PHYML 2.4.6 a program that computes maximum likelihood phylogenies from DNA or AA homologous sequences S. Guindon and O. Gascuel Guindon, S. and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol., 52, 696-704 phylogeny phyml phyml perl "phyml" 1 alignment Sequence Alignment perl " $value" 2 12 readseq_ok_alig perl 1 data_type Data type 0 1 perl (defined $value)? " $value" : "" 3 inputopt Input Options format Format i s i perl " $value" 4 datasets Number of data sets to analyse 1 perl " $value" 5 bootstrap_sets Number of bootstraps sets to analyse (only works with one data set to analyse) 2 perl ($datasets == 1)? " $value" : " 0" 6 control_opt Control Options model Substitution model JC69 K2P F81 HKY F84 TN93 GTR JTT MtREV Dayhoff WAG perl " $value" 7 kappa Transition/transversion ratio (only for DNA sequences) 4 perl " $value" 8 perl $data_type == 0 && not $kappa_e Either enter a value or ask for an estimate (see following option). kappa_e Estimate Transition/transversion ratio? (only for DNA sequences) 1 perl ($value)? " e" : "" 8 perl $data_type == 0 Either enter a value for the ratio (see previous option) or ask for an estimate. invar Proportion of invariable sites 0.0 perl " $value" perl not $invar_e 9 Either enter a value or ask for an estimate (see following option). invar_e Estimate proportion of invariable sites? 1 perl ($value)? " e" : "" 9 Either enter a value for the proportion of invariable sites (see previous option) or ask for an estimate. nb_categ number of relative substitution rate categories (ex:4) 1 perl " $value" 10 alpha Gamma distribution parameter perl " $value" perl not $alpha_e 11 Either enter a value or ask for an estimate (see following option). alpha_e Estimate Gamma distribution parameter? 1 perl ($value)? " e" : "" 11 Either enter a value for the gamma distribution (see previous option) or ask for an estimate. opt_topology Optimise tree topology? perl ($value)? " y" : " n" 1 55 opt_lengths Optimise branch lengths and rate parameters? perl ($value)? " y" : " n" 1 56 user_tree Starting tree? 0 perl ($value)? " $user_tree_file" : " BIONJ" 0 50 user_tree_file Starting tree filename (Newick format) perl "" phylip_tree perl 1 perl $user_tree outfiles *.txt outtree_result *tree* phylip_tree perl 1