© Copyright 1986-2006 by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.
Dolmove is an interactive parsimony program which uses the Dollo and Polymorphism parsimony criteria. It is inspired on Wayne Maddison and David Maddison's marvellous program MacClade, which is written for Apple MacIntosh computers. Dolmove reads in a data set which is prepared in almost the same format as one for the Dollo and polymorhism parsimony program Dollop. It allows the user to choose an initial tree, and displays this tree on the screen. The user can look at different characters and the way their states are distributed on that tree, given the most parsimonious reconstruction of state changes for that particular tree. The user then can specify how the tree is to be rearraranged, rerooted or written out to a file. By looking at different rearrangements of the tree the user can manually search for the most parsimonious tree, and can get a feel for how different characters are affected by changes in the tree topology.
This program is compatible with fewer computer systems than the other programs in PHYLIP. It can be adapted to PCDOS systems or to any system whose screen or terminals emulate DEC VT100 terminals (such as Telnet programs for logging in to remote computers over a TCP/IP network, VT100-compatible windows in the X windowing system, and any terminal compatible with ANSI standard terminals). For any other screen types, there is a generic option which does not make use of screen graphics characters to display the character states. This will be less effective, as the states will be less easy to see when displayed.
The input data file is set up almost identically to the data files for Dollop.
The user interaction starts with the program presenting a menu. The menu looks like this:
Interactive Dollo or polymorphism parsimony, version 3.6 Settings for this run: P Parsimony method? Dollo A Use ancestral states? No F Use factors information? No W Sites weighted? No T Use Threshold parsimony? No, use ordinary parsimony A Use ancestral states in input file? No U Initial tree (arbitrary, user, specify)? Arbitrary 0 Graphics type (IBM PC, ANSI, none)? ANSI L Number of lines on screen? 24 S Width of terminal screen? 80 Are these settings correct? (type Y or the letter for one to change)
The P (Parsimony Method) option is the one that toggles between polymorphism parsimony and Dollo parsimony. The program defaults to Dollo parsimony.
The T (Threshold), F (Factors), A (Ancestors), and 0 (Graphics type) options are the usual ones and are described in the main documentation page and in the Discrete Characters Program documentation page.
The F (Factors) option is used to inform the program which groups of characters are to be counted together in computing the number of characters compatible with the tree. Thus if three binary characters are all factors of the same multistate character, the multistate character will be counted as compatible with the tree only if all three factors are compatible with it.
The X (Mixed Methods option is not available in Dolmove.
The usual W (Weights) option is available in Dolmove. It allows integer weights up to 36, using the symbols 0-9 and A-Z. Increased weight on a step increases both the number of parsimony steps on the character and the contribution it makes to the number of compatibilities.
The T (threshold) option allows a continuum of methods between parsimony and compatibility. Thresholds less than or equal to 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!
The U (initial tree) option allows the user to choose whether the initial tree is to be arbitrary, interactively specified by the user, or read from a tree file. Typing U causes the program to change among the three possibilities in turn. I would recommend that for a first run, you allow the tree to be set up arbitrarily (the default), as the "specify" choice is difficult to use and the "user tree" choice requires that you have available a tree file with the tree topology of the initial tree. Its default name is intree. The program will ask you for its name if it looks for the input tree file and does not find one of this name. If you wish to set up some particular tree you can also do that by the rearrangement commands specified below.
The S (Screen width) option allows the width in characters of the display to be adjusted when more then 80 characters can be displayed on the user's screen.
The L (screen Lines) option allows the user to change the height of the screen (in lines of characters) that is assumed to be available on the display. This may be particularly helpful when displaying large trees on terminals that have more than 24 lines per screen, or on workstation or X-terminal screens that can emulate the ANSI terminals with more than 24 lines.
After the initial menu is displayed and the choices are made, the program then sets up an initial tree and displays it. Below it will be a one-line menu of possible commands, which looks like this:
NEXT? (Options: R # + - S . T U W O F C H ? X Q) (H or ? for Help)
If you type H or ? you will get a single screen showing a description of each of these commands in a few words. Here are slightly more detailed descriptions:
If the A option is used, then the program will infer, for any character whose ancestral state is unknown ("?") whether the ancestral state 0 or 1 will give the fewest changes (according to the criterion in use). If these are tied, then it may not be possible for the program to infer the state in the internal nodes, and many of these will be shown as "?". If the A option is not used, then the program will assume 0 as the ancestral state.
When reconstructing the placement of forward changes and reversions under the Dollo method, keep in mind that each polymorphic state in the input data will require one "last minute" reversion. This is included in the counts. Thus if we have both states 0 and 1 at a tip of the tree the program will assume that the lineage had state 1 up to the last minute, and then state 0 arose in that population by reversion, without loss of state 1.
When Dolmove calculates the number of characters compatible with the tree, it will take the F option into account and count the multistate characters as units, counting a character as compatible with the tree only when all of the binary characters corresponding to it are compatible with the tree.
As we have seen, the initial menu of the program allows you to choose among three screen types (PCDOS, Ansi, and none). If you want to avoid having to make this choice every time, you can change some of the constants in the file phylip.h to have the terminal type initialize itself in the proper way, and recompile. We have tried to have the default values be correct for PC, Macintosh, and Unix screens. If the setting is "none" (which is necessary on Macintosh MacOS 9 screens), the special graphics characters will not be used to indicate nucleotide states, but only letters will be used for the four nucleotides. This is less easy to look at.
The constants that need attention are ANSICRT and IBMCRT. Currently these are both set to "false" on Macintosh MacOS 9 systems, to "true" on MacOS X and on Unix/Linux systems, and IBMCRT is set to "true" on Windows systems. If your system has an ANSI compatible terminal, you might want to find the definition of ANSICRT in phylip.h and set it to "true", and IBMCRT to "false".
Dolmove uses as its numerical criterion the Dollo and polymorphism parsimony methods. The program defaults to carrying out Dollo parsimony.
The Dollo parsimony method was first suggested in print in verbal form by Le Quesne (1974) and was first well-specified by Farris (1977). The method is named after Louis Dollo since he was one of the first to assert that in evolution it is harder to gain a complex feature than to lose it. The algorithm explains the presence of the state 1 by 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:
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 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:
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).
Below is a test data set, but we cannot show the output it generates because of the interactive nature of the program.
5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110