| Package | Description |
|---|---|
| jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
| jebl.evolution