private void clean(){
		if(infiles.size() > 1){
			System.err.println("Trimming is done one file at a time, only the first file will be used.");
		}
		String seqtype = "test";
		if(seqtypeset == "aa"){
			seqtype = "aa";
		}else if (seqtypeset == "nucleotide"){
			seqtype = "nucleotide";
		}
		phyutility.trimsites.TrimSites ts = new phyutility.trimsites.TrimSites(infiles.get(0),seqtype);
		ts.trimAln(cleannum);
		if(cleanmessy == true){
			ts.trimAlnCleanMessy(cleanmessynum);
		}
		if(testForNexus(infiles.get(0))){
			if(out_oth == true){
				ts.printFastaOutfile(outfile);
			}else{
				ts.printNexusOutfile(outfile);
			}
		}else{
			if(out_oth == false){
				ts.printFastaOutfile(outfile);
			}else{
				ts.printNexusOutfile(outfile);
			}
		}
	}