© Copyright 1986-2008 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.
Move is an interactive parsimony program, inspired by Wayne Maddison and David Maddison's marvellous program MacClade, which was written for Macintosh computers. Move reads in a data set which is prepared in almost the same format as one for the mixed method parsimony program Mix. 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 MSDOS 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 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 Mix.
The user interaction starts with the program presenting a menu. The menu looks like this:
Interactive mixed parsimony algorithm, version 3.69 Settings for this run: X Use Mixed method? No P Parsimony method? Wagner A Use ancestral states? No F Use factors information? No O Outgroup root? No, use as outgroup species 1 W Sites weighted? No T Use Threshold parsimony? No, use ordinary parsimony U Initial tree (arbitrary, user, specify)? Arbitrary 0 Graphics type (IBM PC, ANSI, none)? ANSI S Width of terminal screen? 80 L Number of lines on screen? 24 Are these settings correct? (type Y or the letter for one to change)
The P (Parsimony method) option selects among Wagner parsimony and Camin-Sokal parsimony. If X (miXed methods) is selected the P menu item disappears, as it is then irrelevant.
The X (miXed methods), A (Ancestors), F (Factors), O (Outgroup), T (Threshold), 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 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 T (threshold) option allows a continuum of methods between parsimony and compatibility. 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!
The usual W (Weights) option is available in Move. 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 F (Factors) option is available in this program. It is only 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 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:
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".
Move uses as its numerical criterion the Wagner and Camin-Sokal parsimony methods in mixture, where each character can have its method specified separately. The program defaults to carrying out Wagner parsimony.
The Camin-Sokal parsimony method explains the data by assuming that changes 0 --> 1 are allowed but not changes 1 --> 0. Wagner parsimony allows both kinds of changes. (This is under the assumption that 0 is the ancestral state, though the program allows reassignment of the ancestral state, in which case we must reverse the state numbers 0 and 1 throughout this discussion). The criterion is to find the tree which requires the minimum number of changes. The Camin- Sokal method is due to Camin and Sokal (1965) and the Wagner method to Eck and Dayhoff (1966) and to Kluge and Farris (1969).
Here are the assumptions of these two methods:
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