]> 3.6a2 dollop - Dollo and Polymorphism Parsimony Program &phylip_header; dollop dollop perl "dollop < params" 0 infile Input File perl "ln -s $infile infile; " -10 Example input file: 5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110 dollop_opt Dollop options dollop_method Use Polymorphism method (P) 0 perl ($value)? "P\\n" : "" 1 params The Dollo parsimony method (default value) was first suggested in print in verbal form by Le Quesne (1974) and was first well-specified by Farris (1977). It allowing up to one forward change 0-->1 and as many reversions 1-->0 as are necessary to explain the pattern of states seen. The program attempts to minimize the number of 1-->0 reversions necessary. The assumptions of this method are in effect: 1. We know which state is the ancestral one (state 0). 2. The characters are evolving independently. 3. Different lineages evolve independently. 4. The probability of a forward change (0-->1) is small over the evolutionary times involved. 5. The probability of a reversion (1-->0) is also small, but still far larger than the probability of a forward change, so that many reversions are easier to envisage than even one extra forward change. 6. Retention of polymorphism for both states (0 and 1) is highly improbable. 7. The lengths of the segments of the true tree are not so unequal that two changes in a long segment are as probable as one in a short segment. One problem can arise when using additive binary recoding to represent a multistate character as a series of two-state characters. Unlike the Camin-Sokal, Wagner, and Polymorphism methods, the Dollo method can reconstruct ancestral states which do not exist. An example is given in my 1979 paper. It will be necessary to check the output to make sure that this has not occurred. The polymorphism parsimony method was first used by me, and the results published (without a clear specification of the method) by Inger (1967). The method was independently published by Farris (1978a) and by me (1979). The method assumes that we can explain the pattern of states by no more than one origination (0-->1) of state 1, followed by retention of polymorphism along as many segments of the tree as are necessary, followed by loss of state 0 or of state 1 where necessary. The program tries to minimize the total number of polymorphic characters, where each polymorphism is counted once for each segment of the tree in which it is retained. The assumptions of the polymorphism parsimony method are in effect: 1. The ancestral state (state 0) is known in each character. 2. The characters are evolving independently of each other. 3. Different lineages are evolving independently. 4. Forward change (0-->1) is highly improbable over the length of time involved in the evolution of the group. 5. Retention of polymorphism is also improbable, but far more probable that forward change, so that we can more easily envisage much polymorhism than even one additional forward change. 6. Once state 1 is reached, reoccurrence of state 0 is very improbable, much less probable than multiple retentions of polymorphism. 7. The lengths of segments in the true tree are not so unequal that we can more easily envisage retention events occurring in both of two long segments than one retention in a short segment. That these are the assumptions of parsimony methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b), but also read the exchange between Felsenstein and Sober (1986). 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.dollop; cp outtree outtree.dollop; cp outfile outfile.dollop; mv outtree intree; consense < consense.params; cp outtree outtree.consense; cp outfile outfile.consense; mv outtree.dollop outtree; mv infile.dollop infile; mv outfile.dollop 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 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