
                                 fdnamove 



Function

   Interactive DNA parsimony

Description

   Interactive construction of phylogenies from nucleic acid sequences,
   with their evaluation by parsimony and compatibility and the display
   of reconstructed ancestral bases. This can be used to find parsimony
   or compatibility estimates by hand.

Algorithm

   DNAMOVE is an interactive DNA parsimony program, inspired by Wayne
   Maddison and David and Wayne Maddison's marvellous program MacClade,
   which is written for Macintosh computers. DNAMOVE reads in a data set
   which is prepared in almost the same format as one for the DNA
   parsimony program DNAPARS. It allows the user to choose an initial
   tree, and displays this tree on the screen. The user can look at
   different sites and the way the nucleotide 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 sites
   are affected by changes in the tree topology.

   This program uses graphic characters that show the tree to best
   advantage on some computer systems. Its graphic characters will work
   best on MSDOS systems or MSDOS windows in Windows, and to any system
   whose screen or terminals emulate ANSI standard terminals such as old
   Digital VT100 terminals, Telnet programs, or VT100-compatible windows
   in the X windowing system. For any other screen types, (such as
   Macintosh windows) there is a generic option which does not make use
   of screen graphics characters. The program will work well in those
   cases, but the tree it displays will look a bit uglier.

   This program carries out unrooted parsimony (analogous to Wagner
   trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA
   sequences. The method of Fitch (1971) is used to count the number of
   changes of base needed on a given tree.

   The assumptions of this method are exactly analogous to those of MIX:
    1. Each site evolves independently.
    2. Different lineages evolve independently.
    3. The probability of a base substitution at a given site is small
       over the lengths of time involved in a branch of the phylogeny.
    4. The expected amounts of change in different branches of the
       phylogeny do not vary by so much that two changes in a high-rate
       branch are more probable than one change in a low-rate branch.
    5. The expected amounts of change do not vary enough among sites that
       two changes in one site are more probable than one change in
       another.

   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).

   Change from an occupied site to a deletion is counted as one change.
   Reversion from a deletion to an occupied site is allowed and is also
   counted as one change.

Usage

   Here is a sample session with fdnamove


% fdnamove 
Interactive DNA parsimony
Input sequence: dnamove.dat
Input tree file: 

 5 species,  13  sites

Computing steps needed for compatibility in sites ...


  (unrooted)                          19.0 Steps            11 sites compatible

  ,-----------5:Epsilon
--9
  !  ,--------4:Delta
  `--8
     !  ,-----3:Gamma
     `--7
        !  ,--2:Beta
        `--6
           `--1:Alpha

NEXT? (Options: R # + - S . T U W O F H J K L C ? X Q) (? for Help) Do you want
 to write out the tree to a file? (Y or N)
Tree written to file "dnamove.treefile"


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqsetall  (no help text) seqsetall value
  [-intreefile]        tree       (no help text) tree value

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file - Ignore sites with weight zero
   -outgrno            integer    Species number to use as outgroup
   -thresh             toggle     Use threshold parsimony
*  -threshold          float      Threshold value
   -initialtree        menu       Initial tree
   -screenwidth        integer    Width of terminal screen in characters
   -screenlines        integer    Number of lines on screen
   -outtreefile        outfile    Output file name

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outtreefile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) (no help text) seqsetall value Readable sets of
   sequences
   [-intreefile]
   (Parameter 2) (no help text) tree value Phylogenetic tree
   Additional (Optional) qualifiers Allowed values Default
   -weights Weights file - Ignore sites with weight zero Property
   value(s)
   -outgrno Species number to use as outgroup Integer 0 or more 0
   -thresh Use threshold parsimony Toggle value Yes/No No
   -threshold Threshold value Number 1.000 or more 1
   -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 Output file name Output file <sequence>.fdnamove
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   fdnamove reads any normal sequence USAs.

  Input files for usage example

  File: dnamove.dat

   5   13
Alpha     AACGUGGCCA AAU
Beta      AAGGUCGCCA AAC
Gamma     CAUUUCGUCA CAA
Delta     GGUAUUUCGG CCU
Epsilon   GGGAUCUCGG CCC

Output file format

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

  Output files for usage example

  File: dnamove.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
   ednacomp DNA compatibility algorithm
   ednadist Nucleic acid sequence Distance Matrix program
   ednainvar Nucleic acid sequence Invariants method
   ednaml Estimates phylogenies from nucleic acid sequence Maximum
   Likelihood
   ednamlk Estimates phylogenies from nucleic acid sequence Maximum
   Likelihood with molecular clock
   ednapars DNA parsimony algorithm
   ednapenny Penny algorithm for DNA
   eprotdist Protein distance algorithm
   eprotpars Protein parsimony algorithm
   erestml Restriction site Maximum Likelihood method
   eseqboot Bootstrapped sequences algorithm
   fdiscboot Bootstrapped discrete sites algorithm
   fdnacomp DNA compatibility algorithm
   fdnadist Nucleic acid sequence Distance Matrix program
   fdnainvar Nucleic acid sequence Invariants method
   fdnaml Estimates nucleotide phylogeny by maximum likelihood
   fdnamlk Estimates nucleotide phylogeny by maximum likelihood
   fdnapars DNA parsimony algorithm
   fdnapenny Penny algorithm for DNA
   fdolmove Interactive Dollo or Polymorphism Parsimony
   ffreqboot Bootstrapped genetic frequencies algorithm
   fproml Protein phylogeny by maximum likelihood
   fpromlk Protein phylogeny by maximum likelihood
   fprotdist Protein distance algorithm
   fprotpars Protein pasimony algorithm
   frestboot Bootstrapped restriction sites algorithm
   frestdist Computes distance matrix from restriction sites or fragments
   frestml Restriction site maximum Likelihood method
   fseqboot Bootstrapped sequences algorithm
   fseqbootall Bootstrapped sequences algorithm

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.
