
                              EMBOSS: eclique
     _________________________________________________________________
   
                                Program eclique
                                       
Function

   Conversion of PHYLIP's clique
   
Description

   ECLIQUE -- Embossified Compatibility Program
   
   Phylip clique documentation.
   
Usage

   Here is a sample session with eclique using the data:-
     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110


% eclique test

Largest clique program
Output file [eclique.outfile]: stdout
Create a tree file [Y]:
Outgroup root [N]:

Largest clique program, version 3.573c




Largest Cliques
------- -------

Characters: (  1  2  3  6)


  Tree and characters:

     2  1  3  6
     0  0  1  1

             +1-Delta
       +0--1-+
  +--0-+     +--Epsilon
  !    !
  !    +--------Gamma
  !
  +-------------Alpha
  !
  +-------------Beta

remember: this is an unrooted tree!




% more eclique.treefile
(((Delta,Epsilon),Gamma),Alpha,Beta);

Command line arguments

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

   Optional qualifiers:
   -[no]drawtree       bool       Draw tree
   -ancestral          bool       Use ancestral states in input file
   -minclique          bool       Use minimum clique size
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -matrixout          bool       Print out compatibility matrix

   Advanced qualifiers:
   -treefile           outfile    tree file name
   
   Mandatory qualifiers Allowed values Default
   [-infile]
   (Parameter 1) file to read in Input file Required
   [-outfile]
   (Parameter 2) Output file name Output file eclique.outfile
   [-[no]trout]
   (Parameter 3) Create a tree file Yes/No Yes
   -cliqminnum Minimum clique size Any integer value 1
   -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
   -ancestral Use ancestral states in input file Yes/No No
   -minclique Use minimum clique size 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
   -matrixout Print out compatibility matrix Yes/No No
   Advanced qualifiers Allowed values Default
   -treefile tree file name Output file eclique.treefile
   
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
