. 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/JTT_codon . Number of taxa: 10 . Discrete selection: No . Selective constraints on amino acids: optimize? 0 1 : 0.000000 * aa_fitness(a,b) + -3.500000 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.030197 . 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. . ( 0 sec) [ -3748.3003] [Branch lengths ] . ( 0 sec) [ -3748.2958] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.513346 * (1-delta(a,b))] . ( 1 sec) [ -3748.0032] [Branch lengths ] . ( 1 sec) [ -3748.0027] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.509833 * (1-delta(a,b))] . ( 1 sec) [ -3747.8333] [Branch lengths ] . ( 1 sec) [ -3747.8328] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] . ( 1 sec) [ -3747.8107] [Branch lengths ] . ( 1 sec) [ -3747.8107] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] . ( 2 sec) [ -3747.8106] [Branch lengths ] . ( 2 sec) [ -3747.8106] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] . ( 2 sec) [ -3747.8106] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] . Log likelihood of the current tree: -3747.810611. 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/JTT_codon . Number of taxa: 10 . Log-likelihood: -3747.81061 . Unconstrained likelihood: -3479.25308 . Parsimony: 76 . Tree size: 1.02042 . Discrete selection: No . Selective constraints on amino acids: optimize? 0 1 : 0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.029732 . 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 0h0m2s . 2 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'...