Phylip : dollop - Dollo and Polymorphism Parsimony Program (Felsenstein)
Some explanations about the options
Main parameters- Input File
- Example input file:
- 5 6
- Alpha 110110
- Beta 110000
- Gamma 100110
- Delta 001001
- Epsilon 001110
- enter either the name of a file or the actual data
- if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
- OR you can type your data in the next area, or cut and paste it from another application.
- (but not both)
-
Dollop options
- Use Polymorphism method (P)
- The Dollo parsimony method (default value) was firstsuggested in print in verbal form by Le Quesne (1974) and was firstwell-specified by Farris (1977). It allowing up to one forward change0-->1 and as many reversions 1-->0 as are necessary to explain thepattern of states seen. The program attempts to minimize the number of1-->0 reversions necessary. The assumptions of this method are ineffect:
- 1. We know which state is the ancestral one(state 0).
- 2. The characters are evolving independently.
- 3. Different lineages evolveindependently.
- 4. The probability of a forward change(0-->1) is small over the evolutionary times involved.
- 5. The probability of a reversion (1-->0) isalso small, but still far larger than the probability of a forwardchange, so that many reversions are easier to envisage than even oneextra forward change.
- 6. Retention of polymorphism for both states(0 and 1) is highly improbable.
- 7. The lengths of the segments of the truetree are not so unequal that two changes in a long segment are asprobable 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 states in input file (A)
- 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
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User tree options
- Use User tree (default: no, search for best tree) (U)
- 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.
- User Tree file
- Give a tree whenever the infile does not already contain the tree.
- How many tree(s) in the User Tree file
- Give this information whenever the infile does not already contain the tree.
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Output options
- Print out tree (3)
- Tells the program to print a semi-graphical picture of the tree in the outfile.
- Write out trees onto tree file (6)
- 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).
References:
Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Pise form generator version: 5.a (19 Oct 2006 12:37)