. Sum=1.000003 . Scaling frequencies... . The scale_param_b for rate variation over sites has been specified; unreasonable values tend to be estimated for scale and w_0. .......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename: input.phy . Data type: codon . Alphabet size: 64 . Sequence format: interleaved . Number of data sets: 1 . Nb of bootstrapped data sets: 0 . Model name: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0 . Proportion of invariable sites: 0.000000 . Number of substitution categs: 4 for amino acid selection - Number of categs: 4 for Discrete Gamma, 0 for Discrete selection categs - Selection type : 11 . Gamma distribution parameter: 1.000000 . 'Middle' of each class: mean . Codon equilibrium frequencies : empirical . Optimise tree topology: no . Evaluted tree: file "BioNJ" . Optimise branch lengths: yes . Optimise substitution model parameters: yes . Run ID: none . Random seed: 1372469602 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 318 patterns found (out of a total of 1112 sites). . 832 sites without polymorphism (74.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21 Mo of memory space. . ( 1 sec) [ -6644.6871] [Branch lengths ] . ( 2 sec) [ -6640.3243] [Selective constraints on amino acids ][0.725920 * aa_fitness(a,b) + -1.469836 * (1-delta(a,b))] [0.002660 0.500000][0.028869 0.250000][0.082494 0.125000][0.236760 0.125000] . ( 4 sec) [ -6606.9903] [GTR parameters ][rr_val: 0.065736 1.998157 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -6603.9840] [Alpha for w ][ 0.150138] [0.000263 0.500000][0.011738 0.250000][0.063397 0.125000][0.299706 0.125000] . ( 7 sec) [ -6603.9168] [Branch lengths ] . ( 8 sec) [ -6603.8842] [Selective constraints on amino acids ][0.715051 * aa_fitness(a,b) + -1.501326 * (1-delta(a,b))] [0.000260 0.500000][0.011594 0.250000][0.062619 0.125000][0.296029 0.125000] . ( 10 sec) [ -6602.7357] [GTR parameters ][rr_val: 0.059825 2.362759 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -6602.6213] [Alpha for w ][ 0.139185] [0.000181 0.500000][0.010003 0.250000][0.059447 0.125000][0.302697 0.125000] . ( 13 sec) [ -6602.6205] [Branch lengths ] . ( 14 sec) [ -6602.5246] [Selective constraints on amino acids ][0.678883 * aa_fitness(a,b) + -1.527501 * (1-delta(a,b))] [0.000188 0.500000][0.010394 0.250000][0.061771 0.125000][0.314527 0.125000] . ( 15 sec) [ -6602.5146] [GTR parameters ][rr_val: 0.055527 2.371767 1.000000 1.000000 1.000000 1.000000] . ( 17 sec) [ -6602.4920] [Alpha for w ][ 0.136652] [0.000171 0.500000][0.010011 0.250000][0.060942 0.125000][0.316190 0.125000] . ( 18 sec) [ -6602.4919] [Branch lengths ] . ( 19 sec) [ -6602.4622] [Selective constraints on amino acids ][0.661755 * aa_fitness(a,b) + -1.548761 * (1-delta(a,b))] [0.000173 0.500000][0.010108 0.250000][0.061538 0.125000][0.319281 0.125000] . ( 21 sec) [ -6602.4621] [GTR parameters ][rr_val: 0.055095 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 22 sec) [ -6602.4565] [Alpha for w ][ 0.135992] [0.000169 0.500000][0.010008 0.250000][0.061316 0.125000][0.319722 0.125000] . ( 23 sec) [ -6602.4565] [Branch lengths ] . ( 25 sec) [ -6602.4386] [Selective constraints on amino acids ][0.649339 * aa_fitness(a,b) + -1.566844 * (1-delta(a,b))] [0.000170 0.500000][0.010053 0.250000][0.061596 0.125000][0.321182 0.125000] . ( 26 sec) [ -6602.4386] [GTR parameters ][rr_val: 0.054927 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 27 sec) [ -6602.4365] [Alpha