.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data35.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... . 446 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=-10555.099857 . ( 1 sec) [ -10552.4569] [GTR parameters ] . ( 2 sec) [ -10551.5166] [Alpha ][ 0.903985] . ( 2 sec) [ -10551.5166] [Topology ] . ( 2 sec) [ -10484.8412] [Topology ] . ( 4 sec) [ -10473.4165] [Topology ] . ( 5 sec) [ -10469.6529] [Topology ] . ( 6 sec) [ -10468.0389] [Topology ] . ( 7 sec) [ -10467.2638] [Topology ] . ( 8 sec) [ -10466.8540] [Topology ] . ( 9 sec) [ -10466.6391] [Topology ] . ( 10 sec) [ -10466.5171] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.517115 . ( 19 sec) [ -10466.4575] [GTR parameters ] . ( 20 sec) [ -10466.4366] [Alpha ][ 0.917049] . ( 20 sec) [ -10466.4366] [Topology ] . ( 21 sec) [ -10466.3687] [Topology ] . ( 22 sec) [ -10466.3297] [Topology ] . ( 23 sec) [ -10466.3074] [Topology ] . ( 25 sec) [ -10466.2939] [Topology ] . ( 26 sec) [ -10466.2859] [Topology ] . ( 27 sec) [ -10466.2809] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.280895 . ( 37 sec) [ -10466.2807] [GTR parameters ] . ( 37 sec) [ -10466.2805] [Alpha ][ 0.918334] . ( 37 sec) [ -10466.2805] [Topology ] . ( 38 sec) [ -10466.2774] [Topology ] . ( 40 sec) [ -10466.2754] [Topology ] . ( 41 sec) [ -10466.2741] [Topology ] . ( 42 sec) [ -10466.2733] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.273300 . ( 51 sec) [ -10466.2733] [GTR parameters ] . ( 51 sec) [ -10466.2733] [Alpha ][ 0.918334] . ( 51 sec) [ -10466.2733] [Topology ] . ( 52 sec) [ -10466.2728] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 72 sec) [ -10552.4569] [GTR parameters ] . ( 72 sec) [ -10551.5166] [Alpha ][ 0.903985] . ( 72 sec) [ -10548.2201] [ 2456] [depth= 1] . ( 73 sec) [ -10544.6986] [ 2457] [depth= 1] . ( 73 sec) [ -10543.0224] [ 2456] [depth= 1] . ( 73 sec) [ -10543.0115] [ 2457] [depth= 1] . ( 73 sec) [ -10537.9108] [ 2471] [depth= 1] . ( 74 sec) [ -10533.7541] [ 2476] [depth= 1] . ( 74 sec) [ -10532.2155] [ 2474] [depth= 1] . ( 75 sec) [ -10531.9569] [ 2474] [depth= 1] . ( 75 sec) [ -10531.8595] [ 2474] [depth= 1] . ( 75 sec) [ -10531.2566] [ 2474] [depth= 1] . ( 75 sec) [ -10530.2162] [ 2474] [depth= 1] . ( 75 sec) [ -10530.1379] [ 2474] [depth= 1] . ( 75 sec) [ -10527.7675] [ 2477] [depth= 1] . ( 75 sec) [ -10524.4271] [ 2474] [depth= 1] . ( 75 sec) [ -10518.2294] [ 2474] [depth= 1] . ( 76 sec) [ -10516.9900] [ 2473] [depth= 1] . ( 76 sec) [ -10514.9712] [ 2474] [depth= 1] . ( 76 sec) [ -10514.2069] [ 2481] [depth= 1] . ( 77 sec) [ -10509.8468] [ 2474] [depth= 1] . ( 77 sec) [ -10509.4101] [ 2475] [depth= 1] . ( 77 sec) [ -10505.9143] [ 2474] [depth= 1] . ( 78 sec) [ -10474.8207] [Branch lengths ] . ( 79 sec) [ -10474.7433] [GTR parameters ] . ( 79 sec) [ -10474.7227] [Alpha ][ 0.917161] . ( 79 sec) [ -10473.2304] [ 2472] [depth= 1] . ( 79 sec) [ -10473.2158] [ 2473] [depth= 1] . ( 80 sec) [ -10472.6097] [ 2460] [depth= 1] . ( 80 sec) [ -10471.8746] [ 2459] [depth= 1] . ( 85 sec) [ -10467.1145] [Branch lengths ] . ( 85 sec) [ -10467.1076] [GTR parameters ] . ( 85 sec) [ -10467.1065] [Alpha ][ 0.920111] . ( 90 sec) [ -10466.5065] [Branch lengths ] . ( 122 sec) [ -10466.3403] [Branch lengths ] . ( 122 sec) [ -10466.3403] [Topology ] . ( 124 sec) [ -10466.3105] [Topology ] . ( 125 sec) [ -10466.2964] [Topology ] . ( 126 sec) [ -10466.2879] [Topology ] . ( 128 sec) [ -10466.2826] [Topology ] . ( 129 sec) [ -10466.2792] [Topology ] . ( 130 sec) [ -10466.2770] [Topology ] . ( 130 sec) [ -10466.2764] [GTR parameters ] . ( 130 sec) [ -10466.2762] [Alpha ][ 0.918674] . ( 130 sec) [ -10466.2762] [Topology ] . ( 131 sec) [ -10466.2747] [Topology ] . ( 132 sec) [ -10466.2737] [Topology ] . ( 132 sec) [ -10466.2737] [GTR parameters ] . ( 132 sec) [ -10466.2737] [Alpha ][ 0.918674] . ( 132 sec) [ -10466.2737] [Topology ] . ( 133 sec) [ -10466.2731] [Topology ] . ( 133 sec) [ -10466.2731] [GTR parameters ] . ( 133 sec) [ -10466.2731] [Alpha ][ 0.918674] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10466.272790 . Log likelihood obtained after SPR moves : -10466.273076 . Log likelihood of the current tree: -10466.272790. . Printing the most likely tree in file 'data35.phy_phyml_tree.txt'... . Time used 0h2m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo