. 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? 6 : 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? 3 : 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 . 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. . ( 1 sec) [ -6748.5630] [Branch lengths ] . ( 1 sec) [ -6747.1774] [Selective constraints on amino acids ][1.125735 * aa_fitness(a,b) + -1.602781 * (1-delta(a,b))] . ( 2 sec) [ -6708.1338] [GTR parameters ][rr_val: 0.026973 2.533534 0.880761 0.978600 1.004715 1.225774] . ( 3 sec) [ -6697.0340] [Nucleotide equlibrium freqs.][ACGT: 0.309205 0.254483 0.235819 0.200493] . ( 4 sec) [ -6696.3865] [Branch lengths ] . ( 4 sec) [ -6687.2523] [Selective constraints on amino acids ][0.723918 * aa_fitness(a,b) + -1.534058 * (1-delta(a,b))] . ( 5 sec) [ -6685.6955] [GTR parameters ][rr_val: 0.004351 2.944016 0.868682 1.002344 1.062446 1.186469] . ( 7 sec) [ -6685.5260] [Nucleotide equlibrium freqs.][ACGT: 0.318233 0.245132 0.232075 0.204560] . ( 7 sec) [ -6685.2117] [Branch lengths ] . ( 8 sec) [ -6685.0784] [Selective constraints on amino acids ][0.702699 * aa_fitness(a,b) + -1.473327 * (1-delta(a,b))] . ( 9 sec) [ -6685.0583] [GTR parameters ][rr_val: 0.002910 2.993700 0.862571 0.996983 1.063609 1.189627] . ( 10 sec) [ -6685.0559] [Nucleotide equlibrium freqs.][ACGT: 0.318023 0.244851 0.231307 0.205819] . ( 10 sec) [ -6685.0451] [Branch lengths ] . ( 11 sec) [ -6684.9324] [Selective constraints on amino acids ][0.729837 * aa_fitness(a,b) + -1.426083 * (1-delta(a,b))] . ( 12 sec) [ -6684.9321] [GTR parameters ][rr_val: 0.002910 2.986517 0.860687 0.995083 1.062539 1.193572] . ( 12 sec) [ -6684.9319] [Nucleotide equlibrium freqs.][ACGT: 0.317919 0.245101 0.231064 0.205916] . ( 13 sec) [ -6684.9317] [Branch lengths ] . ( 13 sec) [ -6684.8494] [Selective constraints on amino acids ][0.756437 * aa_fitness(a,b) + -1.390831 * (1-delta(a,b))] . ( 14 sec) [ -6684.8490] [GTR parameters ][rr_val: 0.003104 2.985072 0.859512 0.992876 1.062558 1.195541] . ( 14 sec) [ -6684.8490] [Nucleotide equlibrium freqs.][ACGT: 0.317936 0.245274 0.230892 0.205899] . ( 15 sec) [ -6684.8490] [Branch lengths ] . ( 15 sec) [ -6684.8021] [Selective constraints on amino acids ][0.776889 * aa_fitness(a,b) + -1.365171 * (1-delta(a,b))] . ( 16 sec) [ -6684.8018] [GTR parameters ][rr_val: 0.003266 2.982173 0.858486 0.991351 1.061741 1.197904] . ( 16 sec) [ -6684.8018] [Nucleotide equlibrium freqs.][ACGT: 0.317980 0.245402 0.230763 0.205855] . ( 17 sec) [ -6684.8018] [Branch lengths ] . ( 17 sec) [ -6684.7762] [Selective constraints on amino acids ][0.791984 * aa_fitness(a,b) + -1.346152 * (1-delta(a,b))] . ( 17 sec) [ -6684.7762] [GTR parameters ][rr_val: 0.003381 2.982096 0.857704 0.991223 1.061666 1.198002] . ( 18 sec) [ -6684.7761] [Nucleotide equlibrium freqs.][ACGT: 0.318037 0.245489 0.230654 0.205820] . ( 18 sec) [ -6684.7761] [Branch lengths ] . ( 18 sec) [ -6684.7623] [Selective constraints on amino acids ][0.803075 * aa_fitness(a,b) + -1.332120 * (1-delta(a,b))] . ( 20 sec) [ -6684.7621] [GTR parameters ][rr_val: 0.003462 2.978781 0.857130 0.989319 1.060660 1.201041] . ( 20 sec) [ -6684.7620] [Nucleotide equlibrium freqs.][ACGT: 0.318066 0.245544 0.230591 0.205799] . ( 20 sec) [ -6684.7620] [Branch lengths ] . ( 20 sec) [ -6684.7542] [Selective constraints on amino acids ][0.811451 * aa_fitness(a,b) + -1.321683 * (1-delta(a,b))] . ( 21 sec) [ -6684.7542] [GTR parameters ][rr_val: 0.003526 2.978739 0.856662 0.989237 1.060609 1.201068] . ( 21 sec) [ -6684.7542] [Nucleotide equlibrium freqs.][ACGT: 0.318097 0.245591 0.230531 0.205781] . ( 22 sec) [ -6684.7542] [Branch lengths ] . ( 22 sec) [ -6684.7500] [Selective constraints on amino acids ][0.817557 * aa_fitness(a,b) + -1.313989 * (1-delta(a,b))] . ( 22 sec) [ -6684.7500] [GTR parameters ][rr_val: 0.003526 2.978678 0.856287 0.989137 1.060552 1.201146] . ( 23 sec) [ -6684.7500] [Nucleotide equlibrium freqs.][ACGT: 0.318126 0.245623 0.230484 0.205766] . ( 23 sec) [ -6684.7500] [Branch lengths ] . ( 23 sec) [ -6684.7477] [Selective constraints on amino acids ][0.821992 * aa_fitness(a,b) + -1.308307 * (1-delta(a,b))] . ( 24 sec) [ -6684.7477] [GTR parameters ][rr_val: 0.003596 2.978604 0.855976 0.989022 1.060491 1.201262] . ( 24 sec) [ -6684.7477] [Nucleotide equlibrium freqs.][ACGT: 0.318147 0.245641 0.230454 0.205758] . ( 25 sec) [ -6684.7477] [Branch lengths ] . ( 25 sec) [ -6684.7465] [Selective constraints on amino acids ][0.825366 * aa_fitness(a,b) + -1.304109 * (1-delta(a,b))] . ( 26 sec) [ -6684.7463] [GTR parameters ][rr_val: 0.003596 2.976035 0.855942 0.987552 1.059727 1.203742] . ( 26 sec) [ -6684.7463] [Nucleotide equlibrium freqs.][ACGT: 0.318146 0.245659 0.230440 0.205754] . ( 26 sec) [ -6684.7463] [Branch lengths ] . ( 27 sec) [ -6684.7456] [Selective constraints on amino acids ][0.827949 * aa_fitness(a,b) + -1.300963 * (1-delta(a,b))] . ( 28 sec) [ -6684.7456] [GTR parameters ][rr_val: 0.003643 2.976035 0.855942 0.987552 1.059727 1.203742] . ( 28 sec) [ -6684.7456] [Nucleotide equlibrium freqs.][ACGT: 0.318151 0.245676 0.230423 0.205750] . ( 28 sec) [ -6684.7452] [Selective constraints on amino acids ][0.829846 * aa_fitness(a,b) + -1.297927 * (1-delta(a,b))] . ( 29 sec) [ -6684.7452] [GTR parameters ][rr_val: 0.003643 2.976026 0.855796 0.987526 1.059711 1.203739] . ( 29 sec) [ -6684.7452] [Nucleotide equlibrium freqs.][ACGT: 0.318159 0.245685 0.230404 0.205751] . Log likelihood of the current tree: -6684.745191. 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: -6684.74519 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.46728 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.829846 * aa_fitness(a,b) + -1.297927 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.048181 . Scale parameter of Gamma distribution for rate variation over sites: optimize? 0 : -9.000000 . Nulceotide exchangeabilities: optimize? 1 : how_many? 6 : rr_val[i] : 0.003643 2.976026 0.855796 0.987526 1.059711 1.203739 transversion m_[tc][ag] 0.003643 transition/transversion m_tc|ag / m_[tc][ag] 2.976026 T <-> C / transition m_tc / m_tc|ag 1.144204 A <-> G / transition m_ag / m_tc|ag 0.855796 T <-> C / transversion m_tc / m_[tc][ag] 3.405181 A <-> G / transversion m_ag / m_[tc][ag] 2.546871 T <-> A / transversion m_ta / m_[tc][ag] 0.987526 T <-> G / transversion m_tg / m_[tc][ag] 1.059711 C <-> A / transversion m_ca / m_[tc][ag] 1.203739 C <-> G / transversion m_cg / m_[tc][ag] 0.749024 . Nucleotides equilibrium frequencies: optimize? 3 : ACGT : 0.318159 0.245685 0.230404 0.205751 - f(A) = 0.318159 - f(C) = 0.245685 - f(G) = 0.230404 - f(T) = 0.205751 . 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 0h0m29s . 29 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'...