for w ][ 0.135744] [0.000168 0.500000][0.010015 0.250000][0.061511 0.125000][0.321349 0.125000] . ( 29 sec) [ -6602.4365] [Branch lengths ] . ( 30 sec) [ -6602.4241] [Selective constraints on amino acids ][0.639138 * aa_fitness(a,b) + -1.582050 * (1-delta(a,b))] [0.000169 0.500000][0.010050 0.250000][0.061727 0.125000][0.322478 0.125000] . ( 31 sec) [ -6602.4241] [GTR parameters ][rr_val: 0.054830 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 33 sec) [ -6602.4217] [Alpha for w ][ 0.135445] [0.000167 0.500000][0.010004 0.250000][0.061625 0.125000][0.322679 0.125000] . ( 34 sec) [ -6602.4217] [Branch lengths ] . ( 35 sec) [ -6602.4148] [Selective constraints on amino acids ][0.630632 * aa_fitness(a,b) + -1.586737 * (1-delta(a,b))] [0.000169 0.500000][0.010115 0.250000][0.062307 0.125000][0.326247 0.125000] . ( 37 sec) [ -6602.4147] [GTR parameters ][rr_val: 0.054412 2.380441 1.000000 1.000000 1.000000 1.000000] . ( 38 sec) [ -6602.4099] [Alpha for w ][ 0.134843] [0.000165 0.500000][0.010021 0.250000][0.062097 0.125000][0.326660 0.125000] . ( 40 sec) [ -6602.4099] [Branch lengths ] . ( 41 sec) [ -6602.4080] [Selective constraints on amino acids ][0.627497 * aa_fitness(a,b) + -1.591419 * (1-delta(a,b))] [0.000165 0.500000][0.010032 0.250000][0.062166 0.125000][0.327024 0.125000] . ( 42 sec) [ -6602.4080] [GTR parameters ][rr_val: 0.054351 2.378060 1.000000 1.000000 1.000000 1.000000] . ( 44 sec) [ -6602.4068] [Alpha for w ][ 0.134708] [0.000164 0.500000][0.010011 0.250000][0.062119 0.125000][0.327117 0.125000] . ( 45 sec) [ -6602.4068] [Branch lengths ] . ( 47 sec) [ -6602.4055] [Selective constraints on amino acids ][0.623972 * aa_fitness(a,b) + -1.596362 * (1-delta(a,b))] [0.000164 0.500000][0.010027 0.250000][0.062217 0.125000][0.327636 0.125000] . ( 48 sec) [ -6602.4055] [GTR parameters ][rr_val: 0.054351 2.378060 1.000000 1.000000 1.000000 1.000000] . ( 49 sec) [ -6602.4044] [Alpha for w ][ 0.134573] [0.000164 0.500000][0.010006 0.250000][0.062170 0.125000][0.327729 0.125000] . ( 51 sec) [ -6602.4044] [Branch lengths ] . ( 52 sec) [ -6602.4036] [Selective constraints on amino acids ][0.621152 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000164 0.500000][0.010029 0.250000][0.062311 0.125000][0.328474 0.125000] . ( 53 sec) [ -6602.4036] [GTR parameters ][rr_val: 0.054254 2.381835 1.000000 1.000000 1.000000 1.000000] . ( 55 sec) [ -6602.4024] [Alpha for w ][ 0.134439] [0.000163 0.500000][0.010008 0.250000][0.062264 0.125000][0.328567 0.125000] . ( 56 sec) [ -6602.4024] [Branch lengths ] . ( 58 sec) [ -6602.4022] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000164 0.500000][0.010038 0.250000][0.062453 0.125000][0.329569 0.125000] . ( 59 sec) [ -6602.4022] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 60 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 62 sec) [ -6602.4004] [Branch lengths ] . ( 63 sec) [ -6602.4004] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 64 sec) [ -6602.4004] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 66 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 67 sec) [ -6602.4004] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 69 sec) [ -6602.4004] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 70 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . Log likelihood of the current tree: -6602.400402. . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Time used 0h1m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo