The cluster command outputs a .list , .rabund and .sabund files.
The cluster command parameter options are method, cuttoff and precision. No parameters are required.
The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).
- The acceptable methods are furthest, nearest and average. If you do not provide a method the default algorythm is furthest neighbor.
+ The acceptable methods are furthest, nearest and average. If you do not provide a method the default algorithm is furthest neighbor.
The cluster() command outputs three files *.list, *.rabund, and *.sabund. */
vector<string> setParameters();
string getCommandName() { return "cluster"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
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"; }
string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
double cutoff;
+ float adjust;
string showabund, timing;
int precision, length;
ofstream sabundFile, rabundFile, listFile;