. 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-11_mtREV JTT-ML91+mod-0 . Number of taxa: 10 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 1.449950 * aa_fitness(a,b) + -1.500000 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.016440 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : 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 . 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 W 0.004092 TTG L 0.013085 TCG S 0.023906 TAG * 0.000000 TGG W 0.004092 CTT L 0.013085 CCT P 0.018862 CAT H 0.014703 CGT R 0.011556 CTC L 0.013085 CCC P 0.018862 CAC H 0.014703 CGC R 0.011556 CTA L 0.013085 CCA P 0.018862 CAA Q 0.023022 CGA R 0.011556 CTG L 0.013085 CCG P 0.018862 CAG Q 0.023022 CGG R 0.011556 ATT I 0.017401 ACT T 0.020256 AAT N 0.026574 AGT S 0.023906 ATC I 0.017401 ACC T 0.020256 AAC N 0.026574 AGC S 0.023906 ATA M 0.012950 ACA T 0.020256 AAA K 0.026754 AGA * 0.000000 ATG M 0.012950 ACG T 0.020256 AAG K 0.026754 AGG * 0.000000 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. . ( 0 sec) [ -3771.2043] [Branch lengths ] . ( 0 sec) [ -3765.7927] [Selective constraints on amino acids ][1.218590 * aa_fitness(a,b) + -1.751521 * (1-delta(a,b))] . ( 1 sec) [ -3763.7952] [GTR parameters ][rr_val: 0.000000 1.523186 1.061429 1.000000 1.000000 1.000000] . ( 1 sec) [ -3762.6606] [Branch lengths ] . ( 1 sec) [ -3759.9868] [Selective constraints on amino acids ][1.059518 * aa_fitness(a,b) + -1.920203 * (1-delta(a,b))] . ( 1 sec) [ -3759.9578] [GTR parameters ][rr_val: 0.000000 1.603088 1.059788 1.000000 1.000000 1.000000] . ( 2 sec) [ -3759.9403] [Branch lengths ] . ( 2 sec) [ -3758.7219] [Selective constraints on amino acids ][0.958340 * aa_fitness(a,b) + -2.037239 * (1-delta(a,b))] . ( 2 sec) [ -3758.7165] [GTR parameters ][rr_val: 0.000000 1.615168 1.075717 1.000000 1.000000 1.000000] . ( 2 sec) [ -3758.7163] [Branch lengths ] . ( 3 sec) [ -3758.0861] [Selective constraints on amino acids ][0.886895 * aa_fitness(a,b) + -2.122047 * (1-delta(a,b))] . ( 3 sec) [ -3758.0829] [GTR parameters ][rr_val: 0.000000 1.620618 1.088702 1.000000 1.000000 1.000000] . ( 3 sec) [ -3758.0827] [Branch lengths ] . ( 3 sec) [ -3757.7532] [Selective constraints on amino acids ][0.836008 * aa_fitness(a,b) + -2.183290 * (1-delta(a,b))] . ( 4 sec) [ -3757.7516] [GTR parameters ][rr_val: 0.000000 1.625032 1.097969 1.000000 1.000000 1.000000] . ( 4 sec) [ -3757.7513] [Branch lengths ] . ( 4 sec) [ -3757.5775] [Selective constraints on amino acids ][0.799484 * aa_fitness(a,b) + -2.227367 * (1-delta(a,b))] . ( 5 sec) [ -3757.5766] [GTR parameters ][rr_val: 0.000000 1.629131 1.104436 1.000000 1.000000 1.000000] . ( 5 sec) [ -3757.5764] [Branch lengths ] . ( 5 sec) [ -3757.4837] [Selective constraints on amino acids ][0.773027 * aa_fitness(a,b) + -2.259103 * (1-delta(a,b))] . ( 5 sec) [ -3757.4832] [GTR parameters ][rr_val: 0.000000 1.630389 1.109270 1.000000 1.000000 1.000000] . ( 6 sec) [ -3757.4830] [Branch lengths ] . ( 6 sec) [ -3757.4331] [Selective constraints on amino acids ][0.753714 * aa_fitness(a,b) + -2.285765 * (1-delta(a,b))] . ( 6 sec) [ -3757.4327] [GTR parameters ][rr_val: 0.000000 1.630839 1.113779 1.000000 1.000000 1.000000] . ( 6 sec) [ -3757.4327] [Branch lengths ] . ( 7 sec) [ -3757.4057] [Selective constraints on amino acids ][0.739567 * aa_fitness(a,b) + -2.305903 * (1-delta(a,b))] . ( 7 sec) [ -3757.4055] [GTR parameters ][rr_val: 0.000000 1.631621 1.116459 1.000000 