A tool for aligning consensus sequences to reference genomes.
A standalone C++ port of bealign, a part of the BioExt package. The purpose of this program is to align/map sequences in a FASTA file to a reference sequence and output the alignment as another FASTA file.
Key features: * Lightweight and self-contained * Allows codon-aware alignment while handling out-of-frame events * Flexible specification of scoring matrices * OpenMP support
