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diff --git a/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java b/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
deleted file mode 100644
index c3ab8ac..0000000
--- a/src2/fr/orsay/lri/varna/models/templates/BatchBenchmarkPrepare.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/**
- * File written by Raphael Champeimont
- * UMR 7238 Genomique des Microorganismes
- */
-package fr.orsay.lri.varna.models.templates;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import fr.orsay.lri.varna.factories.RNAFactory;
-
-public class BatchBenchmarkPrepare {
-
-	/**
-	 * We assume given directory contains a alignemnt.fasta file,
-	 * of which the first sequence is the consensus structure,
-	 * and the other sequences are aligned nucleotides. 
-	 * The principle is to convert it to a set of secondary structure,
-	 * using the following rule:
-	 * - keep the same nucleotides as in original sequence
-	 * - keep base pairs where both bases of the pair are non-gaps in our sequence
-	 */
-	public void benchmarkAllDir(File rootdir) throws Exception {
-		File seqdir = new File(rootdir, "sequences");
-		if (!seqdir.exists()) {
-			seqdir.mkdir();
-		}
-		
-		File templateFile = new File(rootdir, "template.xml");
-		
-		ArrayList<String> seqnames = new ArrayList<String>();
-		ArrayList<String> sequences = new ArrayList<String>();
-		BatchBenchmark.readFASTA(new File(rootdir, "alignment.fasta"), seqnames, sequences);
-		
-		BufferedWriter outbufASS = new BufferedWriter(new FileWriter(new File(rootdir, "all_secondary_structures.fasta")));
-		
-		String consensusSecStr = sequences.get(0);
-		int[] consensusSecStrInt = RNAFactory.parseSecStr(consensusSecStr);
-		
-		List<File> templates = new ArrayList<File>();
-		for (int i=1; i<seqnames.size(); i++) {
-			String seqname = seqnames.get(i);
-			String sequence = sequences.get(i);
-			String sequenceUngapped = sequence.replaceAll("[\\.-]", "");
-			System.out.println(seqname);
-			String ss = "";
-			String nt = "";
-			for (int j=0; j<sequence.length(); j++) {
-				if (sequence.charAt(j) != '.' && sequence.charAt(j) != '-') {
-					if (consensusSecStr.charAt(j) == '-' || consensusSecStr.charAt(j) == '.') {
-						nt += sequence.charAt(j);
-						ss += '.';
-					} else {
-						int k = consensusSecStrInt[j];
-						// k is the matching base, is it aligned to a base in our sequence?
-						if (sequence.charAt(k) != '.' && sequence.charAt(k) != '-') {
-							nt += sequence.charAt(j);
-							ss += consensusSecStr.charAt(j);
-						} else {
-							nt += sequence.charAt(j);
-							ss += '.';
-						}
-					}
-				}
-			}
-			
-			if (!sequenceUngapped.equals(nt)) {
-				System.out.println(sequenceUngapped);
-				System.out.println(nt);
-				throw new Error("bug");
-			}
-			
-			// We now have the sequence with its secondary structure.
-			File outfile = new File(seqdir, seqname + ".dbn");
-			BufferedWriter outbuf = new BufferedWriter(new FileWriter(outfile));
-			outbuf.write(">" + seqname + "\n");
-			outbuf.write(nt + "\n");
-			outbuf.write(ss + "\n");
-			outbuf.close();
-			
-			outbufASS.write(">" + seqname + "\n");
-			outbufASS.write(ss + "\n");
-			
-			templates.add(templateFile);
-		}
-		
-		outbufASS.close();
-		
-	}
-	
-	public static void main(String[] args) throws Exception {
-		new BatchBenchmarkPrepare().benchmarkAllDir(new File(new File("templates"), "RNaseP_bact_a"));
-	}
-	
-}