changed how we name the make.group groups file, and filter file in filter.seqs, finis...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 877e7c76773ece0f459142e674382fb2747bb8fb..ccf5eebe68f42426f16f2465b68832beb413d2eb 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -182,7 +182,7 @@ AlignCommand::~AlignCommand(){
 void AlignCommand::help(){
        try {
                m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
-               m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
+               m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n");
                m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
                m->mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");
                m->mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");