                                  fdnamove



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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 (aligned) nucleotide sequence set(s): dnamove.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,  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


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

Interactive DNA parsimony
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqsetall  (Aligned) nucleotide sequence set(s)
                                  filename and optional format, or reference
                                  (input USA)
  [-intreefile]        tree       Phylip tree file (optional)

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file - ignore sites with weight zero
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -thresh             toggle     [N] Use threshold parsimony
*  -threshold          float      [1] Threshold value (Number 1.000 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    [*.fdnamove] Phylip tree output file
                                  (optional)

   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 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

   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
                    distmat      Create a distance matrix from a multiple sequence alignment
                    ednacomp     DNA compatibility algorithm
                    ednadist     Nucleic acid sequence Distance Matrix program
                    ednainvar    Nucleic acid sequence Invariants method
                    ednaml       Phylogenies from nucleic acid Maximum Likelihood
                    ednamlk      Phylogenies from nucleic acid Maximum Likelihood with 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 parsimony algorithm
                    frestboot    Bootstrapped restriction sites algorithm
                    frestdist    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.
