commands["read.tree"] = "read.tree";
commands["read.seqs"] = "read.seqs";
commands["bin.seqs"] = "bin.seqs";
+ commands["get.repseqs"] = "get.repseqs";
commands["get.oturep"] = "get.oturep";
commands["cluster"] = "cluster";
commands["deconvolute"] = "deconvolute";
- commands["dist.seqs"] = "dist.seqs";
+ 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["concensus"] = "concensus";
commands["help"] = "help";
commands["filter.seqs"] = "filter.seqs";
+ commands["align.seqs"] = "align.seqs";
commands["quit"] = "quit";