
                                 fdolmove 



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
Input file: dolmove.dat
Input tree file: 


Interactive Dollo or polymorphism parsimony, version 3.6b

 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

NEXT? (Options: R # + - S . T U W O F H J K L C ? X Q) (? for Help) NEXT? (Opti
ons: R # + - S . T U W O F H J K L C ? X Q) (? for Help) Do you want to write o
ut the tree to a file? (Y or N)
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

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing data set
  [-intreefile]        tree       (no help text) tree value

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -ancfile            properties Ancestral states file
   -factorfile         properties Factors file
   -method             menu       Parsimony method
   -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:

   "-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
   [-infile]
   (Parameter 1) File containing data set Discrete states file
   [-intreefile]
   (Parameter 2) (no help text) tree value 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 Parsimony method
   d (Dollo)
   p (Polymorphism)
   d
   -thresh Use threshold parsimony Toggle value Yes/No No
   -threshold Threshold value Number 0.000 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>.fdolmove
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

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
   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
   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 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.
