commands["read.dist"] = "read.dist";
commands["read.otu"] = "read.otu";
commands["read.tree"] = "read.tree";
- commands["read.seqs"] = "read.seqs";
commands["bin.seqs"] = "bin.seqs";
commands["get.oturep"] = "get.oturep";
commands["cluster"] = "cluster";
- commands["deconvolute"] = "deconvolute";
- commands["dist.seqs"] = "dist.seqs";
+ 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["unifrac.unweighted"] = "unifrac.unweighted";
commands["libshuff"] = "libshuff";
commands["tree.shared"] = "tree.shared";
- commands["heatmap"] = "heatmap";
+ 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.line"] = "get.line";
+ commands["get.sabund"] = "get.sabund";
+ commands["get.rabund"] = "get.rabund";
commands["bootstrap.shared"] = "bootstrap.shared";
commands["concensus"] = "concensus";
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["quit"] = "quit";