X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;h=817c4a3290804405bd47582d9b3ec5349c182b43;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=702fd7e14cb80dc57fd62cb0a738bdf3c6fd2bbd;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
index 702fd7e..817c4a3 100644
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -30,8 +30,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "clearcut";			}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	
 	string getHelpString();	
-	string getCitation() { return "The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. http://www.mothur.org/wiki/Clearcut"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
+	string getDescription()		{ return "create a tree from a fasta or phylip file"; }
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }