question: What is libgapmis?
answer: libgapmis is a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis.