| microseq-package | Basic Biological Sequence Analysis | 
| backTranslate | Replace amino acids with codons | 
| findGenes | Finding coding genes | 
| findOrfs | Finding ORFs in genomes | 
| findrRNA | Finding rRNA genes | 
| gff2fasta | Retrieving annotated sequences | 
| gregexpr | Extended 'gregexpr' with substring retrieval | 
| iupac2regex | Ambiguity symbol conversion | 
| lorfs | Longest ORF | 
| microseq | Basic Biological Sequence Analysis | 
| msa2mat | Convert alignment to matrix | 
| msalign | Multiple alignment | 
| msaTrim | Trimming multiple sequence alignments | 
| muscle | Multiple alignment using MUSCLE | 
| orfLength | Length of ORF | 
| readFasta | Read and write FASTA files | 
| readFastq | Read and write FASTQ files | 
| readGFF | Reading and writing GFF-tables | 
| regex2iupac | Ambiguity symbol conversion | 
| reverseComplement | Reverse-complementation of DNA | 
| translate | Translation according to the standard genetic code | 
| writeFasta | Read and write FASTA files | 
| writeFastq | Read and write FASTQ files | 
| writeGFF | Reading and writing GFF-tables |