SeqAn3 3.3.0-rc.1
The Modern C++ library for sequence analysis.
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API Reference
Here is a list of all modules:
[detail level 12]
 Sequence AlignmentThe alignment module contains concepts, algorithms and classes that are related to the computation of pairwise and multiple sequence alignments
 Aligned SequenceProvides seqan3::aligned_sequence, as well as various ranges that model it
 CIGAR ConversionThe CIGAR Conversion submodule contains utility functions to convert a CIGAR to an alignment or vice versa
 ConfigurationProvides configuration elements for the pairwise alignment configuration
 DecoratorThe decorator submodule contains special SeqAn decorators
 Pairwise AlignmentsProvides the algorithmic components for the computation of pairwise alignments
 ScoringProvides the data structures used for scoring alphabets and sequences
 AdaptationProvides alphabet adaptions of some standard char and uint types
 AminoacidProvides the amino acid alphabets and functionality for translation from nucleotide
 CIGARProvides (semi-)alphabets for representing elements in CIGAR strings
 CompositeProvides templates for combining existing alphabets into new alphabet types
 ContainerAlphabet related container
 GapProvides the gap alphabet and functionality to make an alphabet a gapped alphabet
 MaskProvides the mask alphabet and functionality for creating masked composites
 NucleotideProvides the different DNA and RNA alphabet types
 QualityProvides the various quality score types
 RangeAlphabet related ranges
 StructureProvides types to represent single elements of RNA and protein structures
 ViewsAlphabet related views
 Argument Parser
 CoreProvides core functionality used by multiple modules
 AlgorithmProvides core functionality used for algorithms
 ConceptProvides core concepts
 ConfigurationProvides core functionality used to configure configurations
 Debug StreamProvides core functionality used to print seqan3 and std types
 RangeProvides seqan3 general purpose range functionality
 IOThe IO module provides stream handling formatted I/O
 SAM FileProvides files and formats for handling read mapping data
 Sequence FileProvides files and formats for handling sequence data
 StreamThe stream sub-module contains data structures and functions for streaming and tokenization
 Structure FileProvides files and formats for handling structure data
 ViewsIO related views
 SearchData structures and approximate string search algorithms for large collection of text (e.g. DNA)
 ConfigurationData structures and utility functions for configuring search algorithm
 DREAM IndexProvides seqan3::interleaved_bloom_filter
 FM IndexProvides seqan3::fm_index and seqan3::bi_fm_index as well as respective cursors
 k-mer IndexImplementation of shapes for a k-mer Index
 ViewsSearch related views
 charconvThe <charconv> header from C++17's standard library
 newThe <new> header from C++17's standard library
 UtilityProvides additional utility functionality used by multiple modules
 Bloom FilterProvides seqan3:bloom_filter
 Builtin Character OperationsProvides various operations on character types
 ConceptProvides various general purpose concepts
 ContainerProvides various general purpose container and concepts
 RangeThe range module provides general purpose range concepts
 TupleAdditional helper utilities for "tuple" types like std::tuple, std::pair, seqan3::pod_tuple that are not specific to a SeqAn module
 Type ListProvides seqan3::type_list and metaprogramming utilities for working on type lists
 Type PackProvides metaprogramming utilities for working on template parameter packs
 Type TraitsProvides various type traits and their shortcuts
 ViewsViews are "lazy range combinators" that offer modified views onto other ranges