
                             EMBOSS: econsense
     _________________________________________________________________
   
                               Program econsense
                                       
Function

   Conversion of PHYLIP's consense
   
Description

   ECONSENSE -- Embossified consensus tree program
   
   Phylip consense documentation.
   
Usage

   Here is a sample session with econsense using the test data :-
(A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
(A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
(A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
(A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
(A,(B,(E,(G,((F,I),(((J,H),D),C))))));
(A,(B,(E,((F,I),(G,((J,(H,D)),C))))));
(A,(B,(E,((F,I),(G,(((J,H),D),C))))));
(A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));
(A,(B,(E,((G,(F,I)),(((J,H),D),C)))));

% econsense test
Majority-rule and strict consensus tree
Output file [econsense.outfile]: stdout
Create a tree file [Y]:
tree file [econsense.treefile]:

Majority-rule and strict consensus tree program, version 3.573c


Species in order:

  A
  B
  H
  D
  J
  G
  E
  F
  I
  C


Sets included in the consensus tree

Set (species in order)     How many times out of   9.00

.......**.                   9.00
..********                   9.00
..***....*                   6.00
..****.***                   6.00
..***.....                   6.00
..*.*.....                   4.00
..***..***                   2.00


Sets NOT included in consensus tree:

Set (species in order)     How many times out of   9.00

.....**...                   3.00
.....****.                   3.00
..**......                   3.00
.....*****                   3.00
..*.******                   2.00
.....*.**.                   2.00
..****...*                   2.00
....******                   2.00
...*******                   1.00


CONSENSUS TREE:
the numbers at the forks indicate the number
of times the group consisting of the species
which are to the right of that fork occurred
among the trees, out of   9.00 trees

  +---------------------------------------A
  !
  !         +-----------------------------E
  !         !
  !         !                        +----I
  !         !         +------------9.0
  !         !         !              +----F
  !    +--9.0         !
  !    !    !    +--2.0         +---------D
  !    !    !    !    !    +--6.0
  !    !    !    !    !    !    !    +----J
  !    !    !    !    +--6.0    +--4.0
  +--9.0    +--6.0         !         +----H
       !         !         !
       !         !         +--------------C
       !         !
       !         +------------------------G
       !
       +----------------------------------B


  remember: this is an unrooted tree!



% more econsense.treefile
(A:9.0,((E:9.0,(((I:9.0,F:9.0):9.0,((D:9.0,(J:9.0,H:9.0):4.0):6.0,C:9.0):6.0):2
.0,G:9.0):6.0):9.0,
B:9.0):9.0);

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-infile]            infile     file to read in (New Hampshire standard
                                  form)
  [-outfile]           outfile    Output file name
  [-[no]trout]         bool       Create a tree file
  [-treefile]          outfile    tree file name
*  -og                 bool       Outgroup root
*  -outgnum            integer    number of the outgroup

   Optional qualifiers:
   -[no]drawtree       bool       Draw tree
   -root               bool       Trees to be treated as Rooted
   -progress           bool       Print indications of progress of run
   -[no]printsets      bool       Print out the sets of species

   Advanced qualifiers: (none)
   
   Mandatory qualifiers Allowed values Default
   [-infile]
   (Parameter 1) file to read in (New Hampshire standard form) Input file
   Required
   [-outfile]
   (Parameter 2) Output file name Output file econsense.outfile
   [-[no]trout]
   (Parameter 3) Create a tree file Yes/No Yes
   [-treefile]
   (Parameter 4) tree file name Output file econsense.treefile
   -og Outgroup root Yes/No No
   -outgnum number of the outgroup Integer 1 or more 1
   Optional qualifiers Allowed values Default
   -[no]drawtree Draw tree Yes/No Yes
   -root Trees to be treated as Rooted Yes/No No
   -progress Print indications of progress of run Yes/No No
   -[no]printsets Print out the sets of species Yes/No Yes
   Advanced qualifiers Allowed values Default
   (none)
   
Input file

   Must be in New Hampshire standard form.
   
Data files

Notes

   Multiple sequences sets not implemented yet!.
   
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
