. 318 patterns found (out of a total of 1112 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Initial values of parameters . Sequence filename: 20110208_105916.phy . Data type : codon . Sequence format : interleaved . 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 EI-11 . Number of taxa: 10 . Discrete Selection: No . Gamma distribution parameter : estimated - Gamma shape parameter: 1.000000 - 'Middle' of each rate class : mean - Number of categories: 4 . Each rate and its probability: 0 0.136954 0.250000 1 0.476752 0.250000 2 1.000000 0.250000 3 2.386294 0.250000 mean 1.000000 . Selective constraints on amino acids: optimize? 0 1 : 1.000000 * aa_fitness[i,j] + -0.000000 . Scale parameter of Gamma distribution: optimize? 0 : 0.000000 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 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 TTC F 0.012410 TTA L 0.014299 TTG L 0.010072 TCT S 0.028147 TCC S 0.023741 TCA S 0.024910 TCG S 0.008903 TAT Y 0.010701 TAC Y 0.013489 TAA * 0.000000 TAG * 0.000000 TGT C 0.010432 TGC C 0.007194 TGA * 0.000000 TGG W 0.008183 CTT L 0.011871 CTC L 0.012860 CTA L 0.005845 CTG L 0.023561 CCT P 0.023651 CCC P 0.025540 CCA P 0.019424 CCG P 0.006835 CAT H 0.014119 CAC H 0.015288 CAA Q 0.017176 CAG Q 0.028867 CGT R 0.003058 CGC R 0.006115 CGA R 0.007914 CGG R 0.006115 ATT I 0.007644 ATC I 0.016097 ATA I 0.011061 ATG M 0.025899 ACT T 0.028417 ACC T 0.027338 ACA T 0.018165 ACG T 0.007104 AAT N 0.029496 AAC N 0.023651 AAA K 0.027518 AAG K 0.025989 AGT S 0.023741 AGC S 0.033993 AGA R 0.014209 AGG R 0.008813 GTT V 0.014299 GTC V 0.008813 GTA V 0.009083 GTG V 0.020414 GCT A 0.019964 GCC A 0.017986 GCA A 0.014928 GCG A 0.004496 GAT D 0.020234 GAC D 0.035791 GAA E 0.023561 GAG E 0.020683 GGT G 0.004406 GGC G 0.016457 GGA G 0.017716 GGG G 0.011241 . This analysis requires at least 21 Mo of memory space. . ( 4 sec) [ -6709.4108] [Branch lengths ] . ( 6 sec) [ -6704.6719] [Alpha ][ 0.507335] [0.034755 0.250000][0.256677 0.250000][0.825533 0.250000][2.883035 0.250000] . ( 7 sec) [ -6654.1532] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.181049] . ( 11 sec) [ -6653.6912] [Branch lengths ] . ( 13 sec) [ -6653.6815] [Alpha ][ 0.494351] [0.032346 0.250000][0.248212 0.250000][0.816114 0.250000][2.903328 0.250000] . ( 14 sec) [ -6653.6796] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.189090] . ( 18 sec) [ -6653.6702] [Branch lengths ] . ( 20 sec) [ -6653.6701] [Alpha ][ 0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000] . ( 21 sec) [ -6653.6701] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] . ( 25 sec) [ -6653.6698] [Branch lengths ] . ( 27 sec) [ -6653.6698] [Alpha ][ 0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000] . ( 28 sec) [ -6653.6698] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] . ( 30 sec) [ -6653.6698] [Alpha ][ 0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000] . ( 32 sec) [ -6653.6698] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] . Log likelihood of the current tree: -6653.669815. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 20100824-SM04.101103 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier II oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Final values of parameters . Sequence filename: 20110208_105916.phy . Data type : codon . Sequence format : interleaved . 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 EI-11 . Number of taxa: 10 . Log-likelihood: -6653.66982 . Unconstrained likelihood: -5456.53904 . Parsimony: 6068 . Tree size: 0.38774 . Discrete Selection: No . Gamma distribution parameter : estimated - Gamma shape parameter: 0.493554 - 'Middle' of each rate class : mean - Number of categories: 4 . Each rate and its probability: 0 0.032199 0.250000 1 0.247687 0.250000 2 0.815521 0.250000 3 2.904593 0.250000 mean 1.000000 . Selective constraints on amino acids: optimize? 0 1 : 1.000000 * aa_fitness[i,j] + -1.190369 . Scale parameter of Gamma distribution: optimize? 0 : 0.000000 . Nulceotide exchangeabilities: optimize? 0 : how_many? 0 : rr_val[i] : 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 transversion m_[tc][ag] 0.000000 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 TTC F 0.012410 TTA L 0.014299 TTG L 0.010072 TCT S 0.028147 TCC S 0.023741 TCA S 0.024910 TCG S 0.008903 TAT Y 0.010701 TAC Y 0.013489 TAA * 0.000000 TAG * 0.000000 TGT C 0.010432 TGC C 0.007194 TGA * 0.000000 TGG W 0.008183 CTT L 0.011871 CTC L 0.012860 CTA L 0.005845 CTG L 0.023561 CCT P 0.023651 CCC P 0.025540 CCA P 0.019424 CCG P 0.006835 CAT H 0.014119 CAC H 0.015288 CAA Q 0.017176 CAG Q 0.028867 CGT R 0.003058 CGC R 0.006115 CGA R 0.007914 CGG R 0.006115 ATT I 0.007644 ATC I 0.016097 ATA I 0.011061 ATG M 0.025899 ACT T 0.028417 ACC T 0.027338 ACA T 0.018165 ACG T 0.007104 AAT N 0.029496 AAC N 0.023651 AAA K 0.027518 AAG K 0.025989 AGT S 0.023741 AGC S 0.033993 AGA R 0.014209 AGG R 0.008813 GTT V 0.014299 GTC V 0.008813 GTA V 0.009083 GTG V 0.020414 GCT A 0.019964 GCC A 0.017986 GCA A 0.014928 GCG A 0.004496 GAT D 0.020234 GAC D 0.035791 GAA E 0.023561 GAG E 0.020683 GGT G 0.004406 GGC G 0.016457 GGA G 0.017716 GGG G 0.011241 . Time used 0h0m32s . 32 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 '20110208_105916.phy_phyml_tree.txt'...