+
+ outputDir = ""; inputDir = "";
+
+ //initialize list of valid commands
+ commands["read.dist"] = "read.dist";
+ commands["read.otu"] = "read.otu";
+ commands["read.tree"] = "read.tree";
+ commands["bin.seqs"] = "bin.seqs";
+ commands["get.oturep"] = "get.oturep";
+ commands["cluster"] = "cluster";
+ commands["unique.seqs"] = "unique.seqs";
+ commands["dist.seqs"] = "dist.seqs";
+ commands["dist.shared"] = "dist.shared";
+ commands["collect.single"] = "collect.single";
+ commands["collect.shared"] = "collect.shared";
+ commands["rarefaction.single"] = "rarefaction.single";
+ commands["rarefaction.shared"] = "rarefaction.shared";
+ commands["summary.single"] = "summary.single";
+ commands["summary.shared"] = "summary.shared";
+ commands["parsimony"] = "parsimony";
+ commands["unifrac.weighted"] = "unifrac.weighted";
+ commands["unifrac.unweighted"] = "unifrac.unweighted";
+ commands["libshuff"] = "libshuff";
+ commands["tree.shared"] = "tree.shared";
+ commands["heatmap.bin"] = "heatmap.bin";
+ commands["heatmap.sim"] = "heatmap.sim";
+ commands["venn"] = "venn";
+ commands["get.group"] = "get.group";
+ commands["get.label"] = "get.label";
+ commands["get.sabund"] = "get.sabund";
+ commands["get.rabund"] = "get.rabund";
+ commands["bootstrap.shared"] = "bootstrap.shared";
+ //commands["consensus"] = "consensus";
+ commands["help"] = "help";
+ commands["filter.seqs"] = "filter.seqs";
+ commands["align.seqs"] = "align.seqs";
+ commands["summary.seqs"] = "summary.seqs";
+ commands["screen.seqs"] = "screen.seqs";
+ commands["reverse.seqs"] = "reverse.seqs";
+ commands["trim.seqs"] = "trim.seqs";
+ commands["chimera.seqs"] = "chimera.seqs";
+ commands["list.seqs"] = "list.seqs";
+ commands["get.seqs"] = "get.seqs";
+ commands["remove.seqs"] = "get.seqs";
+ commands["system"] = "system";
+ commands["align.check"] = "align.check";
+ commands["get.sharedseqs"] = "get.sharedseqs";
+ commands["get.otulist"] = "get.otulist";
+ commands["quit"] = "quit";
+ commands["hcluster"] = "hcluster";
+ commands["classify.seqs"] = "classify.seqs";
+ commands["phylotype"] = "phylotype";
+ commands["mgcluster"] = "mgcluster";
+ commands["pre.cluster"] = "pre.cluster";
+ commands["pcoa"] = "pcoa";
+ commands["otu.hierarchy"] = "otu.hierarchy";
+ commands["set.dir"] = "set.dir";
+ commands["merge.files"] = "merge.files";
+ commands["parse.list"] = "parse.list";