. 78 patterns found (out of a total of 1112 sites). . 1049 sites without polymorphism (94.33%). . 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 : aa - The number of states: 64 . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of amino acids 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? 2 : 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 . Nucleotides frequencies for codon usage: ACGT : 0.250000 0.250000 0.250000 0.250000 . Codon frequencies: from_sequence? 1 : TTT F 0.011241 TCT S 0.023906 TAT Y 0.012095 TGT C 0.008813 TTC F 0.011241 TCC S 0.023906 TAC Y 0.012095 TGC C 0.008813 TTA L 0.013085 TCA S 0.023906 TAA * 0.000000 TGA * 0.000000 TTG L 0.013085 TCG S 0.023906 TAG * 0.000000 TGG W 0.008183 CTT L 0.013085 CCT P 0.018862 CAT H 0.014703 CGT R 0.007704 CTC L 0.013085 CCC P 0.018862 CAC H 0.014703 CGC R 0.007704 CTA L 0.013085 CCA P 0.018862 CAA Q 0.023022 CGA R 0.007704 CTG L 0.013085 CCG P 0.018862 CAG Q 0.023022 CGG R 0.007704 ATT I 0.011601 ACT T 0.020256 AAT N 0.026574 AGT S 0.023906 ATC I 0.011601 ACC T 0.020256 AAC N 0.026574 AGC S 0.023906 ATA I 0.011601 ACA T 0.020256 AAA K 0.026754 AGA R 0.007704 ATG M 0.025899 ACG T 0.020256 AAG K 0.026754 AGG R 0.007704 GTT V 0.013152 GCT A 0.014344 GAT D 0.028013 GGT G 0.012455 GTC V 0.013152 GCC A 0.014344 GAC D 0.028013 GGC G 0.012455 GTA V 0.013152 GCA A 0.014344 GAA E 0.022122 GGA G 0.012455 GTG V 0.013152 GCG A 0.014344 GAG E 0.022122 GGG G 0.012455 . This analysis requires at least 2 Mo of memory space. . ( 1 sec) [ -3749.3706] [Branch lengths ] . ( 1 sec) [ -3748.8304] [Selective constraints on amino acids ][0.931852 * aa_fitness(a,b) + -1.593850 * (1-delta(a,b))] . ( 1 sec) [ -3742.0228] [GTR parameters ][rr_val: 0.137717 1.648727 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -3736.9762] [Nucleotide equlibrium freqs.][ACGT: 0.384405 0.215022 0.259256 0.141316] . ( 3 sec) [ -3735.9526] [Branch lengths ] . ( 3 sec) [ -3735.6133] [Selective constraints on amino acids ][0.873231 * aa_fitness(a,b) + -1.659519 * (1-delta(a,b))] . ( 4 sec) [ -3735.5456] [GTR parameters ][rr_val: 0.125447 1.521873 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -3735.5381] [Nucleotide equlibrium freqs.][ACGT: 0.384704 0.210257 0.263516 0.141523] . ( 5 sec) [ -3735.5197] [Branch lengths ] . ( 5 sec) [ -3735.3642] [Selective constraints on amino acids ][0.834900 * aa_fitness(a,b) + -1.705719 * (1-delta(a,b))] . ( 5 sec) [ -3735.3637] [GTR parameters ][rr_val: 0.123444 1.529930 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -3735.3598] [Nucleotide equlibrium freqs.][ACGT: 0.384578 0.206814 0.265831 0.142777] . ( 6 sec) [ -3735.3593] [Branch lengths ] . ( 6 sec) [ -3735.2803] [Selective constraints on amino acids ][0.807704 * aa_fitness(a,b) + -1.738471 * (1-delta(a,b))] . ( 7 sec) [ -3735.2800] [GTR parameters ][rr_val: 0.121546 1.535290 1.000000 1.000000 1.000000 1.000000] . ( 7 sec) [ -3735.2782] [Nucleotide equlibrium freqs.][ACGT: 0.384267 0.204591 0.267495 0.143647] . ( 8 sec) [ -3735.2780] [Branch lengths ] . ( 8 sec) [ -3735.2378] [Selective constraints on amino acids ][0.788315 * aa_fitness(a,b) + -1.761605 * (1-delta(a,b))] . ( 8 sec) [ -3735.2376] [GTR parameters ][rr_val: 0.120080 1.539220 1.000000 1.000000 1.000000 1.000000] . ( 9 sec) [ -3735.2367] [Nucleotide equlibrium freqs.][ACGT: 0.383875 0.203028 0.268799 0.144298] . ( 9 sec) [ -3735.2367] [Branch lengths ] . ( 9 sec) [ -3735.2160] [Selective constraints on amino acids ][0.774356 * aa_fitness(a,b) + -1.777960 * (1-delta(a,b))] . ( 9 sec) [ -3735.2159] [GTR parameters ][rr_val: 0.119009 1.542118 1.000000 1.000000 1.000000 1.000000] . ( 10 sec) [ -3735.2155] [Nucleotide equlibrium freqs.][ACGT: 0.384084 0.201855 0.269335 0.144727] . ( 10 sec) [ -3735.2155] [Branch lengths ] . ( 10 sec) [ -3735.2049] [Selective constraints on amino acids ][0.764274 * aa_fitness(a,b) + -1.789405 * (1-delta(a,b))] . ( 11 sec) [ -3735.2049] [GTR parameters ][rr_val: 0.118184 1.544273 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -3735.2046] [Nucleotide equlibrium freqs.][ACGT: 