1.000000 1.000000] . ( 7 sec) [ -3757.4055] [Branch lengths ] . ( 7 sec) [ -3757.3908] [Selective constraints on amino acids ][0.729173 * aa_fitness(a,b) + -2.321218 * (1-delta(a,b))] . ( 7 sec) [ -3757.3907] [GTR parameters ][rr_val: 0.000000 1.632842 1.118514 1.000000 1.000000 1.000000] . ( 8 sec) [ -3757.3907] [Branch lengths ] . ( 8 sec) [ -3757.3827] [Selective constraints on amino acids ][0.721510 * aa_fitness(a,b) + -2.332996 * (1-delta(a,b))] . ( 8 sec) [ -3757.3826] [GTR parameters ][rr_val: 0.000000 1.637815 1.119325 1.000000 1.000000 1.000000] . ( 8 sec) [ -3757.3825] [Branch lengths ] . ( 9 sec) [ -3757.3781] [Selective constraints on amino acids ][0.715835 * aa_fitness(a,b) + -2.342194 * (1-delta(a,b))] . ( 9 sec) [ -3757.3781] [GTR parameters ][rr_val: 0.000000 1.637636 1.120342 1.000000 1.000000 1.000000] . ( 9 sec) [ -3757.3780] [Branch lengths ] . ( 9 sec) [ -3757.3757] [Selective constraints on amino acids ][0.711646 * aa_fitness(a,b) + -2.349442 * (1-delta(a,b))] . ( 10 sec) [ -3757.3757] [GTR parameters ][rr_val: 0.000000 1.638043 1.120456 1.000000 1.000000 1.000000] . ( 10 sec) [ -3757.3756] [Branch lengths ] . ( 10 sec) [ -3757.3744] [Selective constraints on amino acids ][0.708571 * aa_fitness(a,b) + -2.355233 * (1-delta(a,b))] . ( 10 sec) [ -3757.3744] [GTR parameters ][rr_val: 0.000000 1.638672 1.121800 1.000000 1.000000 1.000000] . ( 11 sec) [ -3757.3743] [Branch lengths ] . ( 11 sec) [ -3757.3736] [Selective constraints on amino acids ][0.706264 * aa_fitness(a,b) + -2.360018 * (1-delta(a,b))] . ( 11 sec) [ -3757.3736] [GTR parameters ][rr_val: 0.000000 1.638691 1.121655 1.000000 1.000000 1.000000] . ( 11 sec) [ -3757.3731] [Selective constraints on amino acids ][0.703590 * aa_fitness(a,b) + -2.360018 * (1-delta(a,b))] . ( 12 sec) [ -3757.3730] [GTR parameters ][rr_val: 0.000000 1.644262 1.120886 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -3757.372956. 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-11_mtREV JTT-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -3757.37296 . Unconstrained likelihood: -3479.25308 . Parsimony: 76 . Tree size: 0.90059 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.703590 * aa_fitness(a,b) + -2.360018 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.020695 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.000000 1.644262 1.120886 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 transition/transversion m_tc|ag / m_[tc][ag] 1.644262 T <-> C / transition m_tc / m_tc|ag 0.879114 A <-> G / transition m_ag / m_tc|ag 1.120886 T <-> C / transversion m_tc / m_[tc][ag] 1.445494 A <-> G / transversion m_ag / m_[tc][ag] 1.843029 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 . 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 W 0.004092 TTG L 0.013085 TCG S 0.023906 TAG * 0.000000 TGG W 0.004092 CTT L 0.013085 CCT P 0.018862 CAT H 0.014703 CGT R 0.011556 CTC L 0.013085 CCC P 0.018862 CAC H 0.014703 CGC R 0.011556 CTA L 0.013085 CCA P 0.018862 CAA Q 0.023022 CGA R 0.011556 CTG L 0.013085 CCG P 0.018862 CAG Q 0.023022 CGG R 0.011556 ATT I 0.017401 ACT T 0.020256 AAT N 0.026574 AGT S 0.023906 ATC I 0.017401 ACC T 0.020256 AAC N 0.026574 AGC S 0.023906 ATA M 0.012950 ACA T 0.020256 AAA K 0.026754 AGA * 0.000000 ATG M 0.012950 ACG T 0.020256 AAG K 0.026754 AGG * 0.000000 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 0h0m12s . 12 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'...