Puzzle 5.0 Tree reconstruction for sequences by quartet puzzling and maximum likelihood Strimmer, von Haeseler Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling:A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964-969. phylogeny Puzzle Puzzle perl "Puzzle" 0 stdinput perl " < params" 2 confirm perl "y\\n" 1000 params outfile *.puzzle outtree *.tree phylip_tree perl 1 outdist *.dist phylip_dist perl 1 params params infile Alignement File perl " $infile" 1 12 readseq_ok_alig perl 1 seqtype Is it a DNA or protein sequence perl "" -10 DNA protein control_options Control options approximate Approximate quartet likelihood (v) perl ($value)? "" : "v\\n" 1 1 params puzzling_step Number of puzzling steps (n) perl (defined $value and $value != $vdef)? "n\\n$value\\n" : "" 1000 1 params protein_options Protein options perl $seqtype ne "DNA" protein_model Model of substitution for protein (if no automatic guess) (m) 1 1 0 1 2 3 4 5 6 0 "" 1 "m\\n" 2 "m\\nm\\n" 3 "m\\nm\\nm\\n" 4 "m\\nm\\nm\\nm\\n" 5 "m\\nm\\nm\\nm\\nm\\n" 6 "m\\nm\\nm\\nm\\nm\\nm\\n" The Dayhoff and JTT matrices are for use with proteins encoded on nuclear DNA, and the mtREV24 matrix is for use with proteins encoded on mtDNA. The BLOSUM 62 model is for more distantly related amino acid sequences (Henikoff and Henikoff 1992). perl $seqtype ne "DNA" and ! $guessmodel params dna_options DNA options perl $seqtype eq "DNA" and $dna_model eq "3" ratio Transition/transversion ratio (t) perl (defined $value) ? "t\\n$value\\n" : "" 1 perl $seqtype eq "DNA" params GTR_options GTR model rates GTR_acrate A-C rate (1) perl (defined $value and $value != $vdef) ? "1\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params GTR_agrate A-G rate (2) perl (defined $value and $value != $vdef) ? "2\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params GTR_atrate A-T rate (3) perl (defined $value and $value != $vdef) ? "3\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params GTR_cgrate C-G rate (4) perl (defined $value and $value != $vdef) ? "4\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params GTR_ctrate C-T rate (5) perl (defined $value and $value != $vdef) ? "5\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params GTR_gtrate G-T rate (6) perl (defined $value and $value != $vdef) ? "6\\n$value\\n" : "" 11 perl $seqtype eq "DNA" and $dna_model eq "3" 1.00 params nuc_freq Nucleotids frequencies (in %) (f) perl $seqtype eq "DNA" use_specified Use specified values perl ($value)? "f\\n" : "" 0 50 params a_freq pi(A) perl "$value\\n" 51 perl $use_specified params c_freq pi(C) perl "$value\\n" 52 perl $use_specified params g_freq pi(G) perl "$value\\n" 53 perl $use_specified params dna_model Model of substitution for DNA (m) 1 10 1 2 3 "" 1 "" 2 "m\\n" 3 "m\\nm\\n" The following models are implemented for nucleotides: the Tamura-Nei (TN) model, the Hasegawa et al. (HKY) model, and the Schöniger and von Haeseler (SH) model. The SH model describes the evolution of pairs of dependent nucleotides (pairs are the first and the second nucleotide, the third and the fourth nucleotide and so on). It allows for specification of the transition-transversion ratio. The originally proposed model (Schöniger and von Haeseler 1994) is obtained by setting the transition-transversion parameter to 0.5. The Jukes-Cantor (1969), the Felsenstein (1981), and the Kimura (1980) model are all special cases of the HKY model. perl $seqtype eq "DNA" params constrain_TN Constrain TN model to F84 model (p) perl ($value)? "p\\n" : "" 0 11 perl $seqtype eq "DNA" and $dna_model eq "2" params f84_ratio Expected F84 Transition/transversion ratio perl (defined $value)? "$value\\n" : "" 12 perl $seqtype eq "DNA" and $dna_model eq "2" params y_r Y/R transition parameter (r) perl (defined $value)? "r\\n$value\\n" : "" 13 perl $seqtype eq "DNA" and $dna_model eq "2" params symmetrize_frequencies Symmetrize doublet frequencies (s) perl ($value)? "s\\n" : "" 0 11 perl $seqtype eq "DNA" and $dna_model eq "3" params rate_options Rate heterogeneity options rate_heterogeneity Model of rate heterogeneity (w) 1 20 1 2 3 4 1 "" 2 "w\\n" 3 "w\\nw\\n" 4 "w\\nw\\nw\\n" params alpha Gamma distribution parameter alpha (a) perl (defined $value)? "a\\n$value\\n" : "" 21 perl $rate_heterogeneity eq "2" or $rate_heterogeneity eq "4" params gamma_number Number of Gamma rate categories (c) perl (defined $value and $value != $vdef)? "c\\n$value\\n" : "" 8 21 perl $rate_heterogeneity eq "2" or $rate_heterogeneity eq "4" params invariable Fraction of invariable sites (i) perl (defined $value)? "i\\n$value\\n" : "" 21 perl $rate_heterogeneity eq "3" or $rate_heterogeneity eq "4" params user_tree_options User Tree options user_tree Tree search procedure: User tree (k) perl ($value)? "k\\n" : "" 0 1 params tree_file User Tree file perl ($value)? "$tree_file\\n" : "" 2000 perl $user_tree params no_tree Pairwise distances only (no tree) (k) perl ($value)? "k\\nk\\n" : "" 0 1 params output_options Output options outgroup Display as outgroup (o) perl (defined $value)? "o\\n$value\\n" : "" 1 params branch_length Compute clocklike branch lengths (z) perl ($value)? "z\\n" : "" 0 1 params estimates Parameter estimates (e) 1 1 1 2 "" 1 "" 2 "e\\n" params estimation_by Parameter estimation by (x) 1 1 1 2 "" 1 "" 2 "x\\n" params list_unresolved List unresolved quartets (u) perl ($value)? "u\\n" : "" 0 1 params list_trees List puzzling step trees (j) perl ($value)? "j\\n" : "" 0 1 params