.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data50.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... . 440 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=-10296.740802 . ( 1 sec) [ -10294.9392] [GTR parameters ] . ( 1 sec) [ -10294.7927] [Alpha ][ 0.960616] . ( 1 sec) [ -10294.7927] [Topology ] . ( 2 sec) [ -10235.5620] [Topology ] . ( 4 sec) [ -10223.5704] [Topology ] . ( 5 sec) [ -10220.9334] [Topology ] . ( 6 sec) [ -10219.8027] [Topology ] . ( 6 sec) [ -10219.2500] [Topology ] . ( 7 sec) [ -10218.9647] [Topology ] . ( 8 sec) [ -10218.8140] [Topology ] . ( 9 sec) [ -10218.7333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.733311 . ( 16 sec) [ -10218.6801] [GTR parameters ] . ( 16 sec) [ -10218.3007] [Alpha ][ 1.022180] . ( 16 sec) [ -10218.3007] [Topology ] . ( 16 sec) [ -10218.2286] [Topology ] . ( 17 sec) [ -10218.1933] [Topology ] . ( 18 sec) [ -10218.1745] [Topology ] . ( 19 sec) [ -10218.1645] [Topology ] . ( 20 sec) [ -10218.1591] [Topology ] . ( 21 sec) [ -10218.1562] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.156228 . ( 31 sec) [ -10218.1561] [GTR parameters ] . ( 31 sec) [ -10218.1545] [Alpha ][ 1.026389] . ( 31 sec) [ -10218.1545] [Topology ] . ( 32 sec) [ -10218.1527] [Topology ] . ( 33 sec) [ -10218.1518] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.151758 . ( 41 sec) [ -10218.1517] [GTR parameters ] . ( 41 sec) [ -10218.1517] [Alpha ][ 1.026389] . ( 41 sec) [ -10218.1517] [Topology ] . ( 42 sec) [ -10218.1512] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 59 sec) [ -10294.9392] [GTR parameters ] . ( 59 sec) [ -10294.7927] [Alpha ][ 0.960616] . ( 61 sec) [ -10292.1127] [ 2297] [depth= 1] . ( 61 sec) [ -10290.6536] [ 2295] [depth= 1] . ( 61 sec) [ -10290.1125] [ 2294] [depth= 1] . ( 61 sec) [ -10289.4637] [ 2297] [depth= 1] . ( 61 sec) [ -10288.9441] [ 2297] [depth= 1] . ( 61 sec) [ -10286.3863] [ 2302] [depth= 2] . ( 61 sec) [ -10286.0752] [ 2303] [depth= 1] . ( 62 sec) [ -10286.0115] [ 2299] [depth= 1] . ( 62 sec) [ -10284.9665] [ 2298] [depth= 2] . ( 62 sec) [ -10282.3121] [ 2299] [depth= 1] . ( 62 sec) [ -10281.6755] [ 2298] [depth= 1] . ( 63 sec) [ -10281.5537] [ 2299] [depth= 1] . ( 63 sec) [ -10281.4090] [ 2304] [depth= 2] . ( 64 sec) [ -10281.0173] [ 2296] [depth= 2] . ( 64 sec) [ -10279.5703] [ 2296] [depth= 1] . ( 64 sec) [ -10274.9183] [ 2296] [depth= 1] . ( 64 sec) [ -10274.7389] [ 2299] [depth= 1] . ( 64 sec) [ -10270.0398] [ 2296] [depth= 1] . ( 64 sec) [ -10269.7605] [ 2299] [depth= 1] . ( 65 sec) [ -10268.8129] [ 2296] [depth= 1] . ( 65 sec) [ -10268.6292] [ 2299] [depth= 1] . ( 65 sec) [ -10256.3184] [ 2301] [depth= 2] . ( 65 sec) [ -10223.9581] [Branch lengths ] . ( 66 sec) [ -10223.9128] [GTR parameters ] . ( 66 sec) [ -10223.8016] [Alpha ][ 0.994571] . ( 67 sec) [ -10223.3026] [ 2298] [depth= 1] . ( 68 sec) [ -10223.2835] [ 2297] [depth= 1] . ( 68 sec) [ -10223.2693] [ 2298] [depth= 1] . ( 72 sec) [ -10219.0848] [Branch lengths ] . ( 72 sec) [ -10219.0826] [GTR parameters ] . ( 72 sec) [ -10219.0351] [Alpha ][ 1.017365] . ( 78 sec) [ -10218.3452] [Branch lengths ] . ( 102 sec) [ -10218.2023] [Branch lengths ] . ( 102 sec) [ -10218.2023] [Topology ] . ( 103 sec) [ -10218.1864] [Topology ] . ( 104 sec) [ -10218.1807] [Topology ] . ( 105 sec) [ -10218.1778] [Topology ] . ( 106 sec) [ -10218.1762] [Topology ] . ( 106 sec) [ -10218.1754] [Topology ] . ( 106 sec) [ -10218.1750] [GTR parameters ] . ( 107 sec) [ -10218.1677] [Alpha ][ 1.026316] . ( 107 sec) [ -10218.1677] [Topology ] . ( 107 sec) [ -10218.1668] [Topology ] . ( 108 sec) [ -10218.1668] [GTR parameters ] . ( 108 sec) [ -10218.1668] [Alpha ][ 1.026316] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -10218.1667] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10218.151240 . Log likelihood obtained after SPR moves : -10218.166656 . Log likelihood of the current tree: -10218.151240. . Printing the most likely tree in file 'data50.phy_phyml_tree.txt'... . Time used 0h2m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo