GapsMis

pairwise sequence alignment

Manual


GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps. It focuses on semi-global alignment and it restricts the alignment in containing a variable, but bounded, number of gaps.

This is how it computes a penalty for a gap of n positions :

gap opening penalty + (n - 1) * gap extension penalty

Usage




GapMis is a tool for pairwise sequence alignment with a single gap. It focuses on semi-global alignment and it restricts the alignment in containing at most one gap.

This is how it computes a penalty for a gap of n positions :

gap opening penalty + (n - 1) * gap extension penalty

Usage




GapMis-OMP is the OpenMP-based version of GapMis. It is designed to compute the alignments between all the sequences in a first set of sequences and all those from a second one in parallel.

Usage




libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

Man page