. 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/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 . Nulceotide exchangeabilities: optimize? 1 : how_many? 6 : 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? 3 : 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 : 0.250000 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. . ( 1 sec) [ -3749.3706] [Branch lengths ] . ( 1 sec) [ -3748.8304] [Selective constraints on amino acids ][0.931852 * aa_fitness(a,b) + -1.593850 * (1-delta(a,b))] . ( 2 sec) [ -3740.8066] [GTR parameters ][rr_val: 0.137717 1.635061 1.023915 1.273420 1.159279 1.100343] . ( 3 sec) [ -3736.4322] [Nucleotide equlibrium freqs.][ACGT: 0.380799 0.224130 0.251061 0.144011] . ( 4 sec) [ -3735.4343] [Branch lengths ] . ( 4 sec) [ -3734.9777] [Selective constraints on amino acids ][0.864330 * aa_fitness(a,b) + -1.669212 * (1-delta(a,b))] . ( 5 sec) [ -3734.6417] [GTR parameters ][rr_val: 0.128981 1.481371 1.106414 1.092382 1.129183 1.191721] . ( 6 sec) [ -3734.5826] [Nucleotide equlibrium freqs.][ACGT: 0.390306 0.210181 0.256286 0.143228] . ( 6 sec) [ -3734.5629] [Branch lengths ] . ( 7 sec) [ -3734.3821] [Selective constraints on amino acids ][0.823034 * aa_fitness(a,b) + -1.718978 * (1-delta(a,b))] . ( 7 sec) [ -3734.3731] [GTR parameters ][rr_val: 0.123394 1.485493 1.125878 1.093493 1.119224 1.192702] . ( 8 sec) [ -3734.3664] [Nucleotide equlibrium freqs.][ACGT: 0.391881 0.205492 0.258016 0.144611] . ( 8 sec) [ -3734.3657] [Branch lengths ] . ( 8 sec) [ -3734.2673] [Selective constraints on amino acids ][0.792741 * aa_fitness(a,b) + -1.755543 * (1-delta(a,b))] . ( 9 sec) [ -3734.2643] [GTR parameters ][rr_val: 0.120372 1.491809 1.134791 1.105023 1.116572 1.185845] . ( 10 sec) [ -3734.2618] [Nucleotide equlibrium freqs.][ACGT: 0.392209 0.202761 0.259397 0.145634] . ( 10 sec) [ -3734.2617] [Branch lengths ] . ( 10 sec) [ -3734.2071] [Selective constraints on amino acids ][0.770234 * aa_fitness(a,b) + -1.782585 * (1-delta(a,b))] . ( 11 sec) [ -3734.2053] [GTR parameters ][rr_val: 0.118664 1.497351 1.140632 1.116337 1.116731 1.176611] . ( 11 sec) [ -3734.2042] [Nucleotide equlibrium freqs.][ACGT: 0.392452 0.200911 0.260241 0.146397] . ( 11 sec) [ -3734.2042] [Branch lengths ] . ( 12 sec) [ -3734.1735] [Selective constraints on amino acids ][0.753334 * aa_fitness(a,b) + -1.802635 * (1-delta(a,b))] . ( 12 sec) [ -3734.1725] [GTR parameters ][rr_val: 0.117545 1.501099 1.145013 1.124527 1.117639 1.169463] . ( 13 sec) [ -3734.1719] [Nucleotide equlibrium freqs.][ACGT: 0.392087 0.199690 0.261248 0.146975] . ( 13 sec) [ -3734.1719] [Branch lengths ] . ( 13 sec) [ -3734.1547] [Selective constraints on amino acids ][0.740589 * aa_fitness(a,b) + -1.817469 * (1-delta(a,b))] . ( 14 sec) [ -3734.1541] [GTR parameters ][rr_val: 0.116765 1.503833 1.148050 1.131277 1.118553 1.163354] . ( 14 sec) [ -3734.1538] [Nucleotide equlibrium freqs.][ACGT: 0.392148 0.198754 0.261715 0.147383] . ( 15 sec) [ -3734.1538] [Branch lengths ] . ( 15 sec) [ -3734.1442] [Selective constraints on amino acids ][0.730961 * aa_fitness(a,b) + -1.828357 * (1-delta(a,b))] . ( 15 sec) [ -3734.1439] [GTR parameters ][rr_val: 0.116170 1.505781 1.150529 1.135783 1.119243 1.159308] . ( 16 sec) [ -3734.1437] [Nucleotide equlibrium