. 80 patterns found (out of a total of 81 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Initial values of parameters . Sequence filename: 20110203_144159.txt . Data type : codon . Sequence format : interleaved . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of codons substitution: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11 . Number of taxa: 4 . Discrete Selection: No . Selective constraints on amino acids: optimize? 0 1 : 1.000000 * aa_fitness[i,j] + -9.000000 . Scale parameter of Gamma distribution: optimize? 0 : 0.917608 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.307849 2.215535 1.010220 1.065729 1.085499 0.890831 transversion m_[tc][ag] 0.307849 transition/transversion m_tc|ag / m_[tc][ag] 2.215535 T <-> C / transition m_tc / m_tc|ag 0.989780 A <-> G / transition m_ag / m_tc|ag 1.010220 T <-> C / transversion m_tc / m_[tc][ag] 2.192892 A <-> G / transversion m_ag / m_[tc][ag] 2.238178 T <-> A / transversion m_ta / m_[tc][ag] 1.065729 T <-> G / transversion m_tg / m_[tc][ag] 1.085499 C <-> A / transversion m_ca / m_[tc][ag] 0.890831 C <-> G / transversion m_cg / m_[tc][ag] 0.957941 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.268305 0.195920 0.239202 0.296573 - f(A) = 0.268305 - f(C) = 0.195920 - f(G) = 0.239202 - f(T) = 0.296573 . Codon frequencies: from_sequence? 1 : TTT F 0.017102 TTC F 0.020188 TTA L 0.010929 TTG L 0.010929 TCT S 0.014015 TCC S 0.010929 TCA S 0.017102 TCG S 0.010929 TAT Y 0.023275 TAC Y 0.017102 TAA * 0.000000 TAG * 0.000000 TGT C 0.001670 TGC C 0.001670 TGA * 0.000000 TGG W 0.023275 CTT L 0.007843 CTC L 0.004756 CTA L 0.014015 CTG L 0.004756 CCT P 0.020188 CCC P 0.010929 CCA P 0.007843 CCG P 0.007843 CAT H 0.004756 CAC H 0.001670 CAA Q 0.014015 CAG Q 0.014015 CGT R 0.010929 CGC R 0.014015 CGA R 0.014015 CGG R 0.010929 ATT I 0.007843 ATC I 0.010929 ATA I 0.007843 ATG M 0.029447 ACT T 0.004756 ACC T 0.007843 ACA T 0.001670 ACG T 0.001670 AAT N 0.041793 AAC N 0.007843 AAA K 0.060312 AAG K 0.075744 AGT S 0.020188 AGC S 0.010929 AGA R 0.010929 AGG R 0.004756 GTT V 0.007843 GTC V 0.007843 GTA V 0.007843 GTG V 0.014015 GCT A 0.032534 GCC A 0.026361 GCA A 0.026361 GCG A 0.032534 GAT D 0.017102 GAC D 0.026361 GAA E 0.051052 GAG E 0.057225 GGT G 0.014015 GGC G 0.010929 GGA G 0.007843 GGG G 0.014015 . ( 0 sec) [ -1508.5982] [Branch lengths ] . ( 0 sec) [ -1016.8395] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.833107] . ( 0 sec) [ -1010.7654] [Branch lengths ] . ( 0 sec) [ -1009.1840] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.560917] . ( 0 sec) [ -1008.4636] [Branch lengths ] . ( 0 sec) [ -1008.0106] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.414077] . ( 0 sec) [ -1007.7104] [Branch lengths ] . ( 0 sec) [ -1007.4642] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.306712] . ( 0 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] . ( 1 sec) [ -1006.8138] [Branch lengths ] . ( 1 sec) [ -1006.7500] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.090805] . ( 1 sec) [ -1006.7126] [Branch lengths ] . ( 1 sec) [ -1006.6761] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.050341] . ( 1 sec) [ -1006.6563] [Branch lengths ] . ( 1 sec) [ -1006.6352] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -3.017609] . ( 1 sec) [ -1006.6224] [Branch lengths ] . ( 1 sec) [ -1006.6108] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.993609] . ( 1 sec) [ -1006.6042] [Branch lengths ] . ( 1 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] . ( 2 sec) [ -1006.5865] [Branch lengths ] . ( 2 sec) [ -1006.5851] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.946079] . ( 2 sec) [ -1006.5840] [Branch lengths ] . ( 2 sec) [ -1006.5827] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.938081] . ( 2 sec) [ -1006.5817] [Branch lengths ] . ( 2 sec) [ -1006.5805] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.930553] . ( 2 sec) [ -1006.5795] [Branch