classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index ec2f083e987e47f3125f381bd0c1199307dbdaf8..dd61a35bdcf3e45a72a590ec9b430584cc30376d 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -29,7 +29,7 @@ public:
        string getCommandCategory()             { return "Clustering";                  }
     string getOutputFileNameTag(string, string);
        string getHelpString();         
-       string getCitation() { return "Schloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6. \nhttp://www.mothur.org/wiki/Cluster.classic"; }
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
        string getDescription()         { return "cluster your sequences into OTUs using DOTUR’s method"; }
        
        int execute(); 
@@ -37,7 +37,7 @@ public:
        
 private:
        bool abort, hard, sim;
-       string method, fileroot, tag, outputDir, phylipfile, namefile;
+       string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
        double cutoff;
        int precision, length;
        ofstream sabundFile, rabundFile, listFile;