EMBOSS: fdolmove

| 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 3.69.650

     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:6.6.0.0

       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))
       -dothreshold        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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-infile] (Parameter 1) | discretestates | File containing data set | Discrete states file |
[-intreefile] (Parameter 2) | tree | Phylip tree file (optional) | Phylogenetic tree |
Additional (Optional) qualifiers
-weights | properties | Weights file | Property value(s) |
-ancfile | properties | Ancestral states file | Property value(s) |
-factorfile | properties | Factors file | Property value(s) |
-method | list | Parsimony method |
d | (Dollo)
p | (Polymorphism)
| d
-dothreshold | toggle | Use threshold parsimony | Toggle value Yes/No | No
-threshold | float | Threshold value | Number 0.000 or more | 1
-initialtree | list | Initial tree |
a | (Arbitary)
u | (User)
s | (Specify)
| Arbitary
-screenwidth | integer | Width of terminal screen in characters | Any integer value | 80
-screenlines | integer | Number of lines on screen | Any integer value | 24
-outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fdolmove
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outtreefile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 | Estimate 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 | Calculate 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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) 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.

## Comments

    None