lengths ] . ( 2 sec) [ -1006.5783] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.922720] . ( 2 sec) [ -1006.5772] [Branch lengths ] . ( 2 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] . ( 3 sec) [ -1006.5709] [Branch lengths ] . ( 3 sec) [ -1006.5697] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.892736] . ( 3 sec) [ -1006.5687] [Branch lengths ] . ( 3 sec) [ -1006.5677] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.885567] . ( 3 sec) [ -1006.5668] [Branch lengths ] . ( 3 sec) [ -1006.5656] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.878073] . ( 3 sec) [ -1006.5647] [Branch lengths ] . ( 3 sec) [ -1006.5637] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.871011] . ( 3 sec) [ -1006.5628] [Branch lengths ] . ( 3 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] . ( 4 sec) [ -1006.5570] [Branch lengths ] . ( 4 sec) [ -1006.5560] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.842552] . ( 4 sec) [ -1006.5552] [Branch lengths ] . ( 4 sec) [ -1006.5541] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.835392] . ( 4 sec) [ -1006.5533] [Branch lengths ] . ( 4 sec) [ -1006.5523] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.828647] . ( 4 sec) [ -1006.5515] [Branch lengths ] . ( 4 sec) [ -1006.5505] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.821596] . ( 4 sec) [ -1006.5497] [Branch lengths ] . ( 4 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] . ( 5 sec) [ -1006.5446] [Branch lengths ] . ( 5 sec) [ -1006.5437] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.794645] . ( 5 sec) [ -1006.5429] [Branch lengths ] . ( 5 sec) [ -1006.5421] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.788213] . ( 5 sec) [ -1006.5413] [Branch lengths ] . ( 5 sec) [ -1006.5403] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.781481] . ( 5 sec) [ -1006.5396] [Branch lengths ] . ( 5 sec) [ -1006.5388] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.775149] . ( 5 sec) [ -1006.5381] [Branch lengths ] . ( 5 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 ] . ( 6 sec) [ -1006.5341] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.755811] . ( 6 sec) [ -1006.5334] [Branch lengths ] . ( 6 sec) [ -1006.5327] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.749681] . ( 6 sec) [ -1006.5320] [Branch lengths ] . ( 6 sec) [ -1006.5312] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.743283] . ( 6 sec) [ -1006.5305] [Branch lengths ] . ( 6 sec) [ -1006.5298] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.737252] . ( 6 sec) [ -1006.5291] [Branch lengths ] . ( 6 sec) [ -1006.5283] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.730957] . ( 6 sec) [ -1006.5277] [Branch lengths ] . ( 6 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] . ( 7 sec) [ -1006.5249] [Branch lengths ] . ( 7 sec) [ -1006.5243] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.712993] . ( 7 sec) [ -1006.5237] [Branch lengths ] . ( 7 sec) [ -1006.5229] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.706901] . ( 7 sec) [ -1006.5223] [Branch lengths ] . ( 7 sec) [ -1006.5216] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.701158] . ( 7 sec) [ -1006.5211] [Branch lengths ] . ( 7 sec) [ -1006.5203] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.695165] . ( 7 sec) [ -1006.5197] [Branch lengths ] . ( 7 sec) [ -1006.5191] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.689516] . ( 7 sec) [ -1006.5185] [Branch lengths ] . ( 7 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] . ( 8 sec) [ -1006.5161] [Branch lengths ] . ( 8 sec) [ -1006.5154] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.672265] . ( 8 sec) [ -1006.5149] [Branch lengths ] . ( 8 sec) [ -1006.5143] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.666799] . ( 8 sec) [ -1006.5137] [Branch lengths ] . ( 8 sec) [ -1006.5131] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.661094] . ( 8 sec) [ -1006.5126] [Branch lengths ] . ( 8 sec) [ -1006.5120] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.655717] . ( 8 sec) [ -1006.5115] [Branch lengths ] . ( 8 sec) [ -1006.5108] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.650106] . ( 8 sec) [ -1006.5103] [Branch lengths ] . ( 8 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] . ( 9 sec) [ -1006.5082] [Branch lengths ] . ( 9 sec) [ -1006.5076] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.634013] . ( 9 sec) [ -1006.5071] [Branch lengths ] . ( 9 sec) [ -1006.5065] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.628577] . ( 9 sec) [ -1006.5060] [Branch lengths ] . ( 9 sec) [ -1006.5055] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.623323] . ( 9 sec) [ -1006.5050] [Branch lengths ] . ( 9 sec) [ -1006.5045] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.617971] . ( 9 sec) [ -1006.5040] [Branch lengths ] . ( 9 sec) [ -1006.5035] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.612738] . ( 9 sec) [ -1006.5035] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -2.612738] . Log likelihood of the current tree: -1006.503489. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Final values of parameters . Sequence filename: 20110203_144159.txt . Data type : codon . Sequence format : interleaved . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of codons substitution: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11 . Number of taxa: 4 . Log-likelihood: -1006.50349 . Unconstrained likelihood: -354.56409 . Parsimony: 208 . Tree size: 165.83283 . Discrete Selection: No . Selective constraints on amino acids: optimize? 0 1 : 1.000000 * aa_fitness[i,j] + -2.612738 . Scale parameter of Gamma distribution: optimize? 0 : 0.917608 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.307849 2.215535 1.010220 1.065729 1.085499 0.890831 transversion m_[tc][ag] 0.307849 transition/transversion m_tc|ag / m_[tc][ag] 2.215535 T <-> C / transition m_tc / m_tc|ag 0.989780 A <-> G / transition m_ag / m_tc|ag 1.010220 T <-> C / transversion m_tc / m_[tc][ag] 2.192892 A <-> G / transversion m_ag / m_[tc][ag] 2.238178 T <-> A / transversion m_ta / m_[tc][ag] 1.065729 T <-> G / transversion m_tg / m_[tc][ag] 1.085499 C <-> A / transversion m_ca / m_[tc][ag] 0.890831 C <-> G / transversion m_cg / m_[tc][ag] 0.957941 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.268305 0.195920 0.239202 0.296573 - f(A) = 0.268305 - f(C) = 0.195920 - f(G) = 0.239202 - f(T) = 0.296573 . Codon frequencies: from_sequence? 1 : TTT F 0.017102 TTC F 0.020188 TTA L 0.010929 TTG L 0.010929 TCT S 0.014015 TCC S 0.010929 TCA S 0.017102 TCG S 0.010929 TAT Y 0.023275 TAC Y 0.017102 TAA * 0.000000 TAG * 0.000000 TGT C 0.001670 TGC C 0.001670 TGA * 0.000000 TGG W 0.023275 CTT L 0.007843 CTC L 0.004756 CTA L 0.014015 CTG L 0.004756 CCT P 0.020188 CCC P 0.010929 CCA P 0.007843 CCG P 0.007843 CAT H 0.004756 CAC H 0.001670 CAA Q 0.014015 CAG Q 0.014015 CGT R 0.010929 CGC R 0.014015 CGA R 0.014015 CGG R 0.010929 ATT I 0.007843 ATC I 0.010929 ATA I 0.007843 ATG M 0.029447 ACT T 0.004756 ACC T 0.007843 ACA T 0.001670 ACG T 0.001670 AAT N 0.041793 AAC N 0.007843 AAA K 0.060312 AAG K 0.075744 AGT S 0.020188 AGC S 0.010929 AGA R 0.010929 AGG R 0.004756 GTT V 0.007843 GTC V 0.007843 GTA V 0.007843 GTG V 0.014015 GCT A 0.032534 GCC A 0.026361 GCA A 0.026361 GCG A 0.032534 GAT D 0.017102 GAC D 0.026361 GAA E 0.051052 GAG E 0.057225 GGT G 0.014015 GGC G 0.010929 GGA G 0.007843 GGG G 0.014015 . Time used 0h0m9s . 9 seconds oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Suggested citation: S. Guindon & O. Gascuel "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood" Systematic Biology. 2003. 52(5):696-704. Modified for a codon model by Sanzo Miyazawa (sanzo.miyazawa@gmail.com) oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Printing the most likely tree in file '20110203_144159.txt_phyml_tree.txt'...