GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes. Submit online GLASS queries. Download the current GLASS source code. GLASS is supported by the MIT LCS Computation and Biology group and the Whitehead Center for Genome Research. For further information, please refer to the Comparative Genomics website.