diff --git a/src/ecogrep.c b/src/ecogrep.c
new file mode 100644
index 0000000..6d0704c
--- /dev/null
+++ b/src/ecogrep.c
@@ -0,0 +1,289 @@
+#include "libecoPCR/ecoPCR.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <getopt.h>
+
+#define VERSION "0.1"
+
+void freememory(char **tab, int32_t num){
+	int32_t i;
+	for (i=0;i<num-1;i++){
+		ECOFREE(tab[i],"Error in freememory function");	
+	}
+}
+
+int	ispatternmatching(char **line, char **pattern, int32_t numpattern, int32_t error_max){
+	int 			i;
+	SeqPtr 	    	apatseq	= NULL;
+	ecoseq_t      	*seq	= NULL;
+	PatternPtr    	current_patt;
+	
+	seq = new_ecoseq();
+	
+	sscanf(line[4],"%d",&seq->taxid);
+	seq->AC = strdup(line[0]);
+	//seq->DE = strdup(line[]);
+	seq->SQ = strdup(line[18]);
+	seq->SQ_length = strlen(line[18]);
+		
+	apatseq=ecoseq2apatseq(seq,apatseq);
+		
+	for (i=0; i < numpattern ;i++){
+		current_patt = buildPattern(pattern[i],error_max);
+		if(ManberAll(apatseq,current_patt,0,0,apatseq->seqlen))
+			return 1;
+	}
+	return 0;
+}
+
+void printline(char **line, int32_t i){
+	int32_t k=0;
+	for (k=0; k < i; k++)
+		printf("%s |",line[k]);
+	printf("\n\n");			
+}
+
+/* ----------------------------------------------- */
+/* printout help                                   */                                           
+/* ----------------------------------------------- */
+#define PP fprintf(stdout, 
+
+static void PrintHelp()
+{
+        PP      "\n------------------------------------------\n");
+        PP      " ecogrep Version %s\n", VERSION);
+        PP      "------------------------------------------\n");
+        PP      " synopsis : filtering ecoPCR result based on\n");
+        PP      " taxonomic id filter and regular expression pattern\n");
+        PP      " usage: ecogrep [options] database\n");
+        PP      "------------------------------------------\n");
+        PP      " options:\n");
+        PP      " -d    : [D]atabase containing taxonomic information\n\n"); 
+        PP      " -f    : [F]ile name : ecoPCR ouput file\n\n"); 
+        PP      " -h    : [H]elp - print <this> help\n\n");
+        PP      " -i    : [I]gnore taxonomic id\n\n");
+        PP      " -r    : [R]estrict taxomic id\n\n");
+        PP      " -v    : in[V]ert the sense of matching, to select non-matching lines.\n");
+        PP      "------------------------------------------\n");
+        PP      " Pattern : oligonucleotide pattern\n");;
+        PP      "------------------------------------------\n\n");
+        PP		" https://www.grenoble.prabi.fr/trac/ecoPCR/wiki");
+        PP      "------------------------------------------\n\n");
+}
+
+#undef PP
+
+/* ----------------------------------------------- */
+/* printout usage and exit                         */
+/* ----------------------------------------------- */
+
+#define PP fprintf(stderr, 
+
+static void ExitUsage(stat)
+        int stat;
+{
+        PP      "usage: ecogrep [-d database] [-f filename] [-i taxid] [-r taxid] [-v] [-h] <pattern>\n");
+        PP      "type \"ecogrep -h\" for help\n");
+
+        if (stat)
+            exit(stat);
+}
+
+#undef  PP
+
+/* ----------------------------------------------- */
+/* MAIN						                       */
+/* ----------------------------------------------- */
+
+int main(int argc, char **argv){
+	int32_t     	carg 			= 0;
+	int32_t			r				= 0;				// number of restricted taxid
+	int32_t			g				= 0;				// number of ignored taxid
+	int32_t			v				= 0;			
+	int32_t			p				= 0;				// number of pattern
+	int32_t			i				= 0;
+	int32_t			errflag			= 0;
+	int32_t       	error_max		= 0;
+	int32_t			matchingresult 	= 0;
+	
+	ecotaxonomy_t	*taxonomy;
+		
+	char		  	*filename			= NULL;		// stores the datafile name
+	char			*database			= NULL;		// stores the database path (for taxonomy)
+	int32_t		  	*restricted_taxid 	= NULL;		// stores the restricted taxid
+	int32_t       	*ignored_taxid		= NULL;		// stores the ignored taxid
+	char 			**pattern			= NULL;		// stores the regex pattern
+	char 			*line[19]			= {0};		// stores the line 
+	
+	
+	FILE			*file				= NULL;
+	char			*stream				= ECOMALLOC(sizeof(char *)*10000,"error stream buffer allocation"); 
+	int				current_taxid;
+	char 			*buffer; 
+
+	while ((carg = getopt(argc, argv, "f:d:i:r:e:vh")) != -1) {
+
+	    switch (carg) {                              
