.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data69.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) . 46 sites without polymorphism (9.20%). . 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=-11173.737666 . ( 1 sec) [ -11168.5712] [GTR parameters ] . ( 1 sec) [ -11168.2821] [Alpha ][ 0.947402] . ( 1 sec) [ -11168.2821] [Topology ] . ( 2 sec) [ -11068.6753] [Topology ] . ( 3 sec) [ -11049.7537] [Topology ] . ( 4 sec) [ -11045.0305] [Topology ] . ( 5 sec) [ -11043.0991] [Topology ] . ( 6 sec) [ -11042.2218] [Topology ] . ( 7 sec) [ -11041.7763] [Topology ] . ( 8 sec) [ -11041.5398] [Topology ] . ( 8 sec) [ -11041.3785] [Topology ] . ( 9 sec) [ -11040.7455] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -11040.4333] [Topology ] . Before opt ts/t=1.000000 LK=-11040.433323 . ( 18 sec) [ -11040.2647] [GTR parameters ] . ( 18 sec) [ -11040.2022] [Alpha ][ 0.970113] . ( 18 sec) [ -11040.2022] [Topology ] . ( 18 sec) [ -11040.1562] [Topology ] . ( 19 sec) [ -11040.1377] [Topology ] . ( 20 sec) [ -11040.1280] [Topology ] . ( 21 sec) [ -11040.1225] [Topology ] . ( 22 sec) [ -11040.1193] [Topology ] . ( 23 sec) [ -11040.1175] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11040.117474 . ( 30 sec) [ -11040.1173] [GTR parameters ] . ( 30 sec) [ -11040.1167] [Alpha ][ 0.972223] . ( 30 sec) [ -11040.1167] [Topology ] . ( 31 sec) [ -11040.1155] [Topology ] . ( 32 sec) [ -11040.1148] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11040.114800 . ( 38 sec) [ -11040.1148] [GTR parameters ] . ( 38 sec) [ -11040.1148] [Alpha ][ 0.972223] . ( 38 sec) [ -11040.1148] [Topology ] . ( 39 sec) [ -11040.1144] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -11168.5712] [GTR parameters ] . ( 53 sec) [ -11168.2821] [Alpha ][ 0.947402] . ( 53 sec) [ -11150.9127] [ 2657] [depth= 1] . ( 53 sec) [ -11140.4319] [ 2664] [depth= 1] . ( 53 sec) [ -11134.8617] [ 2657] [depth= 1] . ( 53 sec) [ -11125.6557] [ 2647] [depth= 2] . ( 53 sec) [ -11119.7433] [ 2649] [depth= 1] . ( 53 sec) [ -11116.6405] [ 2655] [depth= 1] . ( 54 sec) [ -11116.0627] [ 2664] [depth= 1] . ( 54 sec) [ -11110.9528] [ 2665] [depth= 1] . ( 54 sec) [ -11110.8532] [ 2665] [depth= 1] . ( 54 sec) [ -11110.2055] [ 2667] [depth= 1] . ( 54 sec) [ -11107.6092] [ 2665] [depth= 1] . ( 54 sec) [ -11107.2589] [ 2667] [depth= 1] . ( 55 sec) [ -11106.9879] [ 2665] [depth= 1] . ( 55 sec) [ -11097.5526] [ 2662] [depth= 1] . ( 55 sec) [ -11094.4013] [ 2659] [depth= 1] . ( 55 sec) [ -11093.9512] [ 2654] [depth= 1] . ( 55 sec) [ -11093.3383] [ 2657] [depth= 1] . ( 55 sec) [ -11090.9693] [ 2654] [depth= 1] . ( 55 sec) [ -11089.9107] [ 2653] [depth= 1] . ( 56 sec) [ -11088.6537] [ 2654] [depth= 1] . ( 56 sec) [ -11088.5041] [ 2655] [depth= 3] . ( 56 sec) [ -11088.4910] [ 2659] [depth= 1] . ( 56 sec) [ -11052.7122] [Branch lengths ] . ( 57 sec) [ -11052.4786] [GTR parameters ] . ( 57 sec) [ -11052.4652] [Alpha ][ 0.957957] . ( 57 sec) [ -11052.1142] [ 2661] [depth= 2] . ( 58 sec) [ -11049.1972] [ 2652] [depth= 1] . ( 59 sec) [ -11049.1329] [ 2652] [depth= 1] . ( 60 sec) [ -11049.1015] [ 2652] [depth= 2] . ( 60 sec) [ -11048.7299] [ 2649] [depth= 1] . ( 60 sec) [ -11048.2700] [ 2650] [depth= 2] . ( 60 sec) [ -11046.2905] [ 2646] [depth= 1] . ( 61 sec) [ -11040.4434] [Branch lengths ] . ( 61 sec) [ -11040.4147] [GTR parameters ] . ( 61 sec) [ -11040.4073] [Alpha ][ 0.965838] . ( 65 sec) [ -11039.6810] [Branch lengths ] . ( 89 sec) [ -11039.5589] [Branch lengths ] . ( 89 sec) [ -11039.5589] [Topology ] . ( 89 sec) [ -11039.5416] [Topology ] . ( 90 sec) [ -11039.5340] [Topology ] . ( 91 sec) [ -11039.5296] [Topology ] . ( 92 sec) [ -11039.5270] [Topology ] . ( 93 sec) [ -11039.5254] [Topology ] . ( 94 sec) [ -11039.5244] [Topology ] . ( 94 sec) [ -11039.5235] [GTR parameters ] . ( 94 sec) [ -11039.5215] [Alpha ][ 0.969868] . ( 94 sec) [ -11039.5215] [Topology ] . ( 95 sec) [ -11039.5207] [Topology ] . ( 95 sec) [ -11039.5206] [GTR parameters ] . ( 95 sec) [ -11039.5206] [Alpha ][ 0.969868] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -11039.5203] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11040.114360 . Log likelihood obtained after SPR moves : -11039.520309 . Log likelihood of the current tree: -11039.520309. . Printing the most likely tree in file 'data69.phy_phyml_tree.txt'... . Time used 0h1m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo