grep: unrecognized option `--mechanistic_params 1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25' Usage: grep [OPTION]... PATTERN [FILE]... Try `grep --help' for more information. /usr/local/phylogeny/phyml/bin/phyml -i input_files/20110203_144144.txt -d codon -b 0 -f e --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11" -c 1 --mechanistic_opt 01000 -o lr --mechanistic_params "-9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" --mechanistic_params 1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25 . Sum=1.000003 . Scaling frequencies... .......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename: 20110203_144144.txt . 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 EI-11 . Proportion of invariable sites: 0.000000 . Number of substitution categs: 1 . Codon equilibrium frequencies : empirical . Optimise tree topology: no . Evaluted tree: file "BioNJ" . Optimise branch lengths: yes . Optimise substitution model parameters: no . Run ID: none . Random seed: 1296711704 . Subtree patterns aliasing: no . Version: 20100824-SM04.101103 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 80 patterns found (out of a total of 81 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... . ( 1 sec) [ -1508.5982] [Branch lengths ] . ( 1 sec) [ -1016.8395] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.833107] . ( 1 sec) [ -1010.7654] [Branch lengths ] . ( 1 sec) [ -1009.1840] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.560917] . ( 1 sec) [ -1008.4636] [Branch lengths ] . ( 1 sec) [ -1008.0106] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.414077] . ( 1 sec) [ -1007.7104] [Branch lengths ] . ( 1 sec) [ -1007.4642] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.306712] . ( 1 sec) [ -1007.2736] [Branch lengths ] . ( 1 sec) [ -1007.1011] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.217743] . ( 1 sec) [ -1006.9904] [Branch lengths ] . ( 1 sec) [ -1006.8823] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.145488] . ( 2 sec) [ -1006.8138] [Branch lengths ] . ( 2 sec) [ -1006.7500] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.090805] . ( 2 sec) [ -1006.7126] [Branch lengths ] . ( 2 sec) [ -1006.6761] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.050341] . ( 2 sec) [ -1006.6563] [Branch lengths ] . ( 2 sec) [ -1006.6352] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.017609] . ( 2 sec) [ -1006.6224] [Branch lengths ] . ( 2 sec) [ -1006.6108] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.993609] . ( 2 sec) [ -1006.6042] [Branch lengths ] . ( 2 sec) [ -1006.5980] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.976245] . ( 2 sec) [ -1006.5945] [Branch lengths ] . ( 2 sec) [ -1006.5912] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.963553] . ( 2 sec) [ -1006.5894] [Branch lengths ] . ( 2 sec) [ -1006.5876] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.954268] . ( 3 sec) [ -1006.5865] [Branch lengths ] . ( 3 sec) [ -1006.5851] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.946079] . ( 3 sec) [ -1006.5840] [Branch lengths ] . ( 3 sec) [ -1006.5827] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.938081] . ( 3 sec) [ -1006.5817] [Branch lengths ] . ( 3 sec) [ -1006.5805] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.930553] . ( 3 sec) [ -1006.5795] [Branch lengths ] . ( 3 sec) [ -1006.5783] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.922720] . ( 3 sec) [ -1006.5772] [Branch lengths ] . ( 3 sec) [ -1006.5761] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.915335] . ( 3 sec) [ -1006.5751] [Branch lengths ] . ( 3 sec) [ -1006.5739] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.907617] . ( 3 sec) [ -1006.5729] [Branch lengths ] . ( 3 sec) [ -1006.5718] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.900341] . ( 4 sec) [ -1006.5709] [Branch lengths ] . ( 4 sec) [ -1006.5697] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.892736] . ( 4 sec) [ -1006.5687] [Branch lengths ] . ( 4 sec) [ -1006.5677] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.885567] . ( 4 sec) [ -1006.5668] [Branch lengths ] . ( 4 sec) [ -1006.5656] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.878073] . ( 4 sec) [ -1006.5647] [Branch lengths ] . ( 4 sec) [ -1006.5637] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.871011] . ( 4 sec) [ -1006.5628] [Branch lengths ] . ( 4 sec) [ -1006.5617] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.863629] . ( 4 sec) [ -1006.5608] [Branch lengths ] . ( 4 sec) [ -1006.5598] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.856673] . ( 4 sec) [ -1006.5589] [Branch lengths ] . ( 4 sec) [ -1006.5578] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.849402] . ( 5 sec) [ -1006.5570] [Branch lengths ] . ( 5 sec) [ -1006.5560] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.842552] . ( 5 sec) [ -1006.5552] [Branch lengths ] . ( 5 sec) [ -1006.5541] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.835392] . ( 5 sec) [ -1006.5533] [Branch lengths ] . ( 5 sec) [ -1006.5523] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.828647] . ( 5 sec) [ -1006.5515] [Branch lengths ] . ( 5 sec) [ -1006.5505] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.821596] . ( 5 sec) [ -1006.5497] [Branch lengths ] . ( 5 sec) [ -1006.5488] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.814956] . ( 5 sec) [ -1006.5480] [Branch lengths ] . ( 5 sec) [ -1006.5470] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.808015] . ( 5 sec) [ -1006.5462] [Branch lengths ] . ( 5 sec) [ -1006.5454] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.801479] . ( 6 sec) [ -1006.5446] [Branch lengths ] . ( 6 sec) [ -1006.5437] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.794645] . ( 6 sec) [ -1006.5429] [Branch lengths ] . ( 6 sec) [ -1006.5421] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.788213] . ( 6 sec) [ -1006.5413] [Branch lengths ] . ( 6 sec) [ -1006.5403] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.781481] . ( 6 sec) [ -1006.5396] [Branch lengths ] . ( 6 sec) [ -1006.5388] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.775149] . ( 6 sec) [ -1006.5381] [Branch lengths ] . ( 6 sec) [ -1006.5372] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.768543] . ( 6 sec) [ -1006.5365] [Branch lengths ] . ( 6 sec) [ -1006.5357] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.762314] . ( 6 sec) [ -1006.5350] [Branch lengths ] . ( 7 sec) [ -1006.5341] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.755811] . ( 7 sec) [ -1006.5334] [Branch lengths ] . ( 7 sec) [ -1006.5327] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.749681] . ( 7 sec) [ -1006.5320] [Branch lengths ] . ( 7 sec) [ -1006.5312] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.743283] . ( 7 sec) [ -1006.5305] [Branch lengths ] . ( 7 sec) [ -1006.5298] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.737252] . ( 7 sec) [ -1006.5291] [Branch lengths ] . ( 7 sec) [ -1006.5283] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.730957] . ( 7 sec) [ -1006.5277] [Branch lengths ] . ( 7 sec) [ -1006.5270] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.725023] . ( 7 sec) [ -1006.5263] [Branch lengths ] . ( 7 sec) [ -1006.5256] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.718830] . ( 8 sec) [ -1006.5249] [Branch lengths ] . ( 8 sec) [ -1006.5243] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.712993] . ( 8 sec) [ -1006.5237] [Branch lengths ] . ( 8 sec) [ -1006.5229] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.706901] . ( 8 sec) [ -1006.5223] [Branch lengths ] . ( 8 sec) [ -1006.5216] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.701158] . ( 8 sec) [ -1006.5211] [Branch lengths ] . ( 8 sec) [ -1006.5203] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.695165] . ( 8 sec) [ -1006.5197] [Branch lengths ] . ( 8 sec) [ -1006.5191] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.689516] . ( 8 sec) [ -1006.5185] [Branch lengths ] . ( 8 sec) [ -1006.5178] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.683621] . ( 8 sec) [ -1006.5173] [Branch lengths ] . ( 8 sec) [ -1006.5166] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.678064] . ( 9 sec) [ -1006.5161] [Branch lengths ] . ( 9 sec) [ -1006.5154] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.672265] . ( 9 sec) [ -1006.5149] [Branch lengths ] . ( 9 sec) [ -1006.5143] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.666799] . ( 9 sec) [ -1006.5137] [Branch lengths ] . ( 9 sec) [ -1006.5131] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.661094] . ( 9 sec) [ -1006.5126] [Branch lengths ] . ( 9 sec) [ -1006.5120] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.655717] . ( 9 sec) [ -1006.5115] [Branch lengths ] . ( 9 sec) [ -1006.5108] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.650106] . ( 9 sec) [ -1006.5103] [Branch lengths ] . ( 9 sec) [ -1006.5098] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.644809] . ( 9 sec) [ -1006.5093] [Branch lengths ] . ( 9 sec) [ -1006.5087] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.639289] . ( 10 sec) [ -1006.5082] [Branch lengths ] . ( 10 sec) [ -1006.5076] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.634013] . ( 10 sec) [ -1006.5071] [Branch lengths ] . ( 10 sec) [ -1006.5065] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.628577] . ( 10 sec) [ -1006.5060] [Branch lengths ] . ( 10 sec) [ -1006.5055] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.623323] . ( 10 sec) [ -1006.5050] [Branch lengths ] . ( 10 sec) [ -1006.5045] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.617971] . ( 10 sec) [ -1006.5040] [Branch lengths ] . ( 10 sec) [ -1006.5035] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.612738] . ( 10 sec) [ -1006.5035] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.612738] . Log likelihood of the current tree: -1006.503489. . Printing the most likely tree in file '20110203_144144.txt_phyml_tree.txt'... . Time used 0h0m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo