                                   fclique



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Function

   Largest clique program

Description

   Finds the largest clique of mutually compatible characters, and the
   phylogeny which they recommend, for discrete character data with two
   states. The largest clique (or all cliques within a given size range of
   the largest one) are found by a very fast branch and bound search
   method. The method does not allow for missing data. For such cases the
   T (Threshold) option of PARS or MIX may be a useful alternative.
   Compatibility methods are particular useful when some characters are of
   poor quality and the rest of good quality, but when it is not known in
   advance which ones are which.

Algorithm

   This program uses the compatibility method for unrooted two-state
   characters to obtain the largest cliques of characters and the trees
   which they suggest. This approach originated in the work of Le Quesne
   (1969), though the algorithms were not precisely specified until the
   later work of Estabrook, Johnson, and McMorris (1976a, 1976b). These
   authors proved the theorem that a group of two-state characters which
   were pairwise compatible would be jointly compatible. This program uses
   an algorithm inspired by the Kent Fiala - George Estabrook program
   CLINCH, though closer in detail to the algorithm of Bron and Kerbosch
   (1973). I am indebted to Kent Fiala for pointing out that paper to me,
   and to David Penny for decribing to me his branch-and-bound approach to
   finding largest cliques, from which I have also borrowed. I am
   particularly grateful to Kent Fiala for catching a bug in versions 2.0
   and 2.1 which resulted in those versions failing to find all of the
   cliques which they should. The program computes a compatibility matrix
   for the characters, then uses a recursive procedure to examine all
   possible cliques of characters.

   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.

  ASSUMPTIONS

   Basically the following assumptions are made:
    1. Each character evolves independently.
    2. Different lineages evolve independently.
    3. The ancestral state is not known.
    4. Each character has a small chance of being one which evolves so
       rapidly, or is so thoroughly misinterpreted, that it provides no
       information on the tree.
    5. The probability of a single change in a character (other than in
       the high rate characters) is low but not as low as the probability
       of being one of these "bad" characters.
    6. The probability of two changes in a low-rate character is much less
       than the probability that it is a high-rate character.
    7. The true tree has segments which are not so unequal in length that
       two changes in a long are as easy to envisage as one change in a
       short segment.

   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.

Usage

   Here is a sample session with fclique


% 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

Command line arguments

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


Input file format

   Input to the algorithm is standard, but the "?", "P", and "B" states
   are not allowed. This is a serious limitation of this program. If you
   want to find large cliques in data that have "?" states, I recommend
   that you use fmix instead with the -Threshold option and the value of
   the threshold set to 2.0. The theory underlying this is given in my
   paper on character weighting (Felsenstein, 1981b).

   fclique reads discrete character data with 2 states.

  Input files for usage example

  File: clique.dat

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

Output file format

   fclique writes the cliques to the text output file and a tree to a
   separate output file

  Output files for usage example

  File: clique.fclique


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!



  File: clique.treefile

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

Data files

   None

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                    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

Author(s)

                    This program is an EMBOSS conversion of a program written by Joe
                    Felsenstein as part of his PHYLIP package.

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

                    Written (2004) - Joe Felsenstein, University of Washington.

                    Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.

Comments

None
