PALADIN

PALADIN is a software that efficiently and accurately aligns DNA reads against protein references, enabling the construction of a functional profile of microbial communities. It is based on the Burrows-Wheeler Aligner and provides robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space. PALADIN was tested against existing tools that used nucleotide or protein alignment algorithms and was found to be more accurate and efficient than the popular DNA read mappers BWA and NovoAlign. Compared to four existing protein alignment tools, PALADIN yielded results seven times faster than the best-performing alternative and nearly 8000 times faster than BLASTX, with comparable accuracy.