. 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 LG-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): 0.023919 . 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? 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 . 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. . ( 0 sec) [ -6695.1663] [Branch lengths ] . ( 0 sec) [ -6667.3155] [Selective constraints on amino acids ][0.500459 * aa_fitness(a,b) + -1.588632 * (1-delta(a,b))] . ( 1 sec) [ -6627.8834] [GTR parameters ][rr_val: 0.073087 1.998765 1.000000 1.000000 1.000000 1.000000] . ( 1 sec) [ -6627.7451] [Branch lengths ] . ( 2 sec) [ -6627.0700] [Selective constraints on amino acids ][0.433129 * aa_fitness(a,b) + -1.588632 * (1-delta(a,b))] . ( 2 sec) [ -6624.5533] [GTR parameters ][rr_val: 0.060850 2.548208 1.000000 1.000000 1.000000 1.000000] . ( 2 sec) [ -6624.5515] [Branch lengths ] . ( 2 sec) [ -6624.4588] [Selective constraints on amino acids ][0.412069 * aa_fitness(a,b) + -1.559889 * (1-delta(a,b))] . ( 3 sec) [ -6624.4153] [GTR parameters ][rr_val: 0.053329 2.578588 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -6624.4153] [Branch lengths ] . ( 4 sec) [ -6624.3933] [Selective constraints on amino acids ][0.418373 * aa_fitness(a,b) + -1.536844 * (1-delta(a,b))] . ( 4 sec) [ -6624.3927] [GTR parameters ][rr_val: 0.052715 2.585475 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -6624.3927] [Branch lengths ] . ( 4 sec) [ -6624.3731] [Selective constraints on amino acids ][0.426769 * aa_fitness(a,b) + -1.520046 * (1-delta(a,b))] . ( 5 sec) [ -6624.3731] [GTR parameters ][rr_val: 0.052770 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 5 sec) [ -6624.3731] [Branch lengths ] . ( 5 sec) [ -6624.3619] [Selective constraints on amino acids ][0.433172 * aa_fitness(a,b) + -1.507546 * (1-delta(a,b))] . ( 6 sec) [ -6624.3619] [GTR parameters ][rr_val: 0.052823 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -6624.3619] [Branch lengths ] . ( 6 sec) [ -6624.3557] [Selective constraints on amino acids ][0.438042 * aa_fitness(a,b) + -1.498433 * (1-delta(a,b))] . ( 7 sec) [ -6624.3557] [GTR parameters ][rr_val: 0.052890 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 7 sec) [ -6624.3557] [Branch lengths ] . ( 7 sec) [ -6624.3523] [Selective constraints on amino acids ][0.441614 * aa_fitness(a,b) + -1.491796 * (1-delta(a,b))] . ( 8 sec) [ -6624.3523] [GTR parameters ][rr_val: 0.052947 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 8 sec) [ -6624.3523] [Branch lengths ] . ( 8 sec) [ -6624.3505] [Selective constraints on amino acids ][0.444127 * aa_fitness(a,b) + -1.486769 * (1-delta(a,b))] . ( 9 sec) [ -6624.3505] [GTR parameters ][rr_val: 0.052947 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 9 sec) [ -6624.3505] [Branch lengths ] . ( 9 sec) [ -6624.3495] [Selective constraints on amino acids ][0.446082 * aa_fitness(a,b) + -1.483106 * (1-delta(a,b))] . ( 10 sec) [ -6624.3495] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 10 sec) [ -6624.3495] [Branch lengths ] . ( 10 sec) [ -6624.3489] [Selective constraints on amino acids ][0.447536 * aa_fitness(a,b) + -1.480435 * (1-delta(a,b))] . ( 10 sec) [ -6624.3489] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -6624.3487] [Selective constraints on amino acids ][0.448576 * aa_fitness(a,b) + -1.477765 * (1-delta(a,b))] . ( 11 sec) [ -6624.3487] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -6624.348650. 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 LG-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -6624.34865 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.35526 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.448576 * aa_fitness(a,b) + -1.477765 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.069430 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.053000 transition/transversion m_tc|ag / m_[tc][ag] 2.594985 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] 2.594985 A <-> G / transversion m_ag / m_[tc][ag] 2.594985 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 . 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 0h0m11s . 11 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'...