/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_161501/input.phy -d aa -b 0 --mechanistic_opt 11063 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0001 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace . 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: aa . 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: 1 . Amino acid 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: 1372835701 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 78 patterns found (out of a total of 1112 sites). . 1049 sites without polymorphism (94.33%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 2 Mo of memory space. . ( 1 sec) [ -3749.3706] [Branch lengths ] . ( 1 sec) [ -3748.8304] [Selective constraints on amino acids ][0.931852 * aa_fitness(a,b) + -1.593850 * (1-delta(a,b))] . ( 2 sec) [ -3740.8066] [GTR parameters ][rr_val: 0.137717 1.635061 1.023915 1.273420 1.159279 1.100343] . ( 3 sec) [ -3736.4322] [Nucleotide equlibrium freqs.][ACGT: 0.380799 0.224130 0.251061 0.144011] . ( 4 sec) [ -3735.4343] [Branch lengths ] . ( 4 sec) [ -3734.9777] [Selective constraints on amino acids ][0.864330 * aa_fitness(a,b) + -1.669212 * (1-delta(a,b))] . ( 5 sec) [ -3734.6417] [GTR parameters ][rr_val: 0.128981 1.481371 1.106414 1.092382 1.129183 1.191721] . ( 6 sec) [ -3734.5826] [Nucleotide equlibrium freqs.][ACGT: 0.390306 0.210181 0.256286 0.143228] . ( 6 sec) [ -3734.5629] [Branch lengths ] . ( 7 sec) [ -3734.3821] [Selective constraints on amino acids ][0.823034 * aa_fitness(a,b) + -1.718978 * (1-delta(a,b))] . ( 7 sec) [ -3734.3731] [GTR parameters ][rr_val: 0.123394 1.485493 1.125878 1.093493 1.119224 1.192702] . ( 8 sec) [ -3734.3664] [Nucleotide equlibrium freqs.][ACGT: 0.391881 0.205492 0.258016 0.144611] . ( 8 sec) [ -3734.3657] [Branch lengths ] . ( 8 sec) [ -3734.2673] [Selective constraints on amino acids ][0.792741 * aa_fitness(a,b) + -1.755543 * (1-delta(a,b))] . ( 9 sec) [ -3734.2643] [GTR parameters ][rr_val: 0.120372 1.491809 1.134791 1.105023 1.116572 1.185845] . ( 10 sec) [ -3734.2618] [Nucleotide equlibrium freqs.][ACGT: 0.392209 0.202761 0.259397 0.145634] . ( 10 sec) [ -3734.2617] [Branch lengths ] . ( 10 sec) [ -3734.2071] [Selective constraints on amino acids ][0.770234 * aa_fitness(a,b) + -1.782585 * (1-delta(a,b))] . ( 11 sec) [ -3734.2053] [GTR parameters ][rr_val: 0.118664 1.497351 1.140632 1.116337 1.116731 1.176611] . ( 11 sec) [ -3734.2042] [Nucleotide equlibrium freqs.][ACGT: 0.392452 0.200911 0.260241 0.146397] . ( 11 sec) [ -3734.2042] [Branch lengths ] . ( 12 sec) [ -3734.1735] [Selective constraints on amino acids ][0.753334 * aa_fitness(a,b) + -1.802635 * (1-delta(a,b))] . ( 12 sec) [ -3734.1725] [GTR parameters ][rr_val: 0.117545 1.501099 1.145013 1.124527 1.117639 1.169463] . ( 13 sec) [ -3734.1719] [Nucleotide equlibrium freqs.][ACGT: 0.392087 0.199690 0.261248 0.146975] . ( 13 sec) [ -3734.1719] [Branch lengths ] . ( 13 sec) [ -3734.1547] [Selective constraints on amino acids ][0.740589 * aa_fitness(a,b) + -1.817469 * (1-delta(a,b))] . ( 14 sec) [ -3734.1541] [GTR parameters ][rr_val: 0.116765 1.503833 1.148050 1.131277 1.118553 1.163354] . ( 14 sec) [ -3734.1538] [Nucleotide equlibrium freqs.][ACGT: 0.392148 0.198754 0.261715 0.147383] . ( 15 sec) [ -3734.1538] [Branch lengths ] . ( 15 sec) [ -3734.1442] [Selective constraints on amino acids ][0.730961 * aa_fitness(a,b) + -1.828357 * (1-delta(a,b))] . ( 15 sec) [ -3734.1439] [GTR parameters ][rr_val: 0.116170 1.505781 1.150529 1.135783 1.119243 1.159308] . ( 16 sec) [ -3734.1437] [Nucleotide equlibrium freqs.][ACGT: 0.392103 0.198026 0.262181 0.147691] . ( 16 sec) [ -3734.1437] [Branch lengths ] . ( 16 sec) [ -3734.1383] [Selective constraints on amino acids ][0.723692 * aa_fitness(a,b) + -1.836244 * (1-delta(a,b))] . ( 17 sec) [ -3734.1382] [GTR parameters ][rr_val: 0.115712 1.507301 1.152469 1.140215 1.120512 1.156864] . ( 18 sec) [ -3734.1381] [Nucleotide equlibrium freqs.][ACGT: 0.392008 0.197512 0.262520 0.147961] . ( 18 sec) [ -3734.1380] [Branch lengths ] . ( 18 sec) [ -3734.1351] [Selective constraints on amino acids ][0.718172 * aa_fitness(a,b) + -1.841894 * (1-delta(a,b))] . ( 19 sec) [ -3734.1350] [GTR parameters ][rr_val: 0.115367 1.507668 1.153437 1.140034 1.119735 1.155254] . ( 19 sec) [ -3734.1349] [Nucleotide equlibrium freqs.][ACGT: 0.391952 0.197056 0.262886 0.148106] . ( 19 sec) [ -3734.1349] [Branch lengths ] . ( 20 sec) [ -3734.1334] [Selective constraints on amino acids ][0.714141 * aa_fitness(a,b) + -1.845628 * (1-delta(a,b))] . ( 20 sec) [ -3734.1333] [GTR parameters ][rr_val: 0.115080 1.509872 1.154901 1.145707 1.120505 1.150606] . ( 20 sec) [ -3734.1333] [Nucleotide equlibrium freqs.][ACGT: 0.391879 0.196854 0.262933 0.148334] . ( 21 sec) [ -3734.1332] [Branch lengths ] . ( 21 sec) [ -3734.1323] [Selective constraints on amino acids ][0.710876 * aa_fitness(a,b) + -1.849004 * (1-delta(a,b))] . ( 21 sec) [ -3734.1323] [GTR parameters ][rr_val: 0.115080 1.509837 1.155562 1.145763 1.120407 1.150349] . ( 22 sec) [ -3734.1323] [Nucleotide equlibrium freqs.][ACGT: 0.391858 0.196614 0.263099 0.148429] . ( 22 sec) [ -3734.1320] [Selective constraints on amino acids ][0.708866 * aa_fitness(a,b) + -1.849004 * (1-delta(a,b))] . ( 22 sec) [ -3734.1320] [GTR parameters ][rr_val: 0.114287 1.510125 1.155191 1.145906 1.120576 1.150249] . ( 23 sec) [ -3734.1319] [Nucleotide equlibrium freqs.][ACGT: 0.391930 0.196308 0.263278 0.148484] . Log likelihood of the current tree: -3734.131925. . 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 0h0m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo