.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data52.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... . 402 patterns found. (out of a total of 500 sites) . 89 sites without polymorphism (17.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8218.396581 . ( 1 sec) [ -8207.7729] [GTR parameters ] . ( 1 sec) [ -8207.7661] [Alpha ][ 0.989870] . ( 1 sec) [ -8207.7661] [Topology ] . ( 1 sec) [ -8163.5971] [Topology ] . ( 2 sec) [ -8152.0230] [Topology ] . ( 3 sec) [ -8148.9805] [Topology ] . ( 4 sec) [ -8148.3847] [Topology ] . ( 5 sec) [ -8148.1924] [Topology ] . ( 5 sec) [ -8148.1169] [Topology ] . ( 6 sec) [ -8148.0838] [Topology ] . ( 7 sec) [ -8148.0686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -8148.0526] [Topology ] . Before opt ts/t=1.000000 LK=-8148.052643 . ( 14 sec) [ -8148.0125] [GTR parameters ] . ( 14 sec) [ -8147.8819] [Alpha ][ 1.031898] . ( 14 sec) [ -8147.8819] [Topology ] . ( 15 sec) [ -8147.8615] [Topology ] . ( 16 sec) [ -8147.8543] [Topology ] . ( 17 sec) [ -8147.8510] [Topology ] . ( 18 sec) [ -8147.8494] [Topology ] . ( 19 sec) [ -8147.8487] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8147.848700 . ( 26 sec) [ -8147.8487] [GTR parameters ] . ( 26 sec) [ -8147.8478] [Alpha ][ 1.035389] . ( 26 sec) [ -8147.8478] [Topology ] . ( 27 sec) [ -8147.8473] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8147.847272 . ( 32 sec) [ -8147.8473] [GTR parameters ] . ( 32 sec) [ -8147.8473] [Alpha ][ 1.035389] . ( 32 sec) [ -8147.8473] [Topology ] . ( 33 sec) [ -8147.8470] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -8207.7729] [GTR parameters ] . ( 45 sec) [ -8207.7661] [Alpha ][ 0.989870] . ( 45 sec) [ -8200.2689] [ 1686] [depth= 1] . ( 46 sec) [ -8189.6151] [ 1684] [depth= 2] . ( 46 sec) [ -8186.8223] [ 1682] [depth= 1] . ( 47 sec) [ -8185.0261] [ 1681] [depth= 1] . ( 47 sec) [ -8183.3290] [ 1682] [depth= 1] . ( 47 sec) [ -8181.6192] [ 1685] [depth= 1] . ( 47 sec) [ -8179.5564] [ 1682] [depth= 1] . ( 47 sec) [ -8178.0386] [ 1685] [depth= 1] . ( 48 sec) [ -8177.7409] [ 1686] [depth= 1] . ( 48 sec) [ -8177.0168] [ 1688] [depth= 1] . ( 48 sec) [ -8176.9467] [ 1686] [depth= 1] . ( 48 sec) [ -8150.1030] [Branch lengths ] . ( 49 sec) [ -8150.0646] [GTR parameters ] . ( 49 sec) [ -8150.0095] [Alpha ][ 1.016763] . ( 52 sec) [ -8148.8127] [Branch lengths ] . ( 66 sec) [ -8148.7884] [ 1686] [depth= 1] . ( 68 sec) [ -8148.0969] [ 1682] [depth= 1] . ( 71 sec) [ -8147.9014] [Branch lengths ] . ( 72 sec) [ -8147.8990] [GTR parameters ] . ( 72 sec) [ -8147.8796] [Alpha ][ 1.033547] . ( 72 sec) [ -8147.8796] [Topology ] . ( 72 sec) [ -8147.8659] [Topology ] . ( 73 sec) [ -8147.8618] [Topology ] . ( 74 sec) [ -8147.8601] [Topology ] . ( 75 sec) [ -8147.8593] [Topology ] . ( 75 sec) [ -8147.8593] [GTR parameters ] . ( 75 sec) [ -8147.8591] [Alpha ][ 1.035226] . ( 75 sec) [ -8147.8591] [Topology ] . ( 76 sec) [ -8147.8587] [Topology ] . ( 76 sec) [ -8147.8587] [GTR parameters ] . ( 76 sec) [ -8147.8587] [Alpha ][ 1.035226] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -8147.8583] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8147.847031 . Log likelihood obtained after SPR moves : -8147.858315 . Log likelihood of the current tree: -8147.847031. . Printing the most likely tree in file 'data52.phy_phyml_tree.txt'... . Time used 0h1m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo