| microseq-package | Basic Biological Sequence Analysis |
| amplicon | Primer matching |
| cmalign | Multiple alignment using Infernal |
| Fasta | Read and write FASTA files |
| gregexpr | Extended 'gregexpr' with substring retrieval |
| iupac2regex | Ambiguity symbol conversion |
| microseq | Basic Biological Sequence Analysis |
| msalign | Multiple alignment |
| msaTrim | Trimming multiple sequence alignments |
| muscle | Multiple alignment using MUSCLE |
| plot.Fasta | Plotting and summary of 'Fasta' objects |
| plot.Fastq | Plotting and summary of 'Fastq' objects |
| readFasta | Read and write FASTA files |
| readFastq | Read and write FASTQ files |
| regex2iupac | Ambiguity symbol conversion |
| reverseComplement | Reverse-complementation of DNA |
| summary.Fasta | Plotting and summary of 'Fasta' objects |
| summary.Fastq | Plotting and summary of 'Fastq' objects |
| translate | Translation according to the standard genetic code |
| uipac2regex | Ambiguity symbol conversion |
| writeFasta | Read and write FASTA files |
| writeFastq | Read and write FASTQ files |