eclique

Program eclique

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Function

Description

Phylip clique documentation.

Usage

% eclique Largest clique program Phylip clique program input file: clique.dat Use minimum clique size [N]: Outgroup root [N]: Phylip clique program output file [eclique.outfile]: Create a tree file [Y]: Phylip tree output file [eclique.treefile]:

Go to the input files for this example
Go to the output files for this example

Command line arguments

Largest clique program
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip clique program input file
   -minclique          toggle     [N] Use minimum clique size
*  -cliqminnum         integer    [1] Minimum clique size (Any integer value)
   -og                 toggle     [N] Outgroup root
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
  [-outfile]           outfile    [eclique.outfile] Phylip clique program
                                  output file
   -[no]trout          boolean    [Y] Create a tree file
  [-treefile]          outfile    [eclique.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -ancestral          boolean    [N] Use ancestral states in input file
   -[no]drawtree       boolean    [Y] Draw tree
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -matrixout          boolean    [N] Print out compatibility matrix

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-treefile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-infile] (Parameter 1)	infile	Phylip clique program input file	Input file	Required
-minclique	toggle	Use minimum clique size	Toggle value Yes/No	No
-cliqminnum	integer	Minimum clique size	Any integer value	1
-og	toggle	Outgroup root	Toggle value Yes/No	No
-outgnum	integer	Number of the outgroup	Integer 1 or more	1
[-outfile] (Parameter 2)	outfile	Phylip clique program output file	Output file	eclique.outfile
-[no]trout	boolean	Create a tree file	Boolean value Yes/No	Yes
[-treefile] (Parameter 3)	outfile	Phylip tree output file	Output file	eclique.treefile
Additional (Optional) qualifiers
-ancestral	boolean	Use ancestral states in input file	Boolean value Yes/No	No
-[no]drawtree	boolean	Draw tree	Boolean value Yes/No	Yes
-printdata	boolean	Print out the data at start of run	Boolean value Yes/No	No
-progress	boolean	Print indications of progress of run	Boolean value Yes/No	No
-matrixout	boolean	Print out compatibility matrix	Boolean value Yes/No	No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	Any string
"-treefile" associated outfile qualifiers
-odirectory3 -odirectory_treefile	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

Input files for usage example

File: clique.dat

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

Output files for usage example

File: eclique.outfile

Largest clique program, version 3.57c.650




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!

File: eclique.treefile

(((Delta,Epsilon),Gamma),Alpha,Beta);

Data files

Notes

Notes

References

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

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.

History

Target users

Comments

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