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PALADIN is a protein sequence alignment tool based on the BWA source. Like BWA, it aligns sequences via read-mapping using BWT. PALADIN, however, offers the novel approach of aligning in the protein space. During the index phase, it processes the reference genome's nucleotide sequences and GTF/GFF annotation containing CDS entries, first converting these transcripts into the corresponding protein sequences, then creating the BWT and suffix array from these proteins. During the alignment phase, it attempts to find ORFs in the read sequences, then converts these to protein sequences, and aligns to the reference protein sequences.
PALADIN currently only supports single-end reads, and BWA-MEM based alignment. It makes use of many BWA parameters and is therefore compatible with many of its command line arguments.
