. 318 patterns found (out of a total of 1112 sites). . 832 sites without polymorphism (74.82%). . Computing pairwise distances... . Building BioNJ tree... oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM10 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Initial values of parameters . Sequence filename: input.phy . Sequence format : interleaved . Data type : codon - The number of states: 64 . 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 JTT-ML91+mod-0 . Number of taxa: 10 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 1.000000 * aa_fitness(a,b) + -1.500000 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.030050 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : 0.738272 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.636937 1.570502 1.137439 0.728588 0.940053 1.188633 transversion m_[tc][ag] 0.636937 transition/transversion m_tc|ag / m_[tc][ag] 1.570502 T <-> C / transition m_tc / m_tc|ag 0.862561 A <-> G / transition m_ag / m_tc|ag 1.137439 T <-> C / transversion m_tc / m_[tc][ag] 1.354654 A <-> G / transversion m_ag / m_[tc][ag] 1.786350 T <-> A / transversion m_ta / m_[tc][ag] 0.728588 T <-> G / transversion m_tg / m_[tc][ag] 0.940053 C <-> A / transversion m_ca / m_[tc][ag] 1.188633 C <-> G / transversion m_cg / m_[tc][ag] 1.142727 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.228869 0.232315 0.309043 0.229772 - f(A) = 0.228869 - f(C) = 0.232315 - f(G) = 0.309043 - f(T) = 0.229772 . Codon frequencies: from_sequence? 1 : TTT F 0.010072 TCT S 0.028147 TAT Y 0.010701 TGT C 0.010432 TTC F 0.012410 TCC S 0.023741 TAC Y 0.013489 TGC C 0.007194 TTA L 0.014299 TCA S 0.024910 TAA * 0.000000 TGA * 0.000000 TTG L 0.010072 TCG S 0.008903 TAG * 0.000000 TGG W 0.008183 CTT L 0.011871 CCT P 0.023651 CAT H 0.014119 CGT R 0.003058 CTC L 0.012860 CCC P 0.025540 CAC H 0.015288 CGC R 0.006115 CTA L 0.005845 CCA P 0.019424 CAA Q 0.017176 CGA R 0.007914 CTG L 0.023561 CCG P 0.006835 CAG Q 0.028867 CGG R 0.006115 ATT I 0.007644 ACT T 0.028417 AAT N 0.029496 AGT S 0.023741 ATC I 0.016097 ACC T 0.027338 AAC N 0.023651 AGC S 0.033993 ATA I 0.011061 ACA T 0.018165 AAA K 0.027518 AGA R 0.014209 ATG M 0.025899 ACG T 0.007104 AAG K 0.025989 AGG R 0.008813 GTT V 0.014299 GCT A 0.019964 GAT D 0.020234 GGT G 0.004406 GTC V 0.008813 GCC A 0.017986 GAC D 0.035791 GGC G 0.016457 GTA V 0.009083 GCA A 0.014928 GAA E 0.023561 GGA G 0.017716 GTG V 0.020414 GCG A 0.004496 GAG E 0.020683 GGG G 0.011241 . This analysis requires at least 7 Mo of memory space. . ( 1 sec) [ -6668.3708] [Branch lengths ] . ( 1 sec) [ -6668.0797] [Selective constraints on amino acids ][1.009856 * aa_fitness(a,b) + -1.596913 * (1-delta(a,b))] . ( 1 sec) [ -6642.3126] [GTR parameters ][rr_val: 0.088147 2.340645 1.137439 0.728588 0.940053 1.188633] . ( 1 sec) [ -6642.1835] [Branch lengths ] . ( 2 sec) [ -6635.6696] [Selective constraints on amino acids ][0.680359 * aa_fitness(a,b) + -1.596913 * (1-delta(a,b))] . ( 2 sec) [ -6635.0061] [GTR parameters ][rr_val: 0.050922 2.468683 1.137439 0.728588 0.940053 1.188633] . ( 2 sec) [ -6635.0013] [Branch lengths ] . ( 3 sec) [ -6634.9424] [Selective constraints on amino acids ][0.651315 * aa_fitness(a,b) + -1.591193 * (1-delta(a,b))] . ( 