remove probabilties by read

4 files changed, 2 insertions, 2 deletions

diff --git a/doc/cli.markdown b/doc/cli.markdown
index d4a1bb9..843bae9 100644
--- a/doc/cli.markdown
+++ b/doc/cli.markdown
@@ -73,7 +73,6 @@ multifasta\_to\_otu's arguments:
   OTU's)
   -t, --trained-matrix, the trained matrix
   -f, --trained-fasta, the fasta file database of sequences
-  -d, --output-directory, quikr output directory
   -l, --lamb, specify what size of lambda to use (the default value is 10,000)
   -k, --kmer, specify what size of kmer to use, (default value is 6)
   -j, --jobs, specifies how many jobs to run at once, (default=number of CPUs)
diff --git a/doc/index.markdown b/doc/index.markdown
index 738bc47..93688bc 100644
--- a/doc/index.markdown
+++ b/doc/index.markdown
@@ -1,7 +1,6 @@
 # Quikr #
 This is the homepage for quikr.
 
-
 ## What is Quikr ##
 Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that
 utilizes sparsity promoting ideas from the field of compressed sensing to
@@ -23,6 +22,8 @@ scripts, and matlab scripts.
 + [Python documentation](python.html)
 + [Command Line Utilities](cli.html)
 
+## Contact ##                                   
+For issues with the python implementation, contact gailro@gmail.com
 
 ## Contributors ##
 + David Koslicki
diff --git a/src/nbc/count b/src/nbc/count
deleted file mode 100755
index 21b4e60..0000000
--- a/src/nbc/count
+++ /dev/null
diff --git a/src/nbc/probabilities-by-read b/src/nbc/probabilities-by-read
deleted file mode 100755
index 08908cc..0000000
--- a/src/nbc/probabilities-by-read
+++ /dev/null