The Maximum Compatibility Problem
---------------------------------

We describe the reconstruction of a phylogeny for a set of taxa (taxonomic
units), in the language of lparse (Version 1.0.13) as in 

 "Character-based cladistics and answer set programming," 
 by D. R. Brooks, E. Erdem, J. W. Minett, and D. Ringe, 
 in Proc. of PADL'05, 2005.

In the file cladistics-basic.tar.gz you will find the following files:

	Alcataenia  Chinese  Indo-European  README  phylogeny.lp

The file phylogeny.lp describes the reconstruction of a phylogeny for a 
given set of taxa (taxonomic units). The files Alcataenia, Chinese, and
Indo-European describe the preprocessed datasets for 9 Alcataenia species, 
7 Chinese dialects, and 24 Indo-European languages respectively. 

With these files, we can generate phylogenies with at most n incompatible 
characters, for Chinese dialects, Indo-European languages, and Alcataenia 
species, using cmodels (with zchaff). For instance, a phylogeny for Chinese 
dialects, with at most 6 incompatible characters, can be generated by the 
command

   	lparse -d none -c n=6 Chinese phylogeny.lp | cmodels -zc .

The results for each dataset are summarized in Sections 6--8. 