0.384104 0.200992 0.269865 0.145038] . ( 11 sec) [ -3735.2046] [Branch lengths ] . ( 12 sec) [ -3735.1992] [Selective constraints on amino acids ][0.756948 * aa_fitness(a,b) + -1.797333 * (1-delta(a,b))] . ( 12 sec) [ -3735.1992] [GTR parameters ][rr_val: 0.117588 1.545850 1.000000 1.000000 1.000000 1.000000] . ( 12 sec) [ -3735.1991] [Nucleotide equlibrium freqs.][ACGT: 0.384029 0.200373 0.270321 0.145277] . ( 13 sec) [ -3735.1991] [Branch lengths ] . ( 13 sec) [ -3735.1964] [Selective constraints on amino acids ][0.751618 * aa_fitness(a,b) + -1.802716 * (1-delta(a,b))] . ( 13 sec) [ -3735.1963] [GTR parameters ][rr_val: 0.117161 1.545850 1.000000 1.000000 1.000000 1.000000] . ( 14 sec) [ -3735.1963] [Nucleotide equlibrium freqs.][ACGT: 0.383931 0.199938 0.270680 0.145451] . ( 14 sec) [ -3735.1963] [Branch lengths ] . ( 14 sec) [ -3735.1949] [Selective constraints on amino acids ][0.747740 * aa_fitness(a,b) + -1.806230 * (1-delta(a,b))] . ( 14 sec) [ -3735.1949] [GTR parameters ][rr_val: 0.116878 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 15 sec) [ -3735.1949] [Nucleotide equlibrium freqs.][ACGT: 0.383834 0.199631 0.270938 0.145597] . ( 15 sec) [ -3735.1948] [Branch lengths ] . ( 15 sec) [ -3735.1942] [Selective constraints on amino acids ][0.744905 * aa_fitness(a,b) + -1.809626 * (1-delta(a,b))] . ( 16 sec) [ -3735.1942] [GTR parameters ][rr_val: 0.117002 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 16 sec) [ -3735.1942] [Nucleotide equlibrium freqs.][ACGT: 0.383737 0.199525 0.271001 0.145737] . ( 16 sec) [ -3735.1940] [Selective constraints on amino acids ][0.743047 * aa_fitness(a,b) + -1.809626 * (1-delta(a,b))] . ( 16 sec) [ -3735.1939] [GTR parameters ][rr_val: 0.116200 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 17 sec) [ -3735.1939] [Nucleotide equlibrium freqs.][ACGT: 0.383822 0.199219 0.271180 0.145780] . Log likelihood of the current tree: -3735.193909. 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 : aa - The number of states: 64 . Data set: #1 . Tree topology: fixed . Optimise branch lengths : yes . Initial tree: BioNJ . Model of amino acids substitution: /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -3735.19391 . Unconstrained likelihood: -3479.25308 . Parsimony: 76 . Tree size: 0.52476 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.743047 * aa_fitness(a,b) + -1.809626 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.033478 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.116200 1.547835 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.116200 transition/transversion m_tc|ag / m_[tc][ag] 1.547835 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] 1.547835 A <-> G / transversion m_ag / m_[tc][ag] 1.547835 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 : 0.383822 0.199219 0.271180 0.145780 - f(A) = 0.383822 - f(C) = 0.199219 - f(G) = 0.271180 - f(T) = 0.145780 . Nucleotides frequencies for codon usage: ACGT : 0.250000 0.250000 0.250000 0.250000 . Codon frequencies: from_sequence? 1 : TTT F 0.011241 TCT S 0.023906 TAT Y 0.012095 TGT C 0.008813 TTC F 0.011241 TCC S 0.023906 TAC Y 0.012095 TGC C 0.008813 TTA L 0.013085 TCA S 0.023906 TAA * 0.000000 TGA * 0.000000 TTG L 0.013085 TCG S 0.023906 TAG * 0.000000 TGG W 0.008183 CTT L 0.013085 CCT P 0.018862 CAT H 0.014703 CGT R 0.007704 CTC L 0.013085 CCC P 0.018862 CAC H 0.014703 CGC R 0.007704 CTA L 0.013085 CCA P 0.018862 CAA Q 0.023022 CGA R 0.007704 CTG L 0.013085 CCG P 0.018862 CAG Q 0.023022 CGG R 0.007704 ATT I 0.011601 ACT T 0.020256 AAT N 0.026574 AGT S 0.023906 ATC I 0.011601 ACC T 0.020256 AAC N 0.026574 AGC S 0.023906 ATA I 0.011601 ACA T 0.020256 AAA K 0.026754 AGA R 0.007704 ATG M 0.025899 ACG T 0.020256 AAG K 0.026754 AGG R 0.007704 GTT V 0.013152 GCT A 0.014344 GAT D 0.028013 GGT G 0.012455 GTC V 0.013152 GCC A 0.014344 GAC D 0.028013 GGC G 0.012455 GTA V 0.013152 GCA A 0.014344 GAA E 0.022122 GGA G 0.012455 GTG V 0.013152 GCG A 0.014344 GAG E 0.022122 GGG G 0.012455 . Time used 0h0m17s . 17 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'...