.6641] [Topology ] . ( 132 sec) [ -9848.6631] [GTR parameters ] . ( 132 sec) [ -9848.6621] [Alpha ][ 0.927075] . ( 132 sec) [ -9848.6621] [Topology ] . ( 133 sec) [ -9848.6601] [Topology ] . ( 134 sec) [ -9848.6586] [Topology ] . ( 135 sec) [ -9848.6576] [Topology ] . ( 136 sec) [ -9848.6568] [Topology ] . ( 136 sec) [ -9848.6568] [GTR parameters ] . ( 137 sec) [ -9848.6568] [Alpha ][ 0.927075] . ( 137 sec) [ -9848.6568] [Topology ] . ( 138 sec) [ -9848.6562] [Topology ] . ( 138 sec) [ -9848.6562] [GTR parameters ] . ( 138 sec) [ -9848.6562] [Alpha ][ 0.927075] . Checking for NNIs, optimizing five branches... . ( 149 sec) [ -9847.9913] [Topology ] . Checking for NNIs, optimizing five branches... . ( 158 sec) [ -9847.8159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 169 sec) [ -9847.8158] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9847.807318 . Log likelihood obtained after SPR moves : -9847.815789 . Log likelihood of the current tree: -9847.807318. . Printing the most likely tree in file 'data91.phy_phyml_tree.txt'... . Time used 0h3m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo