|   | fmove | 
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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:6.6.0.0
   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    [0] 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    [80] Width of terminal screen in characters
                                  (Any integer value)
   -screenlines        integer    [24] 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
 | 
| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-infile] (Parameter 1) | discretestates | File containing data set | Discrete states file | |||||||
| [-intreefile] (Parameter 2) | 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 | 
 | Wagner | ||||||
| -outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 | ||||||
| -threshold | float | Threshold value | Number 0.000 or more | $(infile.discretesize) | ||||||
| -initialtree | list | Initial tree | 
 | Arbitary | ||||||
| -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 | ||||||||||
| (none) | ||||||||||
| Associated qualifiers | ||||||||||
| "-outtreefile" associated outfile qualifiers | ||||||||||
| -odirectory | string | Output directory | Any string | |||||||
| General qualifiers | ||||||||||
| -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
 | 
| (Epsilon,(Delta,(Gamma,(Beta,Alpha)))); | 
| Program name | Description | 
|---|---|
| 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.
None