. 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_155844.phy . 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] + -0.000000 . Scale parameter of Gamma distribution: optimize? 0 : 0.000000 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 transition/transversion m_tc|ag / m_[tc][ag] 1.000000 T <-> C / transition m_tc / m_tc|ag 1.000000 A <-> G / transition m_ag / m_tc|ag 1.000000 T <-> C / transversion m_tc / m_[tc][ag] 1.000000 A <-> G / transversion m_ag / m_[tc][ag] 1.000000 T <-> A / transversion m_ta / m_[tc][ag] 1.000000 T <-> G / transversion m_tg / m_[tc][ag] 1.000000 C <-> A / transversion m_ca / m_[tc][ag] 1.000000 C <-> G / transversion m_cg / m_[tc][ag] 1.000000 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.250000 0.250000 0.250000 0.250000 - f(A) = 0.250000 - f(C) = 0.250000 - f(G) = 0.250000 - f(T) = 0.250000 . 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) [ -1023.3543] [Branch lengths ] . ( 1 sec) [ -1020.8254] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.546303] . ( 1 sec) [ -1016.7033] [Branch lengths ] . ( 1 sec) [ -1016.6561] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.478491] . ( 1 sec) [ -1016.6026] [Branch lengths ] . ( 1 sec) [ -1016.6014] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467479] . ( 1 sec) [ -1016.5996] [Branch lengths ] . ( 1 sec) [ -1016.5996] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.466590] . ( 1 sec) [ -1016.5994] [Branch lengths ] . ( 1 sec) [ -1016.5994] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467749] . ( 1 sec) [ -1016.5994] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467749] . Log likelihood of the current tree: -1016.599406. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Final values of parameters . Sequence filename: 20110203_155844.phy . 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: -1016.59941 . Unconstrained likelihood: -354.56409 . Parsimony: 208 . Tree size: 72.47804 . Discrete Selection: No . Selective constraints on amino acids: optimize? 0 1 : 1.000000 * aa_fitness[i,j] + -0.467749 . Scale parameter of Gamma distribution: optimize? 0 : 0.000000 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 transition/transversion m_tc|ag / m_[tc][ag] 1.000000 T <-> C / transition m_tc / m_tc|ag 1.000000 A <-> G / transition m_ag / m_tc|ag 1.000000 T <-> C / transversion m_tc / m_[tc][ag] 1.000000 A <-> G / transversion m_ag / m_[tc][ag] 1.000000 T <-> A / transversion m_ta / m_[tc][ag] 1.000000 T <-> G / transversion m_tg / m_[tc][ag] 1.000000 C <-> A / transversion m_ca / m_[tc][ag] 1.000000 C <-> G / transversion m_cg / m_[tc][ag] 1.000000 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.250000 0.250000 0.250000 0.250000 - f(A) = 0.250000 - f(C) = 0.250000 - f(G) = 0.250000 - f(T) = 0.250000 . 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 0h0m1s . 1 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_155844.phy_phyml_tree.txt'...