| ## EMBOSS: edolpenny

# Program edolpenny

## Function

Conversion of PHYLIP's dolpenny

## Description

EDOLPENNY - Branch and bound to find all most parsimonious trees for Dollo, polymorphism parsimony criteria

Phylip dolpenny documentation.

## Usage

Here is a sample session with edolpenny using the data:-

        7    6
    Alpha1    110110
    Alpha2    110110
    Beta1     110000
    Beta2     110000
    Gamma1    100110
    Delta     001001
    Epsilon   001110

    % edolpenny test

    Penny algorithm Dollo or polymorphism
    Output file [edolpenny.outfile]: stdout
    Dollo Parsimony method (else Polymorphis) [Y]:
    Create a tree file [Y]:
    Output treefile name [edolpenny.treefile]:

    Penny algorithm for Dollo or polymorphism parsimony, version 3.573c
     branch-and-bound to find all most parsimonious trees

    Dollo parsimony method

    requires a total of              3.000

        3 trees in all found

      +-----------------Delta
      !
    --2  +--------------Epsilon
      !  !
      +--3  +-----------Gamma1
         !  !
         +--6  +--------Alpha2
            !  !
            +--1     +--Beta2
               !  +--5
               +--4  +--Beta1
                  !
                  +-----Alpha1

      +-----------------Delta
      !
    --2  +--------------Epsilon
      !  !
      +--3  +-----------Gamma1
         !  !
         +--6        +--Beta2
            !  +-----5
            !  !     +--Beta1
            +--4
               !     +--Alpha2
               +-----1
                     +--Alpha1

      +-----------------Delta
      !
    --2  +--------------Epsilon
      !  !
      +--3  +-----------Gamma1
         !  !
         !  !        +--Beta2
         +--6     +--5
            !  +--4  +--Beta1
            !  !  !
            +--1  +-----Alpha2
               !
               +--------Alpha1

    % more edolpenny.treefile
    (Delta,(Epsilon,(Gamma1,(Alpha2,((Beta2,Beta1),Alpha1)))))[0.3333];
    (Delta,(Epsilon,(Gamma1,((Beta2,Beta1),(Alpha2,Alpha1)))))[0.3333];
    (Delta,(Epsilon,(Gamma1,(((Beta2,Beta1),Alpha2),Alpha1))))[0.3333];

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-datafile]          infile     data file
      [-outfile]           outfile    Output file name
      [-[no]dollo]         bool       Dollo Parsimony method (else Polymorphis)
    *  -valthresh          float      threshold value
    *  -datasets           integer    number of sets
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name

       Optional qualifiers:
       -numgroups          integer    How many groups of 100 trees
       -howoften           integer    How often to report, in trees
       -simple             bool       Branch and bound is simple
       -ancest             bool       Use ancestral states in input file
       -multsets           bool       Analyze multiple data sets
       -printdata          bool       Print out the data at start of run
       -progress           bool       Print indications of progress of run
       -steps              bool       Print out steps in each site
       -statesatnodes      bool       Print states at all nodes of tree
       -[no]drawtree       bool       Draw tree

       Advanced qualifiers:
       -thresh             bool       Use Threshold parsimony

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-datafile] (Parameter 1) | data file | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | edolpenny.outfile
[-[no]dollo] (Parameter 3) | Dollo Parsimony method (else Polymorphis) | Yes/No | Yes
-valthresh | threshold value | Number 1.000 or more | 1.0
-datasets | number of sets | Integer 2 or more | 2
[-[no]trout] (Parameter 4) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | edolpenny.treefile
Optional qualifiers | Allowed values | Default
-numgroups | How many groups of 100 trees | Any integer value | 1000
-howoften | How often to report, in trees | Any integer value | 100
-simple | Branch and bound is simple | Yes/No | No
-ancest | Use ancestral states in input file | Yes/No | No
-multsets | Analyze multiple data sets | Yes/No | No
-printdata | Print out the data at start of run | Yes/No | No
-progress | Print indications of progress of run | Yes/No | No
-steps | Print out steps in each site | Yes/No | No
-statesatnodes | Print states at all nodes of tree | Yes/No | No
-[no]drawtree | Draw tree | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-thresh | Use Threshold parsimony | Yes/No | No

## Input file format

## Output file format

## Data files

## Notes

## References

## Warnings

## Diagnostics

## Exit status

## Known bugs

## See also

## Author(s)

(c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## Priority

## Target users

## Comments