+	        case 'f':
+	           filename = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on filename allocation");
+	           strcpy(filename,optarg);
+	           break;
+
+	        case 'd':
+	           database = ECOMALLOC(strlen(optarg)+1,
+	           						"Error on datafile allocation");
+	           strcpy(database,optarg);
+	           break;
+	
+	        case 'i':   
+	           ignored_taxid = ECOREALLOC(	ignored_taxid,
+	           								sizeof(int32_t)*(g+1),
+	           								"Error on ignored_taxid reallocation");
+	           sscanf(optarg,"%d",&ignored_taxid[g]);
+	           g++;
+	           break;
+	        
+	        case 'r': 
+	           restricted_taxid = ECOREALLOC(	restricted_taxid, 
+	           									sizeof(int32_t)*(r+1),
+	           									"Error on restricted_taxid reallocation");  
+	           sscanf(optarg,"%d",&restricted_taxid[r]);
+	           r++;
+	           break;
+	           	           
+	        case 'v':     
+	           v = 1;
+	           break;
+	           
+	        case 'h':     
+	           PrintHelp();
+           	   exit(0);
+	           break;
+	           
+	        case 'e':	
+	          sscanf(optarg,"%d",&error_max);
+    	      break;
+	           
+	        case '?':
+            	errflag++;
+	     }
+	}
+	
+	/**
+	 * Get the leftover command line arguments back 
+	 * and check the pattern is not more than 32 character long
+	 */
+	pattern = ECOMALLOC(sizeof *pattern * (argc - optind), "Error in pattern allocation");
+	for (p=0 ; argc > optind ; optind++, p++){
+		if (strlen(argv[optind]) <= 32)
+			pattern[p] = strdup(argv[optind]);
+		else
+		{
+			printf("# Sorry, ecogrep doesn't handle pattern longer than 32 characters.\
+					\n# Please correct this one : %s\n",argv[optind]);
+			exit(0);
+		}
+	}
+	
+	/**
+	 * try to get the database name from environment variable
+	 * if no database name specified in the -d option
+	 
+	if (!database && getenv("ECOPCRDB"))
+		database = getenv("ECOPCRDB");
+	else
+		errflag++;
+	*/
+	
+	/**
+	 * check everything required is provided
+	 */			
+	if (!filename ||
+		!database ||
+		(!p && restricted_taxid == NULL && ignored_taxid == NULL))
+		errflag++;
+	
+	if (errflag)
+    	ExitUsage(errflag);
+	
+	/**
+	* Open the ecoPCR file
+	*/
+	if (filename)
+	{
+		 if( (file = fopen(filename, "r")) == NULL)
+		 	ECOERROR(ECO_IO_ERROR,"Cannot open the file !");
+	}
+
+	/**
+	* Get the taxonomy back
+	*/
+	taxonomy = read_taxonomy(database);
+	 
+	/**
+	* Parse the stream
+	*/ 
+	while( fgets(stream, 10000, file) ){
+	 		
+	 	if (stream[0]!= '#')
+	 	{
+	 		for(	i=0, buffer = strtok(stream,"|");
+					buffer != NULL;
+					i++, buffer = strtok(NULL,"|"))
+			{
+				line[i] = strdup(buffer);
+			}
+			
+			sscanf(line[4],"%d",&current_taxid);
+						
+			if(!v) // normal mode
+			{ 			
+	 			if ( (r > 0) && !(eco_is_taxid_included(	taxonomy, 
+		                            						restricted_taxid, 
+		                            						r, 
+		                            						current_taxid)) 
+			   	   )
+			   	   continue;
+			   	   
+			    if ( (g > 0) && (eco_is_taxid_included(	taxonomy, 
+			                                 			ignored_taxid, 
+			                                 			g, 
+			                                 			current_taxid))
+			       )
+			       continue;
+			}
+			 	
+			else // v mode, invert ignore and restrict taxid
+			{
+				if ( (r > 0) && (eco_is_taxid_included(	taxonomy, 
+		                            					restricted_taxid, 
+		                            					r, 
+		                            					current_taxid)) 
+			   	   )
+			   	   continue;
+			    if ( (g > 0) && !(eco_is_taxid_included(	taxonomy, 
+			                                 				ignored_taxid, 
+			                                 				g, 
+			                                 				current_taxid))
+			       )
+			       continue;
+			}
+			 
+			if ( p == 0 || (ispatternmatching(line,pattern,p,error_max)))		 
+			{    	
+     			printline(line,i);
+     			matchingresult++;
+			}		     	
+	 	}
+	}
+	 
+	printf("# %d matching result\n",matchingresult);
+	
+	freememory(line,i);
+	freememory(pattern,p);
+	ECOFREE(pattern,"Error in free pattern");
+	ECOFREE(stream,"Error in free stream");
+	return 0;
+}
\ No newline at end of file