AlignedSequence is a class containing the single aligned unit of alignment.

This class defines generic properties of any alignment algorithm.

An ordered list of matches between two a pair of sequences

Clustering is a process in which individual matches are grouped in larger set called Cluster. The matches in cluster are decided based on paramters like fixed difference allowed, maximum difference allowed, minimum score and separation factor that should be satisfied. This class implements IClusterBuilder interface.

Represents a alignment object in terms of delta. Delta is an encoded representation of alignments between input sequences. It contains the start and end indices of alignment in reference and query sequence followed by error values and list of integer in following lines. Each integer represent an insertion (+ve) in reference sequence and deletion (-ve) in reference sequence. This class represents such alignment with required properties and utility methods.

Base class for dynamic programming alignment algorithms, including NeedlemanWunsch, SmithWaterman and PairwiseOverlap. The basic reference for this code (including NW, SW and Overlap) is Chapter 2 in Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison; Cambridge Press; 1998 The variable names in these classes follow the notation in Durbin et al.

Base class for all aligner algorithms. Provides storage and read/write operations for the grid.

Implements algorithm to extend given pair of sequences in specified direction. This implementation is specific to NUCmer.

Implements the NeedlemanWunsch algorithm for global alignment. See Chapter 2 in Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison; Cambridge Press; 1998.

NUCmer is a system for rapidly aligning entire genomes or very large DNA sequences. It allows alignment of multiple reference sequences to multiple query sequences. This is commonly used to identify the position and orientation of set of sequence contigs in relation to finished sequence.

This class extends MUMmerAttributes and adds NUCmer specific attributes required to run the NUCmer algorithm.

Class which uses nucmer to perform an alignment.

PairwiseAlignedSequence is a class containing the single aligned unit of pairwise alignment.

This class implements IAlignmentAttributes interface and defines all the parameters required to run any pairwise algorithm.

Pairwise Overlap alignment implementation using affine gap model.

Implements the pair-wise overlap alignment algorithm described in Chapter 2 of Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison; Cambridge Press; 1998.

Pairwise Overlap alignment implementation using simple gap model.

Base class for our pair-wise sequence aligners. This implements the core shared portions of the Smith-Waterman and Needleman-Wunsch aligners.

Optimum score maxtrix cell

A simple implementation of IPairwiseSequenceAlignment that stores the results as list of Aligned Sequences.

SequenceAligners class is an abstraction class which provides instances and lists of all Aligners currently supported by Bio.

A simple implementation of ISequenceAlignment that stores the result of an alignment.

Implements the SmithWaterman algorithm for partial alignment. See Chapter 2 in Biological Sequence Analysis; Durbin, Eddy, Krogh and Mitchison; Cambridge Press; 1998.

An ordered list of clusters between two sequences A and B

Position details of cell with best score.

Interface to hold single aligned unit of alignment.

Aligners will implements this interface to list the attributes supported or required.

Contract defined to implement class that creates clusters. Takes list of maximum unique matches as input and creates clusters

Multiple sequences alignment interface. Multiple sequence alignment (MSA) is used to align three or more sequences in preparation for further analysis. More info on MSA can be found at http://en.wikipedia.org/wiki/Multiple_sequence_alignment)

A sequence alignment algorithm that aligns exactly two sequences. This may diverge from ISequenceAligner at some point; meanwhile, it's important to maintain the distinction (e.g., assembly requires a pairwise algorithm).

An IPairwiseSequenceAlignment is the result of running a Pairwise alignment algorithm on a set of two sequences.

A sequence aligner is an algorithm which takes N sequences as input and produces an alignment of the sequences as output.

An ISequenceAlignment is the result of running an alignment algorithm on a set of two or more sequences. This could be a pairwise alignment, an MSA (multiple sequence alignment), or an overlap alignment of the sort needed for sequence assembly.

Algorith-specific weight function

Enum to indicate method to use while calculating score of a cluster.