%%% README
	by Kenji Fukumzu, The Institute of Statistical Mathematics, 
	Feb 24, 2016

This directory includes Matlab codes for clustering gene trees.  
These codes are used for generating the results in 
     "Multi-locus Phylogenetic Analysis with Gene Tree Clustering"
      by Ruriko Yoshida, Kenji Fukumizu, and Chrysafis Vogiatzis


These codes require the following toolboxes.  Download them in some directories, and set path so that they can be accessed by these codes. 

1) drtoolbox:  by van der Maaten
            https://lvdmaaten.github.io/drtoolbox/
2) Ncut_9:  by Timothee Cour, Stella Yu, Jianbo Shi
            http://www.timotheecour.com/software/ncut/ncut.html

The BHV geodesic data and Euclidean distance data must be included 
in directories, which are to be specified in the codes. 


Usage: 
There are two main functions: 

gene_clustering_EUCdata(method,ncluster)
gene_clustering_BHVdata(method,ncluster)

"method" specifies a clustering method: "Ncut", "Kmean" or "Hclust" (hierarchical clustering with average linkage). 
"ncluster" is the number of clusters.  Note; for evalutation, the current version supports only ncluster = 2 (two clusters).


The image files are generated in ResultsImg directory, and the files of cluster information are in ResltsClst.  Make these directory when you run the codes in a new directory. 




