]> 3.6a2 consense - Consensus tree program &phylip_header; consense consense perl "consense < params" 0 infile Trees File perl "ln -sf $infile intree; " -10 phylip_tree perl 1 type Consensus type MRE Majority rule (extended) S Strict MR Majority rule ML Ml (M-sub-L) MRE MRE "" S "C\\n" MR "C\\nC\\n" ML "C\\nC\\nC\\n" params output Output options print_tree Print out tree (3) perl ($value)? "" : "3\\n" 1 1 Tells the program to print a semi-graphical picture of the tree in the outfile. params print_treefile Write out trees onto tree file (4) perl ($value)? "" : "4\\n" 1 1 Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas). params printdata Print out the data at start of run (1) perl ($value)? "1\\n" : "" 0 1 params indent_tree Indent treefile perl " && indenttree -o outtree.indent outtree" 0 1000 other_options Other options outgroup Outgroup (default, use as outgroup species 1) (O) perl ($value && $value != $vdef)? "O\\n$value\\n" : "" 1 1 params Please enter a value greater than 0 perl $value < 1 rooted Trees to be treated as rooted perl ($value)? "R\\n" : "" 0 1 params outfile outfile treefile perl $print_treefile outtree phylip_tree perl 1 indented_treefile perl $print_treefile && $indent_tree outtree.indent params params confirm perl "Y\\n" 1000 params terminal_type perl "T\\n" -1 params tmp_params *.params