amplicon                Primer matching
cmalign                 Multiple alignment using Infernal
gregexpr                Extended 'gregexpr' with substring retrieval
microseq-package        Basic Biological Sequence Analysis
msaTrim                 Trimming multiple sequence alignments
msalign                 Multiple alignment
muscle                  Multiple alignment using MUSCLE
plot.Fasta              Plotting and summary of 'Fasta' objects
readFasta and writeFasta
                        Read and write FASTA files
readFastq               Read FASTQ files
reverseComplement       Reverse-complementation of DNA
translate               Translation according to the standard genetic
                        code
