]> 3.6a2 kitsch - Fitch-Margoliash and Least Squares Methods with Evolutionary Clock &phylip_header; kitsch kitsch perl "kitsch < params" 0 infile Distances matrix File perl "ln -sf $infile infile; " -5 phylip_dist perl 1 fitch_options Fitch options method Program method F Fitch-Margoliash M Minimum Evolution F F "" M "D\\n" 1 params negative_branch Negative branch lengths allowed (-) perl ($value)? "-\\n" : "" 0 1 params power Power (P) perl (defined $value && $value != $vdef)? "P\\n$value\\n" : "" 2.0 1 For the Fitch-Margoliash method, which is the default method with this program, P is 2.0. For the Cavalli-Sforza and Edwards least squares method it should be set to 0 (so that the denominator is always 1). An intermediate method is also available in which P is 1.0, and any other value of P, such as 4.0 or -2.3, can also be used. This generates a whole family of methods. Please read the documentation (man distance). params jumble_opt Randomize options jumble Randomize (jumble) input order (J) perl ($value)? "J\\n$jumble_seed\\n$times\\n" : "" 0 20 params perl $user_tree 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 perl $jumble && ( ! $neighbor) bootstrap Bootstrap options multiple_dataset Analyze multiple data sets (M) perl ($value)? "M\\n$datasets_nb\\n" : "" 0 10 params datasets_nb How many data sets perl "" 9 there must be no more than 1000 datasets for this server perl $value > 1000 perl $multiple_dataset consense Compute a consensus tree perl ($value) ? "; cp infile infile.kitsch; cp outtree outtree.kitsch; mv outfile outfile.kitsch; mv outtree intree; consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.kitsch outtree; mv infile.kitsch infile; mv outfile.kitsch 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 $consense outtree.consense user_tree_opt User tree options user_tree Use User tree (default: no, search for best tree) (U) perl ($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 bootstrap your dataset and give a user tree at the same time perl $user_tree && $seqboot 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 >> intree; " : "" -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 perl $tree_file output Output options print_tree Print out tree (3) perl ($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" 1 1000 other_options Other options 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