.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data66.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... . 442 patterns found. (out of a total of 500 sites) . 56 sites without polymorphism (11.20%). . 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=-10526.728407 . ( 2 sec) [ -10524.4761] [GTR parameters ] . ( 2 sec) [ -10524.4715] [Alpha ][ 0.992621] . ( 2 sec) [ -10524.4715] [Topology ] . ( 3 sec) [ -10465.5610] [Topology ] . ( 4 sec) [ -10455.2547] [Topology ] . ( 5 sec) [ -10452.8768] [Topology ] . ( 6 sec) [ -10452.0332] [Topology ] . ( 7 sec) [ -10451.6737] [Topology ] . ( 8 sec) [ -10451.5056] [Topology ] . ( 9 sec) [ -10451.4234] [Topology ] . ( 9 sec) [ -10451.3821] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.382088 . ( 17 sec) [ -10451.3223] [GTR parameters ] . ( 17 sec) [ -10451.1965] [Alpha ][ 1.029002] . ( 18 sec) [ -10451.1965] [Topology ] . ( 18 sec) [ -10451.1604] [Topology ] . ( 19 sec) [ -10451.1442] [Topology ] . ( 20 sec) [ -10451.1360] [Topology ] . ( 21 sec) [ -10451.1319] [Topology ] . ( 22 sec) [ -10451.1297] [Topology ] . ( 23 sec) [ -10451.1286] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.128613 . ( 29 sec) [ -10451.1286] [GTR parameters ] . ( 29 sec) [ -10451.1276] [Alpha ][ 1.032220] . ( 30 sec) [ -10451.1276] [Topology ] . ( 30 sec) [ -10451.1269] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.126877 . ( 39 sec) [ -10451.1269] [GTR parameters ] . ( 39 sec) [ -10451.1269] [Alpha ][ 1.032220] . ( 39 sec) [ -10451.1269] [Topology ] . ( 40 sec) [ -10451.1265] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 60 sec) [ -10524.4761] [GTR parameters ] . ( 60 sec) [ -10524.4715] [Alpha ][ 0.992621] . ( 60 sec) [ -10524.0190] [ 2365] [depth= 1] . ( 61 sec) [ -10522.0793] [ 2364] [depth= 1] . ( 61 sec) [ -10521.8108] [ 2365] [depth= 1] . ( 61 sec) [ -10520.1996] [ 2376] [depth= 2] . ( 61 sec) [ -10518.3449] [ 2374] [depth= 1] . ( 62 sec) [ -10517.2983] [ 2377] [depth= 1] . ( 62 sec) [ -10513.7615] [ 2393] [depth= 1] . ( 62 sec) [ -10508.2770] [ 2377] [depth= 1] . ( 62 sec) [ -10508.1422] [ 2383] [depth= 3] . ( 63 sec) [ -10501.5856] [ 2371] [depth= 3] . ( 64 sec) [ -10460.1834] [Branch lengths ] . ( 65 sec) [ -10460.1404] [GTR parameters ] . ( 65 sec) [ -10460.1321] [Alpha ][ 1.002010] . ( 65 sec) [ -10459.0427] [ 2366] [depth= 1] . ( 66 sec) [ -10458.7659] [ 2350] [depth= 1] . ( 66 sec) [ -10458.7055] [ 2352] [depth= 1] . ( 66 sec) [ -10458.4142] [ 2350] [depth= 1] . ( 66 sec) [ -10457.9983] [ 2350] [depth= 1] . ( 68 sec) [ -10451.8408] [Branch lengths ] . ( 69 sec) [ -10451.8213] [GTR parameters ] . ( 69 sec) [ -10451.7622] [Alpha ][ 1.026487] . ( 71 sec) [ -10451.1997] [Branch lengths ] . ( 93 sec) [ -10451.1386] [Branch lengths ] . ( 93 sec) [ -10451.1386] [Topology ] . ( 94 sec) [ -10451.1333] [Topology ] . ( 95 sec) [ -10451.1317] [Topology ] . ( 96 sec) [ -10451.1309] [Topology ] . ( 96 sec) [ -10451.1304] [GTR parameters ] . ( 96 sec) [ -10451.1274] [Alpha ][ 1.032200] . ( 96 sec) [ -10451.1274] [Topology ] . ( 97 sec) [ -10451.1267] [Topology ] . ( 97 sec) [ -10451.1267] [GTR parameters ] . ( 97 sec) [ -10451.1267] [Alpha ][ 1.032200] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10451.126529 . Log likelihood obtained after SPR moves : -10451.126729 . Log likelihood of the current tree: -10451.126529. . Printing the most likely tree in file 'data66.phy_phyml_tree.txt'... . Time used 0h1m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo