.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data21.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... . 451 patterns found. (out of a total of 500 sites) . 45 sites without polymorphism (9.00%). . 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=-10442.050381 . ( 2 sec) [ -10438.0065] [GTR parameters ] . ( 2 sec) [ -10437.9885] [Alpha ][ 1.014348] . ( 2 sec) [ -10437.9885] [Topology ] . ( 2 sec) [ -10372.8235] [Topology ] . ( 4 sec) [ -10365.3616] [Topology ] . ( 4 sec) [ -10363.0571] [Topology ] . ( 5 sec) [ -10362.0626] [Topology ] . ( 6 sec) [ -10361.5856] [Topology ] . ( 7 sec) [ -10361.3468] [Topology ] . ( 8 sec) [ -10361.2242] [Topology ] . ( 9 sec) [ -10361.1605] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10361.160492 . ( 16 sec) [ -10361.1203] [GTR parameters ] . ( 16 sec) [ -10361.1152] [Alpha ][ 1.021447] . ( 16 sec) [ -10361.1152] [Topology ] . ( 17 sec) [ -10361.0795] [Topology ] . ( 18 sec) [ -10361.0607] [Topology ] . ( 19 sec) [ -10361.0508] [Topology ] . ( 19 sec) [ -10361.0455] [Topology ] . ( 20 sec) [ -10361.0427] [Topology ] . ( 21 sec) [ -10361.0412] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10361.041191 . ( 28 sec) [ -10361.0410] [GTR parameters ] . ( 28 sec) [ -10361.0410] [Alpha ][ 1.021447] . ( 28 sec) [ -10361.0410] [Topology ] . ( 29 sec) [ -10361.0402] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -10438.0065] [GTR parameters ] . ( 44 sec) [ -10437.9885] [Alpha ][ 1.014348] . ( 44 sec) [ -10437.7956] [ 2397] [depth= 1] . ( 44 sec) [ -10436.3584] [ 2398] [depth= 1] . ( 44 sec) [ -10434.9893] [ 2397] [depth= 1] . ( 45 sec) [ -10434.7881] [ 2401] [depth= 1] . ( 45 sec) [ -10433.6224] [ 2400] [depth= 1] . ( 45 sec) [ -10432.3945] [ 2405] [depth= 1] . ( 45 sec) [ -10428.9415] [ 2400] [depth= 1] . ( 45 sec) [ -10427.0585] [ 2399] [depth= 1] . ( 45 sec) [ -10413.7179] [ 2405] [depth= 1] . ( 45 sec) [ -10410.1481] [ 2407] [depth= 1] . ( 46 sec) [ -10405.9416] [ 2399] [depth= 1] . ( 47 sec) [ -10404.2320] [ 2400] [depth= 1] . ( 47 sec) [ -10403.5151] [ 2399] [depth= 1] . ( 47 sec) [ -10367.2144] [Branch lengths ] . ( 47 sec) [ -10367.1608] [GTR parameters ] . ( 48 sec) [ -10367.1597] [Alpha ][ 1.017659] . ( 48 sec) [ -10366.2503] [ 2396] [depth= 1] . ( 48 sec) [ -10366.0461] [ 2393] [depth= 1] . ( 49 sec) [ -10365.0204] [ 2395] [depth= 1] . ( 51 sec) [ -10361.6255] [Branch lengths ] . ( 52 sec) [ -10361.6165] [GTR parameters ] . ( 52 sec) [ -10361.6157] [Alpha ][ 1.020418] . ( 56 sec) [ -10361.1462] [Branch lengths ] . ( 79 sec) [ -10361.0869] [Branch lengths ] . ( 79 sec) [ -10361.0869] [Topology ] . ( 80 sec) [ -10361.0811] [Topology ] . ( 81 sec) [ -10361.0790] [Topology ] . ( 82 sec) [ -10361.0779] [Topology ] . ( 83 sec) [ -10361.0774] [Topology ] . ( 83 sec) [ -10361.0763] [GTR parameters ] . ( 83 sec) [ -10361.0763] [Alpha ][ 1.020418] . ( 83 sec) [ -10361.0763] [Topology ] . ( 84 sec) [ -10361.0759] [Topology ] . ( 84 sec) [ -10361.0759] [GTR parameters ] . ( 84 sec) [ -10361.0759] [Alpha ][ 1.020418] . Checking for NNIs, optimizing five branches... . ( 91 sec) [ -10361.0736] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -10361.0731] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10361.040201 . Log likelihood obtained after SPR moves : -10361.073061 . Log likelihood of the current tree: -10361.040201. . Printing the most likely tree in file 'data21.phy_phyml_tree.txt'... . Time used 0h1m45s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo