]> 3.6a2 pars - Discrete character parsimony &phylip_header; pars pars perl "pars < 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 pars_opt Pars options search_opt Search option (S) 0 0 "" 1 "S\\nY\\n" 2 "S\\nN\\n" 0 More thorough search 1 Rearrange on one best tree 2 Less thorough 1 params PARS is a general parsimony program which carries out the Wagner parsimony method with multiple states. Wagner parsimony allows changes among all states. The criterion is to find the tree which requires the minimum number of changes. The Wagner method was originated by Eck and Dayhoff (1966) and by Kluge and Farris (1969). Here are its assumptions: 1. Ancestral states are unknown. 2. Different characters evolve independently. 3. Different lineages evolve independently. 4. Changes to all other states are equally probable (Wagner). 5. These changes are a priori improbable over the evolutionary time spans involved in the differentiation of the group in question. 6. Other kinds of evolutionary event such as retention of polymorphism are far less probable than these state changes. 7. Rates of evolution in different lineages are sufficiently low that two changes in a long segment of the tree are far less probable than one change in a short segment. PARS can handle both bifurcating and multifurcating trees. In doing its search for most parsimonious trees, it adds species not only by creating new forks in the middle of existing branches, but it also tries putting them at the end of new branches which are added to existing forks. Thus it searches among both bifurcating and multifurcating trees. If a branch in a tree does not have any characters which might change in that branch in the most parsimonious tree, it does not save that tree. Thus in any tree that results, a branch exists only if some character has a most parsimonious reconstruction that would involve change in that branch. save_trees Number of trees to save? (V) params 100 perl (defined $value && $value != $vdef) ? "V\\n$value\\n" : "" 1 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 weight_opt Weight options weights Weighted sites (W) perl (defined $value && $value) ? "W\\n" : "" 1 params The weights follow the format described in the main documentation file, with integer weights from 0 to 35 allowed by using the characters 0, 1, 2, ..., 9 and A, B, ... Z. weight_file Weight file perl "ln -s $weight_file weights; " -9 perl $weights user_tree_opt User tree options user_tree Use User tree (default: no, search for best tree) (U) perl ($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\\nD\\n$datasets_nb\\n$multi_seed\\n$multi_times\\n" : "" 0 10 params datasets_nb How many data sets perl "" 9 enter a value > 0 ; there must be no more than 1000 datasets for this server perl ($value > 1000) || ($value < 0) perl $multiple_dataset multi_seed Random number seed (must be odd) perl "" 19 Random number seed must be odd perl $value <= 0 || (($value % 2) == 0) perl $multiple_dataset multi_times Number of times to jumble perl "" 1 19 consense Compute a consensus tree perl ($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 ($value)? " && indenttree -o outtree.indent outtree" : "" 0 1000 parcimony_opt Parcimony options use_threshold Use Threshold parsimony (T) perl ($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