The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences
BLAST
Dotmatcher
Draw a threshold dotplot of two sequence
Dotpath
Draw a non-overlapping wordmatch dotplot of two sequences
Dottup
Display a wordmatch dotplot of two sequences
Needle
Needleman-Wunsch global alignment of two sequences
PM-Bdiversity
Beta diversity PERMANOVA and ANOSIM tests and plotting using distance matrices
PM-extract-rna
Extracting ribosomal RNA fragments from metagenomic sequencing data.
PM-parallel-meta
Profiling microbial community composition from sequencing data.
Polydot
Draw dotplots for all-against-all comparison of a sequence set
Water
Smith-Waterman local alignment of sequences