. 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 : -9.000000 . 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. . ( 0 sec) [ -6681.2580] [Branch lengths ] . ( 0 sec) [ -6678.6712] [Selective constraints on amino acids ][1.168880 * aa_fitness(a,b) + -1.650910 * (1-delta(a,b))] . ( 0 sec) [ -6649.2557] [GTR parameters ][rr_val: 0.026297 2.507914 1.137439 0.728588 0.940053 1.188633] . ( 1 sec) [ -6647.6696] [Branch lengths ] . ( 1 sec) [ -6639.8575] [Selective constraints on amino acids ][0.787490 * aa_fitness(a,b) + -1.686613 * (1-delta(a,b))] . ( 1 sec) [ -6639.2358] [GTR parameters ][rr_val: 0.007644 2.739832 1.137439 0.728588 0.940053 1.188633] . ( 2 sec) [ -6639.0097] [Branch lengths ] . ( 2 sec) [ -6638.7657] [Selective constraints on amino acids ][0.725935 * aa_fitness(a,b) + -1.703271 * (1-delta(a,b))] . ( 3 sec) [ -6638.7608] [GTR parameters ][rr_val: 0.006153 2.743685 1.137439 0.728588 0.940053 1.188633] . ( 3 sec) [ -6638.7534] [Branch lengths ] . ( 3 sec) [ -6638.7379] [Selective constraints on amino acids ][0.712055 * aa_fitness(a,b) + -1.714169 * (1-delta(a,b))] . ( 3 sec) [ -6638.7377] [GTR parameters ][rr_val: 0.005843 2.740941 1.137439 0.728588 0.940053 1.188633] . ( 4 sec) [ -6638.7376] [Branch lengths ] . ( 4 sec) [ -6638.7332] [Selective constraints on amino acids ][0.705412 * aa_fitness(a,b) + -1.721650 * (1-delta(a,b))] . ( 4 sec) [ -6638.7332] [GTR parameters ][rr_val: 0.005753 2.740941 1.137439 0.728588 0.940053 1.188633] . ( 5 sec) [ -6638.7332] [Branch lengths ] . ( 5 sec) [ -6638.7312] [Selective constraints on amino acids ][0.701021 * aa_fitness(a,b) + -1.726949 * (1-delta(a,b))] . ( 5 sec) [ -6638.7312] [GTR parameters ][rr_val: 0.005703 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 6 sec) [ -6638.7312] [Branch lengths ] . ( 6 sec) [ -6638.7301] [Selective constraints on amino acids ][0.697803 * aa_fitness(a,b) + -1.730722 * (1-delta(a,b))] . ( 6 sec) [ -6638.7301] [GTR parameters ][rr_val: 0.005663 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 7 sec) [ -6638.7301] [Branch lengths ] . ( 7 sec) [ -6638.7297] [Selective constraints on amino acids ][0.695600 * aa_fitness(a,b) + -1.733956 * (1-delta(a,b))] . ( 7 sec) [ -6638.7297] [GTR parameters ][rr_val: 0.005652 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 8 sec) [ -6638.7294] [Selective constraints on amino acids ][0.693760 * aa_fitness(a,b) + -1.733956 * (1-delta(a,b))] . ( 8 sec) [ -6638.7294] [GTR parameters ][rr_val: 0.005581 2.744708 1.137439 0.728588 0.940053 1.188633] . Log likelihood of the current tree: -6638.729415. 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: -6638.72941 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.48929 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.693760 * aa_fitness(a,b) + -1.733956 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.039388 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : -9.000000 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.005581 2.744708 1.137439 0.728588 0.940053 1.188633 transversion m_[tc][ag] 0.005581 transition/transversion m_tc|ag / m_[tc][ag] 2.744708 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] 2.367478 A <-> G / transversion m_ag / m_[tc][ag] 3.121937 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 0h0m8s . 8 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'...