]> 3.6a2 neighbor - Neighbor-Joining and UPGMA methods &phylip_header; neighbor neighbor perl "neighbor < params" 0 distance_method Distance method perl ($value eq "upgma") ? "N\\n" : "" neighbor 1 neighbor Neighbor-joining upgma UPGMA params infile Distances matrix File perl "ln -sf $infile infile; " -10 phylip_dist perl 1 jumble_opt Randomize options jumble Randomize (jumble) input order (J) perl ($value) ? "J\\n$jumble_seed\\n" : "" 0 20 params perl not $multiple_dataset jumble_seed Random number seed for jumble (must be odd) perl "" 19 Random number seed must be odd perl $value <= 0 || (($value % 2) == 0) perl $jumble bootstrap Bootstrap options multiple_dataset Analyze multiple data sets (M) perl ($value) ? "M\\n$datasets_nb\\n$multiple_seed\\n" : "" 0 10 params datasets_nb How many data sets perl "" 9 there must be no more than 1000 datasets for this server perl $value > 1000 perl $multiple_dataset multiple_seed Random number seed for multiple dataset (must be odd) perl "" Random number seed must be odd perl $value <= 0 || (($value % 2) == 0) perl $multiple_dataset params consense Compute a consensus tree perl ($value)? "; cp infile infile.neighbor; cp outtree outtree.neighbor; mv outfile outfile.neighbor; mv outtree intree; consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.neighbor outtree; mv infile.neighbor infile; mv outfile.neighbor outfile" : "" 0 10 perl $multiple_dataset && $print_treefile consense_confirm perl "Y\\n" 1000 perl $consense consense.params consense_terminal_type perl "T\\n" -2 perl $consense consense.params consense_outfile perl $consense outfile.consense consense_treefile perl $consense outtree.consense phylip_tree perl 1 output Output options print_tree Print out tree (3) perl ($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 ($value)? "" : "4\\n" 1 1 Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas). params indent_tree Indent treefile perl " && indenttree -o outtree.indent outtree" 0 1000 printdata Print out the data at start of run (1) perl ($value)? "1\\n" : "" 0 1 params other_options Other options outgroup Outgroup species (default, use as outgroup species 1) (O) perl (defined $value && $value != $vdef)? "O\\n$value\\n" : "" 1 1 params Please enter a value greater than 0 perl defined $value && $value < 1 perl $distance_method eq "neighbor" triangular Matrix format square 1 square Square lower Lower-triangular upper Upper-triangular square "" lower "L\\n" upper "R\\n" 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 "0\\n" -1 params tmp_params *.params