.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2770_86x1628_2006.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... . 571 patterns found. (out of a total of 1628 sites) . 1267 sites without polymorphism (77.83%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -5881.3955] [GTR parameters ] . ( 3 sec) [ -5881.3763] [Alpha ][ 1.039147] . ( 3 sec) [ -5881.3763] [Topology ] . ( 6 sec) [ -5840.5187] [Topology ] . ( 8 sec) [ -5831.9227] [Topology ] . ( 11 sec) [ -5825.2712] [Topology ] . ( 13 sec) [ -5824.3381] [Topology ] . ( 15 sec) [ -5824.2227] [Topology ] . ( 18 sec) [ -5824.2058] [Topology ] . ( 20 sec) [ -5824.2023] [Topology ] . ( 22 sec) [ -5824.2014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5824.0941] [GTR parameters ] . ( 38 sec) [ -5823.9485] [Alpha ][ 1.159997] . ( 38 sec) [ -5823.9485] [Topology ] . ( 41 sec) [ -5823.9480] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -5823.9479] [GTR parameters ] . ( 56 sec) [ -5823.9479] [Alpha ][ 1.159997] . ( 56 sec) [ -5823.9479] [Topology ] . ( 58 sec) [ -5823.9478] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 89 sec) [ -5881.3955] [GTR parameters ] . ( 89 sec) [ -5881.3763] [Alpha ][ 1.039147] . ( 90 sec) [ -5880.5971] [ 518] [depth= 1] . ( 90 sec) [ -5880.0235] [ 518] [depth= 1] . ( 90 sec) [ -5879.6552] [ 518] [depth= 1] . ( 90 sec) [ -5879.6115] [ 518] [depth= 1] . ( 91 sec) [ -5873.8661] [ 517] [depth= 1] . ( 91 sec) [ -5873.4203] [ 517] [depth= 1] . ( 91 sec) [ -5873.1945] [ 517] [depth= 1] . ( 92 sec) [ -5871.1004] [ 517] [depth= 2] . ( 92 sec) [ -5870.9911] [ 517] [depth= 2] . ( 93 sec) [ -5870.9400] [ 517] [depth= 1] . ( 93 sec) [ -5870.9271] [ 517] [depth= 2] . ( 93 sec) [ -5870.9154] [ 517] [depth= 1] . ( 94 sec) [ -5869.2789] [ 517] [depth= 1] . ( 94 sec) [ -5868.9431] [ 517] [depth= 1] . ( 94 sec) [ -5868.7479] [ 517] [depth= 1] . ( 95 sec) [ -5868.0867] [ 517] [depth= 3] . ( 95 sec) [ -5868.0291] [ 517] [depth= 1] . ( 95 sec) [ -5867.9488] [ 517] [depth= 1] . ( 98 sec) [ -5856.0675] [ 515] [depth= 4] . ( 99 sec) [ -5855.4154] [ 515] [depth= 1] . ( 100 sec) [ -5854.9416] [ 515] [depth= 1] . ( 100 sec) [ -5848.7736] [ 513] [depth= 1] . ( 101 sec) [ -5844.2807] [ 512] [depth= 2] . ( 103 sec) [ -5844.0683] [ 512] [depth= 1] . ( 104 sec) [ -5844.0464] [ 512] [depth= 1] . ( 109 sec) [ -5843.9813] [ 512] [depth= 1] . ( 109 sec) [ -5843.8187] [ 512] [depth= 1] . ( 109 sec) [ -5843.8039] [ 512] [depth= 1] . ( 111 sec) [ -5843.7888] [ 512] [depth= 1] . ( 113 sec) [ -5843.1350] [ 512] [depth= 1] . ( 113 sec) [ -5842.5610] [ 512] [depth= 1] . ( 116 sec) [ -5842.3305] [ 512] [depth= 2] . ( 116 sec) [ -5842.1627] [ 512] [depth= 2] . ( 117 sec) [ -5841.8969] [ 512] [depth= 1] . ( 117 sec) [ -5841.8809] [ 512] [depth= 2] . ( 117 sec) [ -5841.8298] [ 512] [depth= 1] . ( 118 sec) [ -5841.4085] [ 512] [depth= 1] . ( 118 sec) [ -5841.3910] [ 512] [depth= 1] . ( 123 sec) [ -5839.2863] [ 510] [depth= 1] . ( 128 sec) [ -5837.6801] [ 510] [depth= 5] . ( 132 sec) [ -5836.9725] [ 510] [depth= 1] . ( 133 sec) [ -5834.5589] [ 510] [depth= 2] . ( 133 sec) [ -5831.0691] [ 509] [depth= 1] . ( 133 sec) [ -5830.3719] [ 509] [depth= 1] . ( 135 sec) [ -5829.7456] [ 509] [depth= 2] . ( 139 sec) [ -5829.0950] [ 509] [depth= 2] . ( 140 sec) [ -5825.3656] [ 508] [depth= 2] . ( 141 sec) [ -5824.6950] [ 508] [depth= 1] . ( 141 sec) [ -5824.4269] [ 508] [depth= 1] . ( 143 sec) [ -5824.2963] [ 508] [depth= 1] . ( 145 sec) [ -5824.2545] [ 508] [depth= 1] . ( 146 sec) [ -5822.5161] [ 508] [depth= 1] . ( 146 sec) [ -5822.3249] [ 508] [depth= 1] . ( 147 sec) [ -5822.3077] [ 508] [depth= 1] . ( 149 sec) [ -5811.0309] [Branch lengths ] . ( 151 sec) [ -5810.7118] [GTR parameters ] . ( 151 sec) [ -5810.4587] [Alpha ][ 1.204117] . ( 161 sec) [ -5810.3495] [ 508] [depth= 2] . ( 164 sec) [ -5810.3213] [ 508] [depth= 2] . ( 165 sec) [ -5810.3024] [ 508] [depth= 1] . ( 166 sec) [ -5810.2764] [ 508] [depth= 1] . ( 195 sec) [ -5810.2647] [ 508] [depth= 1] . ( 221 sec) [ -5809.8864] [Branch lengths ] . ( 222 sec) [ -5809.8704] [GTR parameters ] . ( 222 sec) [ -5809.8703] [Alpha ][ 1.207420] . ( 251 sec) [ -5809.8574] [ 508] [depth= 1] . ( 326 sec) [ -5809.6359] [Branch lengths ] . ( 326 sec) [ -5809.6359] [GTR parameters ] . ( 326 sec) [ -5809.6359] [Alpha ][ 1.207420] . ( 326 sec) [ -5809.6359] [Topology ] . ( 328 sec) [ -5809.6325] [Topology ] . ( 331 sec) [ -5809.6319] [Topology ] . ( 331 sec) [ -5809.6319] [GTR parameters ] . ( 331 sec) [ -5809.6319] [Alpha ][ 1.207420] . ( 331 sec) [ -5809.6319] [Topology ] . ( 333 sec) [ -5809.6318] [Topology ] . ( 334 sec) [ -5809.6318] [GTR parameters ] . ( 334 sec) [ -5809.6318] [Alpha ][ 1.207420] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5823.947839 . Log likelihood obtained after SPR moves : -5809.631777 . Log likelihood of the current tree: -5809.631777. . Printing the most likely tree in file 'nucleic_M2770_86x1628_2006.phy_phyml_tree.txt'... . Time used 0h5m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 347.79user 0.00system 5:49.70elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps