Please help by correcting and extending the Wiki pages.
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 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.
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 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).
% fmove Interactive mixed method parsimony Phylip character discrete states file: move.dat Phylip tree file (optional): NEXT? (R # + - S . T U W O F H J K L C ? X Q) (? for Help): Q Do you want to write out the tree to a file? (Y or N): Y 5 species, 6 characters Wagner parsimony method Computing steps needed for compatibility in characters... (unrooted) 8.0 Steps 4 chars compatible ,-----------5:Epsilon --9 ! ,--------4:Delta `--8 ! ,-----3:Gamma `--7 ! ,--2:Beta `--6 `--1:Alpha Tree written to file "move.treefile"
Go to the input files for this example
Go to the output files for this example
Interactive mixed method parsimony Version: EMBOSS:126.96.36.199 Standard (Mandatory) qualifiers: [-infile] discretestates File containing data set [-intreefile] tree Phylip tree file (optional) Additional (Optional) qualifiers: -weights properties Weights file -ancfile properties Ancestral states file -factorfile properties Factors file -method menu [Wagner] Choose the method to use (Values: w (Wagner); c (Camin-Sokal); m (Mixed)) -outgrno integer  Species number to use as outgroup (Integer 0 or more) -threshold float [$(infile.discretesize)] Threshold value (Number 0.000 or more) -initialtree menu [Arbitary] Initial tree (Values: a (Arbitary); u (User); s (Specify)) -screenwidth integer  Width of terminal screen in characters (Any integer value) -screenlines integer  Number of lines on screen (Any integer value) -outtreefile outfile [*.fmove] Phylip tree output file (optional) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outtreefile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit
|Standard (Mandatory) qualifiers|
|discretestates||File containing data set||Discrete states file|
|tree||Phylip tree file (optional)||Phylogenetic tree|
|Additional (Optional) qualifiers|
|-weights||properties||Weights file||Property value(s)|
|-ancfile||properties||Ancestral states file||Property value(s)|
|-factorfile||properties||Factors file||Property value(s)|
|-method||list||Choose the method to use||
|-outgrno||integer||Species number to use as outgroup||Integer 0 or more||0|
|-threshold||float||Threshold value||Number 0.000 or more||$(infile.discretesize)|
|-screenwidth||integer||Width of terminal screen in characters||Any integer value||80|
|-screenlines||integer||Number of lines on screen||Any integer value||24|
|-outtreefile||outfile||Phylip tree output file (optional)||Output file||<*>.fmove|
|Advanced (Unprompted) qualifiers|
|"-outtreefile" associated outfile qualifiers|
|-odirectory||string||Output directory||Any string|
|-auto||boolean||Turn off prompts||Boolean value Yes/No||N|
|-stdout||boolean||Write first file to standard output||Boolean value Yes/No||N|
|-filter||boolean||Read first file from standard input, write first file to standard output||Boolean value Yes/No||N|
|-options||boolean||Prompt for standard and additional values||Boolean value Yes/No||N|
|-debug||boolean||Write debug output to program.dbg||Boolean value Yes/No||N|
|-verbose||boolean||Report some/full command line options||Boolean value Yes/No||Y|
|-help||boolean||Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose||Boolean value Yes/No||N|
|-warning||boolean||Report warnings||Boolean value Yes/No||Y|
|-error||boolean||Report errors||Boolean value Yes/No||Y|
|-fatal||boolean||Report fatal errors||Boolean value Yes/No||Y|
|-die||boolean||Report dying program messages||Boolean value Yes/No||Y|
|-version||boolean||Report version number and exit||Boolean value Yes/No||N|
5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110
|eclique||Largest clique program|
|edollop||Dollo and polymorphism parsimony algorithm|
|edolpenny||Penny algorithm Dollo or polymorphism|
|efactor||Multistate to binary recoding program|
|emix||Mixed parsimony algorithm|
|epenny||Penny algorithm, branch-and-bound|
|fclique||Largest clique program|
|fdollop||Dollo and polymorphism parsimony algorithm|
|fdolpenny||Penny algorithm Dollo or polymorphism|
|ffactor||Multistate to binary recoding program|
|fmix||Mixed parsimony algorithm|
|fpars||Discrete character parsimony|
|fpenny||Penny algorithm, branch-and-bound|
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.