.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_2006.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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -5607.7521] [GTR parameters ] . ( 2 sec) [ -5527.3790] [Alpha ][ 0.500960] . ( 2 sec) [ -5525.4341] [ 850] [depth= 1] . ( 2 sec) [ -5523.1508] [ 853] [depth= 1] . ( 2 sec) [ -5519.7480] [ 850] [depth= 1] . ( 2 sec) [ -5507.5690] [ 851] [depth= 1] . ( 3 sec) [ -5504.6039] [ 850] [depth= 1] . ( 3 sec) [ -5504.2033] [ 851] [depth= 1] . ( 3 sec) [ -5499.4790] [ 853] [depth= 2] . ( 3 sec) [ -5496.3204] [ 853] [depth= 1] . ( 3 sec) [ -5496.1446] [ 854] [depth= 2] . ( 4 sec) [ -5495.3779] [ 853] [depth= 1] . ( 4 sec) [ -5492.1844] [ 853] [depth= 1] . ( 4 sec) [ -5491.9547] [ 854] [depth= 1] . ( 4 sec) [ -5491.1091] [ 854] [depth= 1] . ( 4 sec) [ -5490.9140] [ 853] [depth= 1] . ( 4 sec) [ -5490.8549] [ 854] [depth= 1] . ( 4 sec) [ -5490.6489] [ 854] [depth= 1] . ( 4 sec) [ -5483.4840] [ 850] [depth= 2] . ( 5 sec) [ -5483.1862] [ 855] [depth= 1] . ( 5 sec) [ -5482.9207] [ 853] [depth= 3] . ( 5 sec) [ -5481.9203] [ 853] [depth= 1] . ( 5 sec) [ -5476.1793] [ 854] [depth= 1] . ( 5 sec) [ -5476.1352] [ 855] [depth= 1] . ( 6 sec) [ -5475.2624] [ 854] [depth= 1] . ( 7 sec) [ -5474.3623] [ 856] [depth= 1] . ( 7 sec) [ -5471.7260] [ 854] [depth= 1] . ( 7 sec) [ -5466.7703] [ 855] [depth= 2] . ( 7 sec) [ -5466.6433] [ 856] [depth= 1] . ( 8 sec) [ -5466.5185] [ 856] [depth= 1] . ( 8 sec) [ -5466.2310] [ 856] [depth= 1] . ( 8 sec) [ -5466.1849] [ 856] [depth= 1] . ( 8 sec) [ -5466.1505] [ 856] [depth= 1] . ( 9 sec) [ -5466.0112] [ 856] [depth= 1] . ( 9 sec) [ -5465.5315] [ 855] [depth= 1] . ( 10 sec) [ -5465.1329] [ 855] [depth= 1] . ( 11 sec) [ -5465.0288] [ 855] [depth= 1] . ( 13 sec) [ -5464.9186] [ 855] [depth= 1] . ( 13 sec) [ -5464.4882] [ 855] [depth= 1] . ( 13 sec) [ -5464.3524] [ 855] [depth= 1] . ( 13 sec) [ -5464.3328] [ 855] [depth= 1] . ( 14 sec) [ -5463.9965] [ 855] [depth= 2] . ( 14 sec) [ -5463.9039] [ 855] [depth= 2] . ( 14 sec) [ -5463.8295] [ 855] [depth= 2] . ( 16 sec) [ -5439.6568] [Branch lengths ] . ( 17 sec) [ -5438.5202] [GTR parameters ] . ( 17 sec) [ -5397.9063] [Alpha ][ 0.250961] . ( 17 sec) [ -5397.7295] [ 855] [depth= 1] . ( 17 sec) [ -5396.5947] [ 852] [depth= 1] . ( 17 sec) [ -5395.8082] [ 852] [depth= 1] . ( 17 sec) [ -5392.6402] [ 848] [depth= 2] . ( 33 sec) [ -5388.5981] [Branch lengths ] . ( 34 sec) [ -5387.8347] [GTR parameters ] . ( 34 sec) [ -5387.6991] [Alpha ][ 0.241931] . ( 35 sec) [ -5386.6790] [ 852] [depth= 10] . ( 39 sec) [ -5386.4101] [ 854] [depth= 1] . ( 46 sec) [ -5386.3857] [ 854] [depth= 1] . ( 48 sec) [ -5386.3737] [ 854] [depth= 1] . ( 52 sec) [ -5383.0729] [Branch lengths ] . ( 53 sec) [ -5382.7882] [GTR parameters ] . ( 53 sec) [ -5382.7699] [Alpha ][ 0.238803] . ( 62 sec) [ -5382.7556] [ 854] [depth= 1] . ( 70 sec) [ -5382.4119] [Branch lengths ] . ( 71 sec) [ -5382.4080] [GTR parameters ] . ( 71 sec) [ -5382.4079] [Alpha ][ 0.238551] . ( 107 sec) [ -5382.3690] [Branch lengths ] . ( 107 sec) [ -5382.3690] [Topology ] . ( 108 sec) [ -5382.3649] [Topology ] . ( 109 sec) [ -5382.3635] [Topology ] . ( 110 sec) [ -5382.3629] [Topology ] . ( 110 sec) [ -5382.3622] [GTR parameters ] . ( 110 sec) [ -5382.3619] [Alpha ][ 0.238869] . ( 110 sec) [ -5382.3619] [Topology ] . ( 111 sec) [ -5382.3614] [Topology ] . ( 111 sec) [ -5382.3614] [GTR parameters ] . ( 112 sec) [ -5382.3614] [Alpha ][ 0.238869] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.361413. . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Time used 0h1m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 116.46user 0.00system 1:58.71elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps