                                  fdolmove



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Function

   Interactive Dollo or Polymorphism Parsimony

Description

   Interactive construction of phylogenies from discrete character data
   with two states (0 and 1) using the Dollo or polymorphism parsimony
   criteria. 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

   DOLMOVE is an interactive parsimony program which uses the Dollo and
   Polymorphism parsimony criteria. It is inspired on Wayne Maddison and
   David Maddison's marvellous program MacClade, which is written for
   Apple MacIntosh computers. DOLMOVE reads in a data set which is
   prepared in almost the same format as one for the Dollo and polymorhism
   parsimony program DOLLOP. 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 PCDOS 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.

Usage

   Here is a sample session with fdolmove


% fdolmove
Interactive Dollo or Polymorphism Parsimony
Phylip character discrete states file: dolmove.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


Interactive Dollo or polymorphism parsimony, version 3.69

 5 species,   6 characters


Computing steps needed for compatibility in sites ...


(unrooted)                           5.0 Steps             4 chars compatible
Dollo
  ,-----------5:Epsilon
--9
  !  ,--------4:Delta
  `--8
     !  ,-----3:Gamma
     `--7
        !  ,--2:Beta
        `--6
           `--1:Alpha


Tree written to file "dolmove.treefile"



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

Command line arguments

Interactive Dollo or Polymorphism Parsimony
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing data set
  [-intreefile]        tree       Phylip tree file (optional)

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -ancfile            properties Ancestral states file
   -factorfile         properties Factors file
   -method             menu       [d] Parsimony method (Values: d (Dollo); p
                                  (Polymorphism))
   -thresh             toggle     [N] Use threshold parsimony
*  -threshold          float      [1] 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    [*.fdolmove] 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

   fdolmove reads discrete character data with "?", "P", "B" states
   allowed. .

  (0,1) Discrete character data

   These programs are intended for the use of morphological systematists
   who are dealing with discrete characters, or by molecular evolutionists
   dealing with presence-absence data on restriction sites. One of the
   programs (PARS) allows multistate characters, with up to 8 states, plus
   the unknown state symbol "?". For the others, the characters are
   assumed to be coded into a series of (0,1) two-state characters. For
   most of the programs there are two other states possible, "P", which
   stands for the state of Polymorphism for both states (0 and 1), and
   "?", which stands for the state of ignorance: it is the state
   "unknown", or "does not apply". The state "P" can also be denoted by
   "B", for "both".

   There is a method invented by Sokal and Sneath (1963) for linear
   sequences of character states, and fully developed for branching
   sequences of character states by Kluge and Farris (1969) for recoding a
   multistate character into a series of two-state (0,1) characters.
   Suppose we had a character with four states whose character-state tree
   had the rooted form:

               1 ---> 0 ---> 2
                      |
                      |
                      V
                      3


   so that 1 is the ancestral state and 0, 2 and 3 derived states. We can
   represent this as three two-state characters:

                Old State           New States
                --- -----           --- ------
                    0                  001
                    1                  000
                    2                  011
                    3                  101


   The three new states correspond to the three arrows in the above
   character state tree. Possession of one of the new states corresponds
   to whether or not the old state had that arrow in its ancestry. Thus
   the first new state corresponds to the bottommost arrow, which only
   state 3 has in its ancestry, the second state to the rightmost of the
   top arrows, and the third state to the leftmost top arrow. This coding
   will guarantee that the number of times that states arise on the tree
   (in programs MIX, MOVE, PENNY and BOOT) or the number of polymorphic
   states in a tree segment (in the Polymorphism option of DOLLOP,
   DOLMOVE, DOLPENNY and DOLBOOT) will correctly correspond to what would
   have been the case had our programs been able to take multistate
   characters into account. Although I have shown the above character
   state tree as rooted, the recoding method works equally well on
   unrooted multistate characters as long as the connections between the
   states are known and contain no loops.

   However, in the default option of programs DOLLOP, DOLMOVE, DOLPENNY
   and DOLBOOT the multistate recoding does not necessarily work properly,
   as it may lead the program to reconstruct nonexistent state
   combinations such as 010. An example of this problem is given in my
   paper on alternative phylogenetic methods (1979).

   If you have multistate character data where the states are connected in
   a branching "character state tree" you may want to do the binary
   recoding yourself. Thanks to Christopher Meacham, the package contains
   a program, FACTOR, which will do the recoding itself. For details see
   the documentation file for FACTOR.

   We now also have the program PARS, which can do parsimony for unordered
   character states.

  Input files for usage example

  File: dolmove.dat

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

Output file format

   fdolmove output:

   If the A option is used, then the program will infer, for any character
   whose ancestral state is unknown ("?") whether the ancestral state 0 or
   1 will give the fewest changes (according to the criterion in use). If
   these are tied, then it may not be possible for the program to infer
   the state in the internal nodes, and many of these will be shown as
   "?". If the A option is not used, then the program will assume 0 as the
   ancestral state.

   When reconstructing the placement of forward changes and reversions
   under the Dollo method, keep in mind that each polymorphic state in the
   input data will require one "last minute" reversion. This is included
   in the counts. Thus if we have both states 0 and 1 at a tip of the tree
   the program will assume that the lineage had state 1 up to the last
   minute, and then state 0 arose in that population by reversion, without
   loss of state 1.

   When DOLMOVE calculates the number of characters compatible with the
   tree, it will take the F option into account and count the multistate
   characters as units, counting a character as compatible with the tree
   only when all of the binary characters corresponding to it are
   compatible with the tree.

  Output files for usage example

  File: dolmove.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
                    fdnamove     Interactive DNA parsimony
                    fdnapars     DNA parsimony algorithm
                    fdnapenny    Penny algorithm for DNA
                    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.
