fmove

 

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

Interactive mixed method parsimony

Description

Interactive construction of phylogenies from discrete character data with two states (0 and 1). Evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree. This can be used to find parsimony or compatibility estimates by hand.

Algorithm

MOVE is an interactive parsimony program, inspired by Wayne Maddison and David Maddison's marvellous program MacClade, which is written for Apple 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 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:

  1. Ancestral states are known (Camin-Sokal) or unknown (Wagner).
  2. Different characters evolve independently.
  3. Different lineages evolve independently.
  4. Changes 0 --> 1 are much more probable than changes 1 --> 0 (Camin-Sokal) or equally probable (Wagner).
  5. Both of these kinds of changes are a priori improbable over the evolutionary time spans involved in the differentiation of the group in question.
  6. Other kinds of evolutionary event such as retention of polymorphism are far less probable than 0 --> 1 changes.
  7. Rates of evolution in different lineages are sufficiently low that two changes in a long segment of the tree are far less probable than one change 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).

Usage

Here is a sample session with fmove 


% 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

Command line arguments 

Interactive mixed method parsimony
Version: EMBOSS:6.2.0

   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
w (Wagner)
c (Camin-Sokal)
m (Mixed)
 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
a (Arbitary)
u (User)
s (Specify)
 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

Input file format

The fmove input data file is set up almost identically to the data files for MIX.

Input files for usage example

File: move.dat

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

fmove outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: move.treefile

(Epsilon,(Delta,(Gamma,(Beta,Alpha))));

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

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

Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

History

Written (2004) - Joe Felsenstein, University of Washington.

Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.