                                    fmove



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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


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.
