EMBOSS: epenny

| ## EMBOSS: epenny

# Program epenny

## Function

Conversion of PHYLIP's penny

## Description

EPENNY - Embossified branch and bound to find all most parsimonious trees

Phylip penny documentation.

## Usage

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

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

    % epenny test

    Penny algorithm, branch-and-bound to find all most parsimonious trees
    Output file [epenny.outfile]: stdout
    Method
           Wag : Wagner
           Cam : Camin-Sokal
           Mix : Mixed
        prompt : "Choose the method to use
    -method : enter list value [Wag]:
    Create a tree file [Y]:
    Output treefile name [epenny.treefile]:

    Wagner parsimony method

    requires a total of              8.000

        3 trees in all found

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

      remember: this is an unrooted tree!

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

      remember: this is an unrooted tree!

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

      remember: this is an unrooted tree!

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

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-infile]            infile     data file
      [-outfile]           outfile    Output file name
       -method             list       (no help text) list value
    *  -outgnum            integer    number of the outgroup
    *  -valthresh          float      threshold value
    *  -datasets           integer    How many data 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
       -og                 bool       Outgroup root
       -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
       -seqatnodes         bool       Print sequences at all nodes of tree
       -[no]drawtree       bool       Draw tree

       Advanced qualifiers:
       -thresh             bool       Use Threshold parsimony

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | data file | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | epenny.outfile
-method | (no help text) list value |
Wag | (Wagner)
Cam | (Camin-Sokal)
Mix | (Mixed)
prompt | ("Choose the method to use)
| Wag
-outgnum | number of the outgroup | Integer 1 or more | 1
-valthresh | threshold value | Number 1.000 or more | 1.0
-datasets | How many data sets | Any integer value | 0
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | epenny.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
-og | Outgroup root | 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
-seqatnodes | Print sequences 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