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