added dist.shared command

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index 4c72dceaf26d73d8d030641c33ab48d699f495a6..787cc8025a6c62d01be190a63c33e42429fe21a4 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -19,9 +19,12 @@ ValidCommands::ValidCommands() {
                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.shared"]                 = "dist.shared";  //matrix output
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
                commands["rarefaction.single"]  = "rarefaction.single"; 
@@ -42,6 +45,7 @@ ValidCommands::ValidCommands() {
                commands["concensus"]                   = "concensus";
                commands["help"]                                = "help"; 
                commands["filter.seqs"]                 = "filter.seqs";
+               commands["align.seqs"]                  = "align.seqs";
                commands["quit"]                                = "quit";