CLIQUE

CLIQUE 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. Part of Phylip package.

Manual: http://evolution.genetics.washington.edu/phylip/doc/clique.html

Test Data Set

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

Test Output (with all numerical options on)

Largest clique program, version 3.6

 5 species,   6  characters
Species  Character states
-------  --------- ------
Alpha       11011 0
Beta        11000 0
Gamma       10011 0
Delta       00100 1
Epsilon     00111 0

Character Compatibility Matrix (1 if compatible)
--------- ------------- ------ -- -- -----------

                     111..1
                     111..1
                     111..1
                     ...111
                     ...111
                     111111


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!