EMBOSS: ednapenny

| ## EMBOSS: ednapenny

# Program ednapenny

## Function

Conversion of PHYLIP's dnapenny

## Description

EDNAPENNY - Branch and bound to find all most parsimonious trees for nucleic acid sequence parsimony criteria

Phylip dnapenny documentation.

## Usage

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

        8    6
    Alpha1    AAGAAG
    Alpha2    AAGAAG
    Beta1     AAGGGG
    Beta2     AAGGGG
    Gamma1    AGGAAG
    Gamma2    AGGAAG
    Delta     GGAGGA
    Epsilon   GGAAAG

    % ednapenny test

    Penny algorithm for DNA
    Output file [ednapenny.outfile]: stdout
    Create a tree file [Y]:
    Output treefile name [ednapenny.treefile]:

    Penny algorithm for DNA, version 3.573c
     branch-and-bound to find all most parsimonious trees

    requires a total of              8.000

         9 trees in all found

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
      !           +--7  +--Epsilon
    --1           !  !
      !     +-----6  +-----Gamma2
      !     !     !
      !  +--4     +--------Gamma1
      !  !  !
      !  !  !           +--Beta2
      +--2  +-----------5
         !              +--Beta1
         !
         +-----------------Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !           +-----3
      !           !     +--Epsilon
    --1     +-----6
      !     !     !     +--Gamma2
      !     !     +-----7
      !  +--4           +--Gamma1
      !  !  !
      !  !  !           +--Beta2
      +--2  +-----------5
         !              +--Beta1
         !
         +-----------------Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
      !           +--6  +--Epsilon
    --1           !  !
      !     +-----7  +-----Gamma1
      !     !     !
      !  +--4     +--------Gamma2
      !  !  !
      !  !  !           +--Beta2
      +--2  +-----------5
         !              +--Beta1
         !
         +-----------------Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
    --1           +--7  +--Epsilon
      !           !  !
      !  +--------6  +-----Gamma2
      !  !        !
      !  !        +--------Gamma1
      +--2
         !              +--Beta2
         !           +--5
         +-----------4  +--Beta1
                     !
                     +-----Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !           +-----3
    --1           !     +--Epsilon
      !  +--------6
      !  !        !     +--Gamma2
      !  !        +-----7
      +--2              +--Gamma1
         !
         !              +--Beta2
         !           +--5
         +-----------4  +--Beta1
                     !
                     +-----Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
    --1           +--6  +--Epsilon
      !           !  !
      !  +--------7  +-----Gamma1
      !  !        !
      !  !        +--------Gamma2
      +--2
         !              +--Beta2
         !           +--5
         +-----------4  +--Beta1
                     !
                     +-----Alpha2

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
      !           +--7  +--Epsilon
    --1           !  !
      !        +--6  +-----Gamma2
      !        !  !
      !  +-----2  +--------Gamma1
      !  !     !
      +--4     +-----------Alpha2
         !
         !              +--Beta2
         +--------------5
                        +--Beta1

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !           +-----3
      !           !     +--Epsilon
    --1        +--6
      !        !  !     +--Gamma2
      !  +-----2  +-----7
      !  !     !        +--Gamma1
      !  !     !
      +--4     +-----------Alpha2
         !
         !              +--Beta2
         +--------------5
                        +--Beta1

      remember: this is an unrooted tree!

      +--------------------Alpha1
      !
      !                 +--Delta
      !              +--3
      !           +--6  +--Epsilon
    --1           !  !
      !        +--7  +-----Gamma1
      !        !  !
      !  +-----2  +--------Gamma2
      !  !     !
      +--4     +-----------Alpha2
         !
         !              +--Beta2
         +--------------5
                        +--Beta1

      remember: this is an unrooted tree!

    % more ednapenny.treefile
    (Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),(Beta2,Beta1)),Alpha2))[0.1111];
    (Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),(Beta2,Beta1)),Alpha2))[0.1111];
    (Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),(Beta2,Beta1)),Alpha2))[0.1111];
    (Alpha1,((((Delta,Epsilon),Gamma2),Gamma1),((Beta2,Beta1),Alpha2)))[0.1111];
    (Alpha1,(((Delta,Epsilon),(Gamma2,Gamma1)),((Beta2,Beta1),Alpha2)))[0.1111];
    (Alpha1,((((Delta,Epsilon),Gamma1),Gamma2),((Beta2,Beta1),Alpha2)))[0.1111];
    (Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),Alpha2),(Beta2,Beta1)))[0.1111];
    (Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),Alpha2),(Beta2,Beta1)))[0.1111];
    (Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),Alpha2),(Beta2,Beta1)))[0.1111];

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-msf]               seqset     File containing a sequence
      [-outfile]           outfile    Output file name
    *  -outgnum            integer    number of the outgroup
    *  -valthresh          float      threshold value
      [-[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
       -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
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence | Readable sequences | Required
[-outfile] (Parameter 2) | Output file name | Output file | ednapenny.outfile
-outgnum | number of the outgroup | Integer 1 or more | 1
-valthresh | threshold value | Number 1.000 or more | 1.0
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | ednapenny.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
-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