3 sec) [ -6634.9356] [GTR parameters ][rr_val: 0.047854 2.483250 1.137439 0.728588 0.940053 1.188633] . ( 4 sec) [ -6634.9356] [Branch lengths ] . ( 4 sec) [ -6634.9350] [Selective constraints on amino acids ][0.651315 * aa_fitness(a,b) + -1.587295 * (1-delta(a,b))] . ( 4 sec) [ -6634.9350] [GTR parameters ][rr_val: 0.047593 2.483250 1.137439 0.728588 0.940053 1.188633] . ( 5 sec) [ -6634.9340] [Selective constraints on amino acids ][0.654031 * aa_fitness(a,b) + -1.583595 * (1-delta(a,b))] . ( 5 sec) [ -6634.9340] [GTR parameters ][rr_val: 0.047593 2.483250 1.137439 0.728588 0.940053 1.188633] . Log likelihood of the current tree: -6634.933978. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM10 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Final values of parameters . Sequence filename: input.phy . Sequence format : interleaved . Data type : codon - The number of states: 64 . 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 JTT-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -6634.93398 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.36614 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.654031 * aa_fitness(a,b) + -1.583595 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.049184 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : 0.738272 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.047593 2.483250 1.137439 0.728588 0.940053 1.188633 transversion m_[tc][ag] 0.047593 transition/transversion m_tc|ag / m_[tc][ag] 2.483250 T <-> C / transition m_tc / m_tc|ag 0.862561 A <-> G / transition m_ag / m_tc|ag 1.137439 T <-> C / transversion m_tc / m_[tc][ag] 2.141954 A <-> G / transversion m_ag / m_[tc][ag] 2.824545 T <-> A / transversion m_ta / m_[tc][ag] 0.728588 T <-> G / transversion m_tg / m_[tc][ag] 0.940053 C <-> A / transversion m_ca / m_[tc][ag] 1.188633 C <-> G / transversion m_cg / m_[tc][ag] 1.142727 . Nucleotides equilibrium frequencies: optimize? 0 : ACGT : 0.228869 0.232315 0.309043 0.229772 - f(A) = 0.228869 - f(C) = 0.232315 - f(G) = 0.309043 - f(T) = 0.229772 . Codon frequencies: from_sequence? 1 : TTT F 0.010072 TCT S 0.028147 TAT Y 0.010701 TGT C 0.010432 TTC F 0.012410 TCC S 0.023741 TAC Y 0.013489 TGC C 0.007194 TTA L 0.014299 TCA S 0.024910 TAA * 0.000000 TGA * 0.000000 TTG L 0.010072 TCG S 0.008903 TAG * 0.000000 TGG W 0.008183 CTT L 0.011871 CCT P 0.023651 CAT H 0.014119 CGT R 0.003058 CTC L 0.012860 CCC P 0.025540 CAC H 0.015288 CGC R 0.006115 CTA L 0.005845 CCA P 0.019424 CAA Q 0.017176 CGA R 0.007914 CTG L 0.023561 CCG P 0.006835 CAG Q 0.028867 CGG R 0.006115 ATT I 0.007644 ACT T 0.028417 AAT N 0.029496 AGT S 0.023741 ATC I 0.016097 ACC T 0.027338 AAC N 0.023651 AGC S 0.033993 ATA I 0.011061 ACA T 0.018165 AAA K 0.027518 AGA R 0.014209 ATG M 0.025899 ACG T 0.007104 AAG K 0.025989 AGG R 0.008813 GTT V 0.014299 GCT A 0.019964 GAT D 0.020234 GGT G 0.004406 GTC V 0.008813 GCC A 0.017986 GAC D 0.035791 GGC G 0.016457 GTA V 0.009083 GCA A 0.014928 GAA E 0.023561 GGA G 0.017716 GTG V 0.020414 GCG A 0.004496 GAG E 0.020683 GGG G 0.011241 . Time used 0h0m5s . 5 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 'input.phy_phyml_tree.txt'... . Printing the most likely tree in file 'input.phy_phyml_tree.txt'...