The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
cutadapt removes adapter sequences fromnhigh-throughput sequencing data. This is usually necessary when the readnlength of the sequencing machine is longer than the molecule that isnsequenced, for example when sequencing microRNAs.