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

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

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.