fmove

Function

Description

Algorithm

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

% 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

   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. 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

Standard (Mandatory) qualifiers		Allowed values	Default
[-infile] (Parameter 1)	File containing data set	Discrete states file
[-intreefile] (Parameter 2)	Phylip tree file (optional)	Phylogenetic tree
Additional (Optional) qualifiers		Allowed values	Default
-weights	Weights file	Property value(s)
-ancfile	Ancestral states file	Property value(s)
-factorfile	Factors file	Property value(s)
-method	Choose the method to use	w (Wagner) c (Camin-Sokal) m (Mixed)	Wagner
-outgrno	Species number to use as outgroup	Integer 0 or more	0
-threshold	Threshold value	Number 0.000 or more	$(infile.discretesize)
-initialtree	Initial tree	a (Arbitary) u (User) s (Specify)	Arbitary
-screenwidth	Width of terminal screen in characters	Any integer value	80
-screenlines	Number of lines on screen	Any integer value	24
-outtreefile	Phylip tree output file (optional)	Output file	<*>.fmove
Advanced (Unprompted) qualifiers		Allowed values	Default
(none)

Input file format

Input files for usage example

File: move.dat

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

Output file format

Output files for usage example

File: move.treefile

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

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

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

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

Target users