. 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 . Nulceotide exchangeabilities: optimize? 1 : how_many? 6 : rr_val[i] : 0.000100 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000100 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? 3 : 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 0.010072 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) [ -6663.4173] [Branch lengths ] . ( 1 sec) [ -6659.2132] [Selective constraints on amino acids ][0.742027 * aa_fitness(a,b) + -1.495086 * (1-delta(a,b))] . ( 3 sec) [ -6621.6879] [GTR parameters ][rr_val: 0.077509 2.278421 0.964970 0.938863 1.284829 0.934072] . ( 4 sec) [ -6613.5811] [Nucleotide equlibrium freqs.][ACGT: 0.305240 0.256203 0.236512 0.202045] . ( 4 sec) [ -6613.4589] [Branch lengths ] . ( 4 sec) [ -6613.1067] [Selective constraints on amino acids ][0.674006 * aa_fitness(a,b) + -1.465612 * (1-delta(a,b))] . ( 6 sec) [ -6612.4508] [GTR parameters ][rr_val: 0.056531 2.536403 0.971416 0.953876 1.241501 0.962038] . ( 6 sec) [ -6612.4104] [Nucleotide equlibrium freqs.][ACGT: 0.309943 0.253073 0.235316 0.201667] . ( 7 sec) [ -6612.4092] [Branch lengths ] . ( 7 sec) [ -6612.3868] [Selective constraints on amino acids ][0.668219 * aa_fitness(a,b) + -1.440241 * (1-delta(a,b))] . ( 8 sec) [ -6612.3685] [GTR parameters ][rr_val: 0.052214 2.568021 0.970469 0.952756 1.240263 0.964107] . ( 9 sec) [ -6612.3677] [Nucleotide equlibrium freqs.][ACGT: 0.310620 0.252693 0.234962 0.201725] . ( 9 sec) [ -6612.3677] [Branch lengths ] . ( 10 sec) [ -6612.3491] [Selective constraints on amino acids ][0.678078 * aa_fitness(a,b) + -1.420946 * (1-delta(a,b))] . ( 11 sec) [ -6612.3488] [GTR parameters ][rr_val: 0.051708 2.573235 0.969869 0.952054 1.241298 0.964973] . ( 11 sec) [ -6612.3487] [Nucleotide equlibrium freqs.][ACGT: 0.310776 0.252692 0.234806 0.201726] . ( 12 sec) [ -6612.3487] [Branch lengths ] . ( 12 sec) [ -6612.3352] [Selective constraints on amino acids ][0.688187 * aa_fitness(a,b) + -1.406886 * (1-delta(a,b))] . ( 13 sec) [ -6612.3351] [GTR parameters ][rr_val: 0.051708 2.571923 0.969740 0.951977 1.240100 0.966284] . ( 13 sec) [ -6612.3351] [Nucleotide equlibrium freqs.][ACGT: 0.310783 0.252771 0.234728 0.201718] . ( 13 sec) [ -6612.3351] [Branch lengths ] . ( 14 sec) [ -6612.3273] [Selective constraints on amino acids ][0.696112 * aa_fitness(a,b) + -1.396812 * (1-delta(a,b))] . ( 15 sec) [ -6612.3273] [GTR parameters ][rr_val: 0.051784 2.571135 0.969487 0.951572 1.239980 0.966983] . ( 15 sec) [ -6612.3273] [Nucleotide equlibrium freqs.][ACGT: 0.310800 0.252825 0.234669 0.201706] . ( 15 sec) [ -6612.3273] [Branch lengths ] . ( 16 sec) [ -6612.3233] [Selective constraints on amino acids ][0.701815 * aa_fitness(a,b) + -1.389580 * (1-delta(a,b))] . ( 17 sec) [ -6612.3233] [GTR parameters ][rr_val: 0.051836 2.570644 0.969255 0.951496 1.240003 0.967359] . ( 17 sec) [ -6612.3233] [Nucleotide equlibrium freqs.][ACGT: 0.310815 0.252863 0.234623 0.201699] . ( 17 sec) [ -6612.3233] [Branch lengths ] . ( 18 sec) [ -6612.3212] [Selective constraints on amino acids ][0.705891 * aa_fitness(a,b) + -1.384382 * (1-delta(a,b))] . ( 19 sec) [ -6612.3212] [GTR parameters ][rr_val: 0.051888 2.570165 0.969059 0.951314 1.239971 0.967770] . ( 19 sec) [ -6612.3212] [Nucleotide equlibrium freqs.][ACGT: 0.310826 0.252890 0.234590 0.201694] . ( 19 sec) [ -6612.3212] [Branch lengths ] . ( 19 sec) [ -6612.3201] [Selective constraints on amino acids ][0.708837 * aa_fitness(a,b) + -1.380641 * (1-delta(a,b))] . ( 20 sec) [ -6612.3201] [GTR parameters ][rr_val: 0.051888 2.570163 0.969010 0.951302 1.239963 0.967765] . ( 20 sec) [ -6612.3200] [Nucleotide equlibrium freqs.][ACGT: 0.310839 0.252906 0.234565 0.201690] . ( 21 sec) [ -6612.3200] [Branch lengths ] . ( 21 sec) [ -6612.3195] [Selective constraints on amino acids ][0.710931 * aa_fitness(a,b) + -1.377729 * (1-delta(a,b))] . ( 22 sec) [ -6612.3195] [GTR parameters ][rr_val: 0.051888 2.569709 0.968832 0.951085 1.239898 0.968186] . ( 22 sec) [ -6612.3195] [Nucleotide equlibrium freqs.][ACGT: 0.310843 0.252920 0.234547 0.201689] . ( 23 sec) [ -6612.3192] [Selective constraints on amino acids ][0.712564 * aa_fitness(a,b) + -1.374818 * (1-delta(a,b))] . ( 23 sec) [ -6612.3192] [GTR parameters ][rr_val: 0.051888 2.569708 0.968777 0.951074 1.239891 0.968179] . ( 24 sec) [ -6612.3192] [Nucleotide equlibrium freqs.][ACGT: 0.310853 0.252930 0.234525 0.201692] . Log likelihood of the current tree: -6612.319156. 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: -6612.31916 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.35544 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.712564 * aa_fitness(a,b) + -1.374818 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.054553 . Nulceotide exchangeabilities: optimize? 1 : how_many? 6 : rr_val[i] : 0.051888 2.569708 0.968777 0.951074 1.239891 0.968179 transversion m_[tc][ag] 0.051888 transition/transversion m_tc|ag / m_[tc][ag] 2.569708 T <-> C / transition m_tc / m_tc|ag 1.031223 A <-> G / transition m_ag / m_tc|ag 0.968777 T <-> C / transversion m_tc / m_[tc][ag] 2.649941 A <-> G / transversion m_ag / m_[tc][ag] 2.489475 T <-> A / transversion m_ta / m_[tc][ag] 0.951074 T <-> G / transversion m_tg / m_[tc][ag] 1.239891 C <-> A / transversion m_ca / m_[tc][ag] 0.968179 C <-> G / transversion m_cg / m_[tc][ag] 0.840856 . Nucleotides equilibrium frequencies: optimize? 3 : ACGT : 0.310853 0.252930 0.234525 0.201692 - f(A) = 0.310853 - f(C) = 0.252930 - f(G) = 0.234525 - f(T) = 0.201692 . 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 0h0m24s . 24 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'...