]> 3.6a2 dnapars - DNA Parsimony Program &phylip_header; dnapars dnapars perl "dnapars < params" 0 infile Alignement File perl "ln -s $infile infile; " -10 12 readseq_ok_alig perl 1 dnapars_opt Parcimony options use_threshold Use Threshold parsimony (T) perl ($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) Thresholds less than or equal to 1.0 do not have any meaning and should not be used: they will result in a tree dependent only on the input order of species and not at all on the data params use_transversion Use Transversion parsimony (N) perl ($value)? "N\\n" : "" 0 5 params bootstrap Bootstrap options seqboot Perform a bootstrap before analysis perl ($value)? "seqboot < seqboot.params && mv outfile infile && " : "" 0 -5 By selecting this option, the bootstrap will be performed on your sequence file. So you don't need to perform a separated seqboot before. Don't give an already bootstrapped file to the program, this won't work! You must also provide parameters for jumble. method Resampling methods bootstrap 1 bootstrap Bootstrap jackknife Delete-half jackknife permute Permute species for each character permute "J\\nJ\\n" bootstrap "" jackknife "J\\n" 1. The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and its use in phylogeny estimation was introduced by me (Felsenstein, 1985b). It involves creating a new data set by sampling N characters randomly with replacement, so that the resulting data set has the same size as the original, but some characters have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped data sets can be shown statistically to be typical of the variation that you would get from collecting new data sets. The method assumes that the characters evolve independently, an assumption that may not be realistic for many kinds of data. 2. Delete-half-jackknifing. This alternative to the bootstrap involves sampling a random half of the characters, and including them in the data but dropping the others. The resulting data sets are half the size of the original, and no characters are duplicated. The random variation from doing this should be very similar to that obtained from the bootstrap. The method is advocated by Wu (1986). 3. Permuting species within characters. This method of resampling (well, OK, it may not be best to call it resampling) was introduced by Archie (1989) and Faith (1990; see also Faith and Cranston, 1991). It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure. It is used for different purposes than the bootstrap, as it tests not the variation around an estimated tree but the hypothesis that there is no taxonomic structure in the data: if a statistic such as number of steps is significantly smaller in the actual data than it is in replicates that are permuted, then we can argue that there is some taxonomic structure in the data (though perhaps it might be just a pair of sibling species). perl $seqboot seqboot.params seqboot_seed Random number seed (must be odd) perl "$value\\n" 1010 Random number seed must be odd perl $value <= 0 || (($value % 2) == 0) perl $seqboot seqboot.params jumble_message (You may also enter a random number seed for jumble) replicates How many replicates perl ($value && $value != $vdef)? "R\\n$value\\n" : "" 100 1 this server allows no more than 1000 replicates perl $replicates > 1000 perl $seqboot seqboot.params consense Compute a consensus tree perl ($value)? ";cp infile infile.dnapars;mv outtree outtree.dnapars;mv outfile outfile.dnapars;cp outtree.dnapars intree;consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.dnapars outtree; mv infile.dnapars infile; mv outfile.dnapars outfile" : "" 0 10 perl $seqboot && $print_treefile multiple_dataset perl (defined $jumble_seed)? "M\\nD\\n$replicates\\n$jumble_seed\\n$times\\n" : "M\\nD\\n$replicates\\n$seqboot_seed\\n$times\\n" 1 perl $seqboot params bootconfirm perl "y\\n" 1000 perl $seqboot seqboot.params bootterminal_type perl "0\\n" -1 perl $seqboot seqboot.params jumble_opt Randomize options jumble Randomize (jumble) input order (J) perl ($value && ! $seqboot )? "j\\n$jumble_seed\\n$times\\n" : "" 0 20 params jumble_seed Random number seed for jumble (must be odd) perl "" 19 Random number seed for jumble must be odd. perl defined $value && ($value <= 0 || (($value % 2) == 0)) perl $jumble times Number of times to jumble perl "" 1 19 perl $jumble || $seqboot user_tree_opt User tree options user_tree Use User tree (default: no, search for best tree) (U) perl ($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)? "ln -s $tree_file intree; " : "" -1 Give a tree whenever the infile does not already contain the tree. perl $user_tree weight_opt Weight options weights Use weights for sites (W) perl ($value)? "W\\n" : "" 1 params weights_file Weights file perl ($value)? "ln -s $weights_file weights; " : "" -1 perl $weights phylip_weights perl 1 phylip_weights infile output Output options print_tree Print out tree (3) perl ($value)? "" : "3\\n" 1 1 Tells the program to print a semi-graphical picture of the tree in the outfile. params print_steps Print out steps in each site (4) perl ($value)? "5\\n" : "" 0 1 params print_sequences Print sequences at all nodes of tree (5) perl ($value)? "5\\n" : "" 0 1 params print_treefile Write out trees onto tree file (6) perl ($value)? "" : "6\\n" 1 1 Tells the program to save the tree in a tree file (outtree) (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas). params printdata Print out the data at start of run (1) perl ($value)? "1\\n" : "" 0 1 params indent_tree Indent treefile perl ($value)? " && indenttree -o outtree.indent outtree" : "" 0 1000 other_options Other options outgroup Outgroup species (default, use as outgroup species 1) (O) perl ($value && $value != $vdef)? "o\\n$value\\n" : "" 1 1 params Please enter a value greater than 0 perl $value && $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 $consense outfile.consense consense_outgroup perl "O\\n$outgroup\\n" 1000 perl $consense and $outgroup and $outgroup != 1 consense.params consense_treefile perl $consense outtree.consense