freqs.][ACGT: 0.392103 0.198026 0.262181 0.147691] . ( 16 sec) [ -3734.1437] [Branch lengths ] . ( 16 sec) [ -3734.1383] [Selective constraints on amino acids ][0.723692 * aa_fitness(a,b) + -1.836244 * (1-delta(a,b))] . ( 17 sec) [ -3734.1382] [GTR parameters ][rr_val: 0.115712 1.507301 1.152469 1.140215 1.120512 1.156864] . ( 18 sec) [ -3734.1381] [Nucleotide equlibrium freqs.][ACGT: 0.392008 0.197512 0.262520 0.147961] . ( 18 sec) [ -3734.1380] [Branch lengths ] . ( 18 sec) [ -3734.1351] [Selective constraints on amino acids ][0.718172 * aa_fitness(a,b) + -1.841894 * (1-delta(a,b))] . ( 19 sec) [ -3734.1350] [GTR parameters ][rr_val: 0.115367 1.507668 1.153437 1.140034 1.119735 1.155254] . ( 19 sec) [ -3734.1349] [Nucleotide equlibrium freqs.][ACGT: 0.391952 0.197056 0.262886 0.148106] . ( 19 sec) [ -3734.1349] [Branch lengths ] . ( 20 sec) [ -3734.1334] [Selective constraints on amino acids ][0.714141 * aa_fitness(a,b) + -1.845628 * (1-delta(a,b))] . ( 20 sec) [ -3734.1333] [GTR parameters ][rr_val: 0.115080 1.509872 1.154901 1.145707 1.120505 1.150606] . ( 20 sec) [ -3734.1333] [Nucleotide equlibrium freqs.][ACGT: 0.391879 0.196854 0.262933 0.148334] . ( 21 sec) [ -3734.1332] [Branch lengths ] . ( 21 sec) [ -3734.1323] [Selective constraints on amino acids ][0.710876 * aa_fitness(a,b) + -1.849004 * (1-delta(a,b))] . ( 21 sec) [ -3734.1323] [GTR parameters ][rr_val: 0.115080 1.509837 1.155562 1.145763 1.120407 1.150349] . ( 22 sec) [ -3734.1323] [Nucleotide equlibrium freqs.][ACGT: 0.391858 0.196614 0.263099 0.148429] . ( 22 sec) [ -3734.1320] [Selective constraints on amino acids ][0.708866 * aa_fitness(a,b) + -1.849004 * (1-delta(a,b))] . ( 22 sec) [ -3734.1320] [GTR parameters ][rr_val: 0.114287 1.510125 1.155191 1.145906 1.120576 1.150249] . ( 23 sec) [ -3734.1319] [Nucleotide equlibrium freqs.][ACGT: 0.391930 0.196308 0.263278 0.148484] . Log likelihood of the current tree: -3734.131925. 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/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0 . Number of taxa: 10 . Log-likelihood: -3734.13192 . Unconstrained likelihood: -3479.25308 . Parsimony: 76 . Tree size: 0.51407 . Discrete selection: No . Selective constraints on amino acids: optimize? 1 1 : 0.708866 * aa_fitness(a,b) + -1.849004 * (1-delta(a,b)) Mean selective constraints on amino acids (not weighted by frequencies): 0.034176 . Nulceotide exchangeabilities: optimize? 1 : how_many? 6 : rr_val[i] : 0.114287 1.510125 1.155191 1.145906 1.120576 1.150249 transversion m_[tc][ag] 0.114287 transition/transversion m_tc|ag / m_[tc][ag] 1.510125 T <-> C / transition m_tc / m_tc|ag 0.844809 A <-> G / transition m_ag / m_tc|ag 1.155191 T <-> C / transversion m_tc / m_[tc][ag] 1.275767 A <-> G / transversion m_ag / m_[tc][ag] 1.744483 T <-> A / transversion m_ta / m_[tc][ag] 1.145906 T <-> G / transversion m_tg / m_[tc][ag] 1.120576 C <-> A / transversion m_ca / m_[tc][ag] 1.150249 C <-> G / transversion m_cg / m_[tc][ag] 0.583269 . Nucleotides equilibrium frequencies: optimize? 3 : ACGT : 0.391930 0.196308 0.263278 0.148484 - f(A) = 0.391930 - f(C) = 0.196308 - f(G) = 0.263278 - f(T) = 0.148484 . 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 0h0m23s . 23 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'...