
                               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
