.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data2.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... . 454 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . 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=-9801.144178 . ( 1 sec) [ -9799.9617] [GTR parameters ] . ( 1 sec) [ -9797.1449] [Alpha ][ 1.202689] . ( 1 sec) [ -9797.1449] [Topology ] . ( 2 sec) [ -9743.9815] [Topology ] . ( 2 sec) [ -9735.8535] [Topology ] . ( 3 sec) [ -9733.2210] [Topology ] . ( 4 sec) [ -9732.0913] [Topology ] . ( 5 sec) [ -9731.5407] [Topology ] . ( 6 sec) [ -9731.2519] [Topology ] . ( 7 sec) [ -9730.9560] [Topology ] . ( 7 sec) [ -9729.8822] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9729.882213 . ( 14 sec) [ -9729.8433] [GTR parameters ] . ( 14 sec) [ -9729.8272] [Alpha ][ 1.186224] . ( 14 sec) [ -9729.8272] [Topology ] . ( 15 sec) [ -9726.3677] [Topology ] . ( 16 sec) [ -9724.1515] [Topology ] . ( 17 sec) [ -9723.9354] [Topology ] . ( 18 sec) [ -9723.8862] [Topology ] . ( 19 sec) [ -9723.8718] [Topology ] . ( 19 sec) [ -9723.8666] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.866603 . ( 26 sec) [ -9723.8661] [GTR parameters ] . ( 26 sec) [ -9723.8658] [Alpha ][ 1.183900] . ( 26 sec) [ -9723.8658] [Topology ] . ( 27 sec) [ -9723.8635] [Topology ] . ( 28 sec) [ -9723.8622] [Topology ] . ( 29 sec) [ -9723.8615] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.861484 . ( 36 sec) [ -9723.8615] [GTR parameters ] . ( 36 sec) [ -9723.8615] [Alpha ][ 1.183900] . ( 36 sec) [ -9723.8615] [Topology ] . ( 37 sec) [ -9723.8611] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -9799.9617] [GTR parameters ] . ( 50 sec) [ -9797.1449] [Alpha ][ 1.202689] . ( 51 sec) [ -9795.9543] [ 2238] [depth= 1] . ( 51 sec) [ -9795.3567] [ 2243] [depth= 1] . ( 51 sec) [ -9792.7475] [ 2238] [depth= 1] . ( 51 sec) [ -9791.1715] [ 2241] [depth= 1] . ( 51 sec) [ -9791.1134] [ 2241] [depth= 1] . ( 51 sec) [ -9790.5221] [ 2242] [depth= 1] . ( 52 sec) [ -9789.6051] [ 2241] [depth= 1] . ( 52 sec) [ -9774.3044] [ 2260] [depth= 1] . ( 52 sec) [ -9773.3126] [ 2263] [depth= 1] . ( 53 sec) [ -9771.1987] [ 2267] [depth= 1] . ( 53 sec) [ -9769.3226] [ 2263] [depth= 1] . ( 53 sec) [ -9765.0078] [ 2260] [depth= 1] . ( 53 sec) [ -9735.0402] [Branch lengths ] . ( 54 sec) [ -9735.0094] [GTR parameters ] . ( 54 sec) [ -9734.9747] [Alpha ][ 1.179629] . ( 54 sec) [ -9734.9419] [ 2257] [depth= 1] . ( 55 sec) [ -9734.8060] [ 2260] [depth= 1] . ( 57 sec) [ -9732.0306] [Branch lengths ] . ( 57 sec) [ -9732.0301] [GTR parameters ] . ( 57 sec) [ -9732.0301] [Alpha ][ 1.179629] . ( 58 sec) [ -9732.0105] [ 2257] [depth= 1] . ( 60 sec) [ -9731.4085] [Branch lengths ] . ( 60 sec) [ -9731.4082] [GTR parameters ] . ( 60 sec) [ -9731.4080] [Alpha ][ 1.177616] . ( 62 sec) [ -9731.3620] [ 2264] [depth= 1] . ( 74 sec) [ -9731.2125] [ 2239] [depth= 1] . ( 81 sec) [ -9730.9422] [Branch lengths ] . ( 81 sec) [ -9730.9413] [GTR parameters ] . ( 81 sec) [ -9730.9385] [Alpha ][ 1.184179] . ( 81 sec) [ -9730.9385] [Topology ] . ( 82 sec) [ -9730.9101] [Topology ] . ( 83 sec) [ -9730.8110] [Topology ] . ( 83 sec) [ -9730.1843] [Topology ] . ( 84 sec) [ -9727.6112] [Topology ] . ( 85 sec) [ -9724.2608] [Topology ] . ( 86 sec) [ -9723.9489] [Topology ] . ( 86 sec) [ -9723.9481] [GTR parameters ] . ( 86 sec) [ -9723.9481] [Alpha ][ 1.182995] . ( 86 sec) [ -9723.9481] [Topology ] . ( 87 sec) [ -9723.8817] [Topology ] . ( 88 sec) [ -9723.8659] [Topology ] . ( 89 sec) [ -9723.8618] [Topology ] . ( 89 sec) [ -9723.8608] [Topology ] . ( 90 sec) [ -9723.8605] [Topology ] . ( 90 sec) [ -9723.8605] [GTR parameters ] . ( 90 sec) [ -9723.8605] [Alpha ][ 1.182995] . ( 91 sec) [ -9723.8605] [Topology ] . ( 91 sec) [ -9723.8604] [Topology ] . ( 91 sec) [ -9723.8604] [GTR parameters ] . ( 92 sec) [ -9723.8604] [Alpha ][ 1.182995] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9723.861076 . Log likelihood obtained after SPR moves : -9723.860371 . Log likelihood of the current tree: -9723.860371. . Printing the most likely tree in file 'data2.phy_phyml_tree.txt'... . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo