. 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 . Discrete gamma model for the variation of selective constraint over sites: . Gamma distribution parameter: - Gamma shape parameter: estimated: 0.300000 - 'Middle' of each rate class : mean - Number of categories: 4 . The values of and their probabilities including those in discrete gamma: 0 0.001650 0.500000 1.000000 wab + -4.402329 1 0.017904 0.250000 1.000000 wab + -2.017845 2 0.051161 0.125000 1.000000 wab + -0.967889 3 0.146832 0.125000 1.000000 wab + 0.089479 mean 0.030050 . Selection type : 11 . 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 . 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 . Nucleotides frequencies for codon usage: ACGT : 0.000000 0.000000 0.000000 0.000000 . 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 21 Mo of memory space. . ( 1 sec) [ -6644.6871] [Branch lengths ] . ( 2 sec) [ -6640.3243] [Selective constraints on amino acids ][0.725920 * aa_fitness(a,b) + -1.469836 * (1-delta(a,b))] [0.002660 0.500000][0.028869 0.250000][0.082494 0.125000][0.236760 0.125000] . ( 4 sec) [ -6606.9903] [GTR parameters ][rr_val: 0.065736 1.998157 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -6603.9840] [Alpha for w ][ 0.150138] [0.000263 0.500000][0.011738 0.250000][0.063397 0.125000][0.299706 0.125000] . ( 7 sec) [ -6603.9168] [Branch lengths ] . ( 8 sec) [ -6603.8842] [Selective constraints on amino acids ][0.715051 * aa_fitness(a,b) + -1.501326 * (1-delta(a,b))] [0.000260 0.500000][0.011594 0.250000][0.062619 0.125000][0.296029 0.125000] . ( 10 sec) [ -6602.7357] [GTR parameters ][rr_val: 0.059825 2.362759 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -6602.6213] [Alpha for w ][ 0.139185] [0.000181 0.500000][0.010003 0.250000][0.059447 0.125000][0.302697 0.125000] . ( 13 sec) [ -6602.6205] [Branch lengths ] . ( 14 sec) [ -6602.5246] [Selective constraints on amino acids ][0.678883 * aa_fitness(a,b) + -1.527501 * (1-delta(a,b))] [0.000188 0.500000][0.010394 0.250000][0.061771 0.125000][0.314527 0.125000] . ( 15 sec) [ -6602.5146] [GTR parameters ][rr_val: 0.055527 2.371767 1.000000 1.000000 1.000000 1.000000] . ( 17 sec) [ -6602.4920] [Alpha for w ][ 0.136652] [0.000171 0.500000][0.010011 0.250000][0.060942 0.125000][0.316190 0.125000] . ( 18 sec) [ -6602.4919] [Branch lengths ] . ( 19 sec) [ -6602.4622] [Selective constraints on amino acids ][0.661755 * aa_fitness(a,b) + -1.548761 * (1-delta(a,b))] [0.000173 0.500000][0.010108 0.250000][0.061538 0.125000][0.319281 0.125000] . ( 21 sec) [ -6602.4621] [GTR parameters ][rr_val: 0.055095 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 22 sec) [ -6602.4565] [Alpha for w ][ 0.135992] [0.000169 0.500000][0.010008 0.250000][0.061316 0.125000][0.319722 0.125000] . ( 23 sec) [ -6602.4565] [Branch lengths ] . ( 25 sec) [ -6602.4386] [Selective constraints on amino acids ][0.649339 * aa_fitness(a,b) + -1.566844 * (1-delta(a,b))] [0.000170 0.500000][0.010053 0.250000][0.061596 0.125000][0.321182 0.125000] . ( 26 sec) [ -6602.4386] [GTR parameters ][rr_val: 0.054927 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 27 sec) [ -6602.4365] [Alpha for w ][ 0.135744] [0.000168 0.500000][0.010015 0.250000][0.061511 0.125000][0.321349 0.125000] . ( 29 sec) [ -6602.4365] [Branch lengths ] . ( 30 sec) [ -6602.4241] [Selective constraints on amino acids ][0.639138 * aa_fitness(a,b) + -1.582050 * (1-delta(a,b))] [0.000169 0.500000][0.010050 0.250000][0.061727 0.125000][0.322478 0.125000] . ( 31 sec) [ -6602.4241] [GTR parameters ][rr_val: 0.054830 2.376122 1.000000 1.000000 1.000000 1.000000] . ( 33 sec) [ -6602.4217] [Alpha for w ][ 0.135445] [0.000167 0.500000][0.010004 0.250000][0.061625 0.125000][0.322679 0.125000] . ( 34 sec) [ -6602.4217] [Branch lengths ] . ( 35 sec) [ -6602.4148] [Selective constraints on amino acids ][0.630632 * aa_fitness(a,b) + -1.586737 * (1-delta(a,b))] [0.000169 0.500000][0.010115 0.250000][0.062307 0.125000][0.326247 0.125000] . ( 37 sec) [ -6602.4147] [GTR parameters ][rr_val: 0.054412 2.380441 1.000000 1.000000 1.000000 1.000000] . ( 38 sec) [ -6602.4099] [Alpha for w ][ 0.134843] [0.000165 0.500000][0.010021 0.250000][0.062097 0.125000][0.326660 0.125000] . ( 40 sec) [ -6602.4099] [Branch lengths ] . ( 41 sec) [ -6602.4080] [Selective constraints on amino acids ][0.627497 * aa_fitness(a,b) + -1.591419 * (1-delta(a,b))] [0.000165 0.500000][0.010032 0.250000][0.062166 0.125000][0.327024 0.125000] . ( 42 sec) [ -6602.4080] [GTR parameters ][rr_val: 0.054351 2.378060 1.000000 1.000000 1.000000 1.000000] . ( 44 sec) [ -6602.4068] [Alpha for w ][ 0.134708] [0.000164 0.500000][0.010011 0.250000][0.062119 0.125000][0.327117 0.125000] . ( 45 sec) [ -6602.4068] [Branch lengths ] . ( 47 sec) [ -6602.4055] [Selective constraints on amino acids ][0.623972 * aa_fitness(a,b) + -1.596362 * (1-delta(a,b))] [0.000164 0.500000][0.010027 0.250000][0.062217 0.125000][0.327636 0.125000] . ( 48 sec) [ -6602.4055] [GTR parameters ][rr_val: 0.054351 2.378060 1.000000 1.000000 1.000000 1.000000] . ( 49 sec) [ -6602.4044] [Alpha for w ][ 0.134573] [0.000164 0.500000][0.010006 0.250000][0.062170 0.125000][0.327729 0.125000] . ( 51 sec) [ -6602.4044] [Branch lengths ] . ( 52 sec) [ -6602.4036] [Selective constraints on amino acids ][0.621152 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000164 0.500000][0.010029 0.250000][0.062311 0.125000][0.328474 0.125000] . ( 53 sec) [ -6602.4036] [GTR parameters ][rr_val: 0.054254 2.381835 1.000000 1.000000 1.000000 1.000000] . ( 55 sec) [ -6602.4024] [Alpha for w ][ 0.134439] [0.000163 0.500000][0.010008 0.250000][0.062264 0.125000][0.328567 0.125000] . ( 56 sec) [ -6602.4024] [Branch lengths ] . ( 58 sec) [ -6602.4022] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000164 0.500000][0.010038 0.250000][0.062453 0.125000][0.329569 0.125000] . ( 59 sec) [ -6602.4022] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 60 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 62 sec) [ -6602.4004] [Branch lengths ] . ( 63 sec) [ -6602.4004] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 64 sec) [ -6602.4004] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 66 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 67 sec) [ -6602.4004] [Selective constraints on amino acids ][0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b))] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . ( 69 sec) [ -6602.4004] [GTR parameters ][rr_val: 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000] . ( 70 sec) [ -6602.4004] [Alpha for w ][ 0.134230] [0.000162 0.500000][0.010005 0.250000][0.062379 0.125000][0.329714 0.125000] . Log likelihood of the current tree: -6602.400402. 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: -6602.40040 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.35816 . Discrete selection: No . Discrete gamma model for the variation of selective constraint over sites: . Gamma distribution parameter: - Gamma shape parameter: estimated: 0.134230 - 'Middle' of each rate class : mean - Number of categories: 4 . The values of and their probabilities including those in discrete gamma: 0 0.000162 0.500000 0.619513 wab + -7.360936 1 0.010005 0.250000 0.619513 wab + -3.239622 2 0.062379 0.125000 0.619513 wab + -1.409498 3 0.329714 0.125000 0.619513 wab + 0.262328 mean 0.051594 . Selection type : 11 . Selective constraints on amino acids: optimize? 1 1 : 0.619513 * aa_fitness(a,b) + -1.599326 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.051594 . Nulceotide exchangeabilities: optimize? 1 : how_many? 2 : rr_val[i] : 0.054104 2.379453 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.054104 transition/transversion m_tc|ag / m_[tc][ag] 2.379453 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] 2.379453 A <-> G / transversion m_ag / m_[tc][ag] 2.379453 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 : 0.000000 0.000000 0.000000 0.000000 . 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 0h1m10s . 70 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'...