Uses of Package
org.biojava.bio.alignment
Packages that use org.biojava.bio.alignment
Package
Description
Classes to generate and describe sequence alignments.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
ABI Trace Handling.
Parser for Phred output
Interfaces and classes for representing sequence similarity search results.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Representation of the Symbols that make up a sequence, and locations within
them.
Classes to support the reading and writing of PHYLIP format.
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Classes in org.biojava.bio.alignment used by org.biojava.bio.alignmentClassDescriptionAn alignment containing multiple SymbolLists.This Interface provides methods for the alignment of bio-sequences.AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.EditableAlignment is an interface that defines methods for shifting bases within an Alignment.The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.A simple implementation of an Alignment.This object is able to read a substitution matrix file and constructs a short matrix in memory.UnequalLengthAlignment has the following behavior.
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Classes in org.biojava.bio.alignment used by org.biojava.bio.chromatogram
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Classes in org.biojava.bio.alignment used by org.biojava.bio.dist
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Classes in org.biojava.bio.alignment used by org.biojava.bio.dp
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Classes in org.biojava.bio.alignment used by org.biojava.bio.program.abi
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Classes in org.biojava.bio.alignment used by org.biojava.bio.program.phred
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Classes in org.biojava.bio.alignment used by org.biojava.bio.search
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Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.homol
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Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.impl
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Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.io
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Classes in org.biojava.bio.alignment used by org.biojava.bio.symbol
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Classes in org.biojava.bio.alignment used by org.biojavax.bio.phylo.io.phylip