: This library provides classes to store and analyse biological sequences. Each position in a sequences is coded by a int. An object implementing the bpp::Alphabet interface is used to make the relation between the int code and its more common character representation. Support for DNA, RNA, protein and codon sequences is provided. The bpp::AlphabetTools provides tools to deal with Alphabet objects. The basic bpp::Sequence class contains the code sequence, a name for the sequence and optionally comments. More elaborated classes can be built by inheriting this class. The bpp::SequenceTools static class provides simple analysis tools, like base frequencies measures, concatenation, etc.

bpp-seq also provides tools to perform in silico: molecular biology, like complementation, transcription, translation, etc. All these methods are particular cases of alphabet translation, and are implemented via the interface bpp::Translator. Of particular interest are the classes bpp::NucleicAcidsReplication, bpp::DNAToRNA and bpp::GeneticCode + derivatives.

: Sequence collections are stored as containers. The simplest container implements the bpp::SequenceContainer interface, providing access to sequences by their name. The bpp::OrderedSequenceContainer adds access by position in the container. The simplest implementation of this interface is the bpp::VectorSequenceContainer, which stores the sequences as a vector of bpp::Sequence objects (or instances inheriting from this class). Input/output from various file formats is provided, including fasta (bpp::Fasta), GenBank (bpp::GenBank) and Mase (bpp::Mase). Tools dealing with containers can be found in the bpp::SequenceContainerTools static class.

Support for alignments is provided via the bpp::SiteContainer interface, which enables site access. Sites are stored as a distinct class, similar to a "vertical" sequence, called bpp::Site. It shares several methods with the bpp::Sequence object, although it does not contain a name but a position attribute. This attribute can be used to track the position of sites when handling alignments (for instance after removing all gap-containing sites). There are currently two implementations of the bpp::SiteContainer interface:

bpp::AlignedSequenceContainer, inheriting from bpp::VectorSequenceContainer and adding the site access. Sequence access is hence in and site access in , n being the total number of sites.
bpp::VectorSiteContainer is a symmetric implementation, storing the data as a vector of bpp::Site objects, providing site access in but sequence access in , m being the total number of sequences. The static classes bpp::SymbolListTools and bpp::SiteContainerTools provide some tools (for instance: pairwise alignment) to deal respectively with bpp::Site and bpp::SiteContainer objects. I/O is provided for several formats, including Clustal (bpp::Clustal) and Phylip (bpp::Phylip).

: Bio++ sequence library also contains support for sequence properties, like amino-acids biochemical properties. The interfaces bpp::AlphabetIndex1 and bpp::AlphabetIndex2 provides methods to deal with indices in 1 and 2 dimensions respectively. Several basic properties are provided, together with input from the AAIndex databases.