commands["get.oturep"] = "get.oturep";
commands["cluster"] = "cluster";
commands["deconvolute"] = "deconvolute";
+ commands["dist.seqs"] = "dist.seqs";
+ commands["dist.shared"] = "dist.shared"; //matrix output
commands["collect.single"] = "collect.single";
commands["collect.shared"] = "collect.shared";
commands["rarefaction.single"] = "rarefaction.single";
commands["unifrac.weighted"] = "unifrac.weighted";
commands["unifrac.unweighted"] = "unifrac.unweighted";
commands["libshuff"] = "libshuff";
- commands["tree.groups"] = "tree.groups";
+ commands["tree.shared"] = "tree.shared";
commands["heatmap"] = "heatmap";
commands["venn"] = "venn";
commands["get.group"] = "get.group";
commands["get.label"] = "get.label";
commands["get.line"] = "get.line";
+ commands["bootstrap.shared"] = "bootstrap.shared";
+ commands["concensus"] = "concensus";
commands["help"] = "help";
+ commands["filter.seqs"] = "filter.seqs";
+ commands["align.seqs"] = "align.seqs";
commands["quit"] = "quit";