]> 3.6a2 mix - Mixed method parsimony &phylip_header; mix mix perl "mix < params" 0 infile Input File perl "ln -s $infile infile; " -10 Example input file: 5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110 mix_opt Mix options use_mixed Use Mixed method (X) 0 perl ($value)? "X\\n" : "" 1 params You have to put on the first line of the input file, after the number of species and the number of characters, the character M, to signal that the Mixture information follows. There then follows, before the species data, a line or lines, the first character the first line being M. There then follow as many characters as are needed to fill out the length of a species name, and one letter for each for each character. These letters are C or S if the character is to be reconstructed according to Camin-Sokal parsimony, W or ? if the character is to be reconstructed according to Wagner parsimony. So if there are 20 characters the line giving the mixture might look like this: Mixture WWWCC WWCWC parsimony_method perl ! $use_mixed Parsimony method (P) perl ($value eq "camin")? "P\\n" : "" neighbor 1 wagner Wagner camin Camin-Sokal params Only if Use Mixed method is disabled. use_ancestral_state Use ancestral states in input file (A) perl ($value)? "A\\n" : "" 1 params There should also be, in the input file after the numbers of species and characters, an A on the first line of the file. There must also be, before the character data, a line or lines giving the ancestral states for each character. It will look like the data for a species (the ancestor). It must start with the letter A in the first column. There then follow enough characters or blanks to complete the full length of a species name (e. g. ANCESTOR). Then the states which are ancestral for the individual characters follow. These may be 0, 1 or ?, the latter indicating that the ancestral state is unknown. Examples: ANCESTOR 0010011 jumble_opt Randomize options jumble Randomize (jumble) input order (J) perl ($value)? "j\\n$jumble_seed\\n$times\\n" : "" 0 20 params jumble_seed Random number seed (must be odd) perl "" 19 Random number seed must be odd perl $value <= 0 || (($value % 2) == 0) perl $jumble times Number of times to jumble perl "" 1 19 user_tree_opt User tree options user_tree Use User tree (default: no, search for best tree) (U) perl ($value)? "U\\n" : "" 0 1 To give your tree to the program, you must normally put it in the alignement file, after the sequences, preceded by a line indicating how many trees you give. Here, this will be automatically appended: just give a treefile and the number of trees in it. you cannot randomize (jumble) your dataset and give a user tree at the same time perl $user_tree && $jumble params tree_file User Tree file perl ($value)? "cat $tree_file >> infile; " : "" -1 Give a tree whenever the infile does not already contain the tree. perl $user_tree tree_nb How many tree(s) in the User Tree file perl "echo $value >> infile; " 1 -2 Give this information whenever the infile does not already contain the tree. perl $tree_file bootstrap Bootstrap options multiple_dataset Analyze multiple data sets (M) perl ($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.mix; cp outtree outtree.mix; cp outfile outfile.mix; mv outtree intree; consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.mix outtree; mv infile.mix infile; mv outfile.mix outfile" : "" 0 10 perl $multiple_dataset && $print_treefile output Output options print_tree Print out tree (3) perl ($value)? "" : "3\\n" 1 1 Tells the program to print a semi-graphical picture of the tree in the outfile. params print_step Print out steps in each character (4) perl ($value)? "4\\n" : "" 0 1 params print_states Print states at all nodes of tree (5) perl ($value)? "5\\n" : "" 0 1 params print_treefile Write out trees onto tree file (6) perl ($value) ? "" : "6\\n" 1 1 Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas). params printdata Print out the data at start of run (1) perl ($value)? "1\\n" : "" 0 1 params indent_tree Indent treefile perl ($value)? " && indenttree -o outtree.indent outtree" : "" 0 1000 pars_opt Parcimony options use_threshold Use Threshold parsimony (T) perl ($value)? "T\\n$threshold\\n" : "" 0 3 params threshold Threshold value (if use threshold parsimony) perl "" 2 perl $use_threshold You must enter a numeric value, greater than 1 perl ($threshold !~ /^\d+(\.\d+)?$/) || ($threshold < 1) params 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