diff --git a/src/seqTools.cpp b/src/seqTools.cpp
new file mode 100644
index 00000000..5f64c491
--- /dev/null
+++ b/src/seqTools.cpp
@@ -0,0 +1,68 @@
+//
+//  seqTools.cpp
+//  StochHMM
+//
+//  Created by Paul Lott on 5/18/12.
+//  Copyright (c) 2012 University of California, Davis. All rights reserved.
+//
+
+#include "seqTools.h"
+
+namespace StochHMM{
+    
+    
+    sequence shuffle(sequence *seq){
+        sequence shuffled_seq(ALPHA_NUM);
+        std::string strSeq=seq->getUndigitized();
+        for(size_t i=0;i<strSeq.size();++i){
+            size_t k = rand() % (strSeq.size());
+            if (k!=i){
+                iter_swap(strSeq.begin()+i, strSeq.begin()+k);
+            }
+        }
+        
+        shuffled_seq.setSeq(strSeq, seq->getTrack());
+        
+        return shuffled_seq;
+    }
+    
+    sequence random_sequence(std::vector<double>& freq, size_t length, track* tr){
+        sequence random_seq(ALPHA_NUM);
+        
+        if (tr==NULL){
+            std::cerr << "Track is not defined" << std::endl;
+            return random_seq;
+        }
+        
+        size_t alphaSize=tr->getAlphaSize();
+        size_t freqSize=freq.size();
+        if (alphaSize!=freqSize){
+            std::cerr << "Frequency distribution size and Alphabet size must be the same." << std::endl;
+            return random_seq;
+        }
+        
+        //Create CDF of frequency distribution
+        std::vector<std::pair<double,std::string> > cdf;
+        double sum = 0.0;
+        for(size_t i=0;i<freqSize;++i){
+            sum+=freq[i];
+            std::pair<double,std::string> val (sum, tr->getAlpha(i));
+            cdf.push_back(val);
+        }
+        
+        //Generate random sequence
+        std::string random_string;
+        for(size_t j=0;j<length;++j){
+            double val = ((double)rand()/((double)(RAND_MAX)+(double)(1))); //Generate random 
+            for (size_t m=0;m<freqSize;++m){ //Check to see which value is 
+                if (cdf[m].first>=val){
+                    random_string+=cdf[m].second;
+                    break;
+                }
+            }
+        }
+        
+        random_seq.setSeq(random_string, tr);
+        return random_seq;
+    }
+}
\ No newline at end of file
diff --git a/src/seqTools.h b/src/seqTools.h
new file mode 100644
index 00000000..6e1c060d
--- /dev/null
+++ b/src/seqTools.h
@@ -0,0 +1,39 @@
+//
+//  seqTools.h
+//  StochHMM
+//
+//  Created by Paul Lott on 5/18/12.
+//  Copyright (c) 2012 University of California, Davis. All rights reserved.
+//
+
+#ifndef StochHMM_seqTools_h
+#define StochHMM_seqTools_h
+#include <iostream>
+#include <string>
+#include <algorithm>
+#include "sequence.h"
+#include "hmm.h"
+namespace StochHMM{
+    sequence shuffle(sequence* seq);
+    
+    sequence random_sequence(std::vector<double> const& freq, size_t , track*);
+    sequence random_sequence(emm*);
+    
+    sequence reverseComplement();
+    sequence translate();
+    
+    
+    void motifScoring();
+    
+    void markov_length_distribution(model*);
+    
+    void markov_generate_sequence(model*);
+    
+//Put in PWM scoring with options for set threshold or determine threshold through shuffling and calculation of FDR(give an FDR threshold)
+    
+    
+}
+
+
+
+#endif