. 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 WAG-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): 0.032331 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : -9.000000 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 1.280529 1.697218 1.315096 0.791060 1.043250 1.228929 transversion m_[tc][ag] 1.280529 transition/transversion m_tc|ag / m_[tc][ag] 1.697218 T <-> C / transition m_tc / m_tc|ag 0.684904 A <-> G / transition m_ag / m_tc|ag 1.315096 T <-> C / transversion m_tc / m_[tc][ag] 1.162431 A <-> G / transversion m_ag / m_[tc][ag] 2.232005 T <-> A / transversion m_ta / m_[tc][ag] 0.791060 T <-> G / transversion m_tg / m_[tc][ag] 1.043250 C <-> A / transversion m_ca / m_[tc][ag] 1.228929 C <-> G / transversion m_cg / m_[tc][ag] 0.936761 . Nucleotides equilibrium frequencies: optimize? 3 : ACGT : 0.151318 0.303167 0.330124 0.215392 - f(A) = 0.151318 - f(C) = 0.303167 - f(G) = 0.330124 - f(T) = 0.215392 . 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 7 Mo of memory space. . ( 0 sec) [ -6824.4953] [Branch lengths ] . ( 0 sec) [ -6811.9406] [Selective constraints on amino acids ][1.382830 * aa_fitness(a,b) + -1.795176 * (1-delta(a,b))] . ( 1 sec) [ -6772.5521] [GTR parameters ][rr_val: 0.054131 2.291978 1.315096 0.791060 1.043250 1.228929] . ( 2 sec) [ -6735.1884] [Nucleotide equlibrium freqs.][ACGT: 0.294968 0.268587 0.236831 0.199614] . ( 3 sec) [ -6733.0917] [Branch lengths ] . ( 3 sec) [ -6711.4859] [Selective constraints on amino acids ][0.715889 * aa_fitness(a,b) + -1.791876 * (1-delta(a,b))] . ( 3 sec) [ -6705.1386] [GTR parameters ][rr_val: 0.008341 3.376388 1.315096 0.791060 1.043250 1.228929] . ( 5 sec) [ -6704.2698] [Nucleotide equlibrium freqs.][ACGT: 0.318264 0.247209 0.229111 0.205416] . ( 5 sec) [ -6703.9047] [Branch lengths ] . ( 5 sec) [ -6703.3389] [Selective constraints on amino acids ][0.630777 * aa_fitness(a,b) + -1.733171 * (1-delta(a,b))] . ( 6 sec) [ -6703.2536] [GTR parameters ][rr_val: 0.004940 3.518256 1.315096 0.791060 1.043250 1.228929] . ( 7 sec) [ -6703.2435] [Nucleotide equlibrium freqs.][ACGT: 0.319362 0.245694 0.227389 0.207554] . ( 7 sec) [ -6703.2047] [Branch lengths ] . ( 7 sec) [ -6703.1166] [Selective constraints on amino acids ][0.649366 * aa_fitness(a,b) + -1.685270 * (1-delta(a,b))] . ( 8 sec) [ -6703.1165] [GTR parameters ][rr_val: 0.004796 3.523439 1.315096 0.791060 1.043250 1.228929] . ( 8 sec) [ -6703.1161] [Nucleotide equlibrium freqs.][ACGT: 0.319227 0.245956 0.226956 0.207861] . ( 8 sec) [ -6703.1150] [Branch lengths ] . ( 9 sec) [ -6703.0412] [Selective constraints on amino acids ][0.674199 * aa_fitness(a,b) + -1.652022 * (1-delta(a,b))] . ( 9 sec) [ -6703.0412] [GTR parameters ][rr_val: 0.004933 3.523439 1.315096 0.791060 1.043250 1.228929] . ( 9 sec) [ -6703.0411] [Nucleotide equlibrium freqs.][ACGT: 0.319210 0.246123 0.226732 0.207935] . ( 10 sec) [ -6703.0411] [Branch lengths ] . ( 10 sec) [ -6703.0031] [Selective constraints on amino acids ][0.692570 * aa_fitness(a,b) + -1.629060 * (1-delta(a,b))] . ( 10 sec) [ -6703.0030] [GTR parameters ][rr_val: 0.005065 3.530428 1.315096 0.791060 1.043250 1.228929] . ( 11 sec) [ -6703.0029] [Nucleotide equlibrium freqs.][ACGT: 0.319375 0.246144 0.226544 0.207936] . ( 11 sec) [ -6703.0029] [Branch lengths ] . ( 12 sec) [ -6702.9846] [Selective constraints on amino acids ][0.705355 * aa_fitness(a,b) + -1.613111 * (1-delta(a,b))] . ( 12 sec) [ -6702.9845] [GTR parameters ][rr_val: 0.005153 3.530428 1.315096 0.791060 1.043250 1.228929] . ( 12 sec) [ -6702.9845] [Nucleotide equlibrium freqs.][ACGT: 