.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data9.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... . 316 patterns found. (out of a total of 500 sites) . 164 sites without polymorphism (32.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5188.828666 . ( 1 sec) [ -5182.3636] [GTR parameters ] . ( 1 sec) [ -5182.3635] [Alpha ][ 0.998896] . ( 1 sec) [ -5182.3635] [Topology ] . ( 2 sec) [ -5158.5937] [Topology ] . ( 3 sec) [ -5155.9177] [Topology ] . ( 4 sec) [ -5155.5437] [Topology ] . ( 5 sec) [ -5155.4587] [Topology ] . ( 6 sec) [ -5155.4345] [Topology ] . ( 7 sec) [ -5155.4267] [Topology ] . ( 7 sec) [ -5155.4241] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5155.424069 . ( 12 sec) [ -5155.4131] [GTR parameters ] . ( 12 sec) [ -5155.4028] [Alpha ][ 1.015610] . ( 12 sec) [ -5155.4028] [Topology ] . ( 13 sec) [ -5155.4010] [Topology ] . ( 14 sec) [ -5155.4004] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5155.400408 . ( 18 sec) [ -5155.4004] [GTR parameters ] . ( 18 sec) [ -5155.4004] [Alpha ][ 1.015610] . ( 18 sec) [ -5155.4004] [Topology ] . ( 19 sec) [ -5155.4002] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 31 sec) [ -5182.3636] [GTR parameters ] . ( 31 sec) [ -5182.3635] [Alpha ][ 0.998896] . ( 32 sec) [ -5182.3360] [ 876] [depth= 1] . ( 32 sec) [ -5181.5259] [ 877] [depth= 1] . ( 32 sec) [ -5179.9695] [ 876] [depth= 1] . ( 32 sec) [ -5179.3411] [ 875] [depth= 1] . ( 33 sec) [ -5176.9973] [ 876] [depth= 1] . ( 33 sec) [ -5176.8402] [ 876] [depth= 1] . ( 33 sec) [ -5174.7927] [ 874] [depth= 1] . ( 33 sec) [ -5174.6594] [ 873] [depth= 1] . ( 34 sec) [ -5174.5811] [ 874] [depth= 1] . ( 34 sec) [ -5174.1271] [ 874] [depth= 2] . ( 34 sec) [ -5173.9853] [ 874] [depth= 1] . ( 35 sec) [ -5173.8692] [ 874] [depth= 1] . ( 35 sec) [ -5173.2085] [ 874] [depth= 1] . ( 35 sec) [ -5172.5776] [ 873] [depth= 1] . ( 35 sec) [ -5172.1389] [ 874] [depth= 1] . ( 35 sec) [ -5172.0627] [ 874] [depth= 1] . ( 35 sec) [ -5172.0309] [ 874] [depth= 1] . ( 35 sec) [ -5170.7349] [ 874] [depth= 1] . ( 35 sec) [ -5170.6631] [ 874] [depth= 1] . ( 36 sec) [ -5170.6383] [ 874] [depth= 1] . ( 36 sec) [ -5170.5211] [ 874] [depth= 1] . ( 36 sec) [ -5170.3762] [ 874] [depth= 1] . ( 37 sec) [ -5158.1596] [Branch lengths ] . ( 37 sec) [ -5158.1513] [GTR parameters ] . ( 37 sec) [ -5158.1471] [Alpha ][ 1.009460] . ( 37 sec) [ -5155.7878] [ 873] [depth= 1] . ( 44 sec) [ -5155.4065] [Branch lengths ] . ( 45 sec) [ -5155.4055] [GTR parameters ] . ( 45 sec) [ -5155.4040] [Alpha ][ 1.015682] . ( 51 sec) [ -5155.4004] [Branch lengths ] . ( 72 sec) [ -5155.4000] [Branch lengths ] . ( 72 sec) [ -5155.4000] [Topology ] . ( 72 sec) [ -5155.4000] [Topology ] . ( 73 sec) [ -5155.4000] [GTR parameters ] . ( 73 sec) [ -5155.4000] [Alpha ][ 1.016698] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5155.400193 . Log likelihood obtained after SPR moves : -5155.400010 . Log likelihood of the current tree: -5155.400010. . Printing the most likely tree in file 'data9.phy_phyml_tree.txt'... . Time used 0h1m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo