+ string parsimonyArray[] = {"random","groups","iters"};
+ commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
+
+ string unifracWeightedArray[] = {"groups","iters"};
+ commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
+
+ string unifracUnweightedArray[] = {"groups","iters"};
+ commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
+
+ string heatmapArray[] = {"groups","line","label","sorted","scale"};
+ commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
+ string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
+ commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
+
+ string summaryseqsArray[] = {"fasta"};
+ commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
+
+ string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+ commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
+
+ string reverseseqsArray[] = {"fasta"};
+ commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
+
+ string trimseqsArray[] = {"fasta", "flip", "oligos", "forward", "reverse", "barcode"};
+ commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
+
+ string vennArray[] = {"groups","line","label","calc"};
+ commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
+
+ string binseqsArray[] = {"fasta","line","label","name", "group"};
+ commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
+
+ string distsharedArray[] = {"line","label","calc","groups"};
+ commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
+
+ string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
+ commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
+
+ string treeGroupsArray[] = {"line","label","calc","groups", "phylip", "column", "name"};
+ commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
+
+ string bootstrapArray[] = {"line","label","calc","groups","iters"};
+ commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
+
+ string concensusArray[] = {};
+ commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
+
+ string distanceArray[] = {"fasta", "calc", "countends", "cutoff", "processors"};
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+ commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
+