0.319360 0.246234 0.226450 0.207956] . ( 13 sec) [ -6702.9845] [Branch lengths ] . ( 13 sec) [ -6702.9757] [Selective constraints on amino acids ][0.714304 * aa_fitness(a,b) + -1.602165 * (1-delta(a,b))] . ( 13 sec) [ -6702.9756] [GTR parameters ][rr_val: 0.005220 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 14 sec) [ -6702.9756] [Nucleotide equlibrium freqs.][ACGT: 0.319430 0.246243 0.226386 0.207941] . ( 14 sec) [ -6702.9756] [Branch lengths ] . ( 15 sec) [ -6702.9714] [Selective constraints on amino acids ][0.720422 * aa_fitness(a,b) + -1.594535 * (1-delta(a,b))] . ( 15 sec) [ -6702.9714] [GTR parameters ][rr_val: 0.005220 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 15 sec) [ -6702.9714] [Nucleotide equlibrium freqs.][ACGT: 0.319438 0.246282 0.226317 0.207963] . ( 16 sec) [ -6702.9714] [Branch lengths ] . ( 16 sec) [ -6702.9694] [Selective constraints on amino acids ][0.724644 * aa_fitness(a,b) + -1.589288 * (1-delta(a,b))] . ( 16 sec) [ -6702.9694] [GTR parameters ][rr_val: 0.005286 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 17 sec) [ -6702.9694] [Nucleotide equlibrium freqs.][ACGT: 0.319449 0.246301 0.226283 0.207967] . ( 17 sec) [ -6702.9694] [Branch lengths ] . ( 17 sec) [ -6702.9684] [Selective constraints on amino acids ][0.727648 * aa_fitness(a,b) + -1.585699 * (1-delta(a,b))] . ( 18 sec) [ -6702.9684] [GTR parameters ][rr_val: 0.005286 3.536256 1.315096 0.791060 1.043250 1.228929] . ( 18 sec) [ -6702.9684] [Nucleotide equlibrium freqs.][ACGT: 0.319456 0.246318 0.226258 0.207968] . ( 18 sec) [ -6702.9684] [Branch lengths ] . ( 19 sec) [ -6702.9679] [Selective constraints on amino acids ][0.729655 * aa_fitness(a,b) + -1.582586 * (1-delta(a,b))] . ( 19 sec) [ -6702.9679] [GTR parameters ][rr_val: 0.005286 3.540820 1.315096 0.791060 1.043250 1.228929] . ( 19 sec) [ -6702.9679] [Nucleotide equlibrium freqs.][ACGT: 0.319544 0.246272 0.226199 0.207984] . ( 20 sec) [ -6702.9677] [Selective constraints on amino acids ][0.731294 * aa_fitness(a,b) + -1.579473 * (1-delta(a,b))] . ( 20 sec) [ -6702.9677] [GTR parameters ][rr_val: 0.005286 3.540820 1.315096 0.791060 1.043250 1.228929] . ( 20 sec) [ -6702.9677] [Nucleotide equlibrium freqs.][ACGT: 0.319529 0.246292 0.226189 0.207989] . Log likelihood of the current tree: -6702.967674. 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 WAG-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -6702.96767 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.49776 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.731294 * aa_fitness(a,b) + -1.579473 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.044623 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : -9.000000 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.005286 3.540820 1.315096 0.791060 1.043250 1.228929 transversion m_[tc][ag] 0.005286 transition/transversion m_tc|ag / m_[tc][ag] 3.540820 T <-> C / transition m_tc / m_tc|ag 0.684904 A <-> G / transition m_ag / m_tc|ag 1.315096 T <-> C / transversion m_tc / m_[tc][ag] 2.425122 A <-> G / transversion m_ag / m_[tc][ag] 4.656518 T <-> A / transversion m_ta / m_[tc][ag] 0.791060 T <-> G / transversion m_tg / m_[tc][ag] 1.043250 C <-> A / transversion m_ca / m_[tc][ag] 1.228929 C <-> G / transversion m_cg / m_[tc][ag] 0.936761 . Nucleotides equilibrium frequencies: optimize? 3 : ACGT : 0.319529 0.246292 0.226189 0.207989 - f(A) = 0.319529 - f(C) = 0.246292 - f(G) = 0.226189 - f(T) = 0.207989 . 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 0h0m20s . 20 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'...