| blosum | Parse blosum from the given file data |
| align.smith_waterman | do the local pairwise sequence alignment via the smith-waterman algorithm |
| HSP | get the high score region(HSP) from the given alignment result |
| align.needleman_wunsch | do the global pairwise sequence alignment via the needleman-wunsch algorithm |
| align.gwANI | run the genome-wide average nucleotide identity(gwANI) calculation for a given nucleotide sequence collection |