]> 3.6a2 clique - Compatibility Program &phylip_header; clique clique perl "clique < params" 0 infile Input File perl "ln -sf $infile infile; " -10 Example input file 5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110 clique_opt Clique options use_ancestral_state Use ancestral states in input file (A) perl ($value) ? "A\\n" : "" 1 params There should also be, in the input file after the numbers of species and characters, an A on the first line of the file. There must also be, before the character data, a line or lines giving the ancestral states for each character. It will look like the data for a species (the ancestor). It must start with the letter A in the first column. There then follow enough characters or blanks to complete the full length of a species name (e. g. ANCESTOR). Then the states which are ancestral for the individual characters follow. These may be 0, 1 or ?, the latter indicating that the ancestral state is unknown. Examples: ANCESTOR 0010011 spec_min_clique_size Specify minimum clique size? (C) perl ($value)? "C\\n$min_clique_size\\n" : "" 0 3 params min_clique_size Minimum clique size perl "" 2 perl $spec_min_clique_size You must enter a numeric value, greater than 0 perl ($min_clique_size !~ /^\d+(\.\d+)?$/) || ($min_clique_size < 0) This option indicates that you wish to specify a minimum clique size and print out all cliques (and their associated trees) greater than or equal to than that size. params bootstrap Bootstrap options multiple_dataset Analyze multiple data sets (M) perl ($value)? "M\\n$datasets_nb\\n" : "" 0 10 params datasets_nb How many data sets perl "" 9 enter a value > 0 ; there must be no more than 1000 datasets for this server perl ($value > 1000) || ($value < 0) perl $multiple_dataset consense Compute a consensus tree perl ($value)? "; cp infile infile.clique; cp outtree outtree.clique; cp outfile outfile.clique; mv treefile intree; consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.clique outtree; mv infile.clique infile; mv outfile.clique outfile" : "" 0 10 perl $multiple_dataset && $print_treefile output Output options print_matrix Print out compatibility matrix (3) perl ($value)? "" : "3\\n" 1 1 params print_tree Print out tree (4) perl ($value)? "" : "4\\n" 1 1 Tells the program to print a semi-graphical picture of the tree in the outfile. params print_treefile Write out trees onto tree file (5) perl ($value)? "" : "5\\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 ($value)? "1\\n" : "" 0 1 params indent_tree Indent treefile perl ($value) ? " && indenttree -o outtree.indent outtree" : "" 0 1000 other_options Other options outgroup Outgroup root (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 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 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