As we know there are many competitive tools which do the multiple sequence alignment. Some of them are able to do the global alignment by changing the score parameters as well. I am wondering if someone knows any tool, or method which uses the paired-end read information for the alignment. In my case, I have a small group of short paired-end reads (50 pairs) sequenced by Illumina. They all come from a very small region of DNA. I want to align these pairs to make the consensus sequence.