|   | fclique | 
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After one pass through all possible cliques, the program knows the size of the largest clique, and during a second pass it prints out the cliques of the right size. It also, along with each clique, prints out the tree suggested by that clique.
The assumptions of compatibility methods have been treated in several of my papers (1978b, 1979, 1981b, 1988b), especially the 1981 paper. For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b), but also read the exchange between Felsenstein and Sober (1986).
A constant available for alteration at the beginning of the program is the form width, "FormWide", which you may want to change to make it as large as possible consistent with the page width available on your output device, so as to avoid the output of cliques and of trees getting wrapped around unnecessarily.
| % fclique Largest clique program Phylip discrete states file: clique.dat Phylip clique program output file [clique.fclique]: Output written to file "clique.fclique" Tree written on file "clique.treefile" Done. | 
Go to the input files for this example
Go to the output files for this example
| 
Largest clique program
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-infile]            discretestates Phylip discrete states file
  [-outfile]           outfile    [*.fclique] Phylip clique program output
                                  file
   Additional (Optional) qualifiers (* if not always prompted):
   -ancfile            properties Phylip ancestral states file (optional)
   -factorfile         properties Phylip multistate factors file (optional)
   -weights            properties Phylip weights file (optional)
   -cliqmin            integer    [0] Minimum clique size (Integer 0 or more)
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fclique] Phylip tree output file
                                  (optional)
   -printdata          boolean    [N] Print data at start of run
   -[no]progress       boolean    [Y] Print indications of progress of run
   -[no]treeprint      boolean    [Y] Print out tree
   -printcomp          boolean    [N] Print out compatibility matrix
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   "-outtreefile" associated qualifiers
   -odirectory         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) | discretestates | Phylip discrete states file | Discrete states file | |
| [-outfile] (Parameter 2) | outfile | Phylip clique program output file | Output file | <*>.fclique | 
| Additional (Optional) qualifiers | ||||
| -ancfile | properties | Phylip ancestral states file (optional) | Property value(s) | |
| -factorfile | properties | Phylip multistate factors file (optional) | Property value(s) | |
| -weights | properties | Phylip weights file (optional) | Property value(s) | |
| -cliqmin | integer | Minimum clique size | Integer 0 or more | 0 | 
| -outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 | 
| -[no]trout | toggle | Write out trees to tree file | Toggle value Yes/No | Yes | 
| -outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fclique | 
| -printdata | boolean | Print data at start of run | Boolean value Yes/No | No | 
| -[no]progress | boolean | Print indications of progress of run | Boolean value Yes/No | Yes | 
| -[no]treeprint | boolean | Print out tree | Boolean value Yes/No | Yes | 
| -printcomp | 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 | |
| "-outtreefile" associated outfile qualifiers | ||||
| -odirectory | 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 | 
fclique reads discrete character data with 2 states.
| 
     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110
 | 
| 
Largest clique program, version 3.69.650
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!
 | 
| (((Delta,Epsilon),Gamma),Alpha,Beta); | 
| Program name | Description | 
|---|---|
| eclique | Largest clique program | 
| edollop | Dollo and polymorphism parsimony algorithm | 
| edolpenny | Penny algorithm Dollo or polymorphism | 
| efactor | Multistate to binary recoding program | 
| emix | Mixed parsimony algorithm | 
| epenny | Penny algorithm, branch-and-bound | 
| fdollop | Dollo and polymorphism parsimony algorithm | 
| fdolpenny | Penny algorithm Dollo or polymorphism | 
| ffactor | Multistate to binary recoding program | 
| fmix | Mixed parsimony algorithm | 
| fmove | Interactive mixed method parsimony | 
| fpars | Discrete character parsimony | 
| fpenny | Penny algorithm, branch-and-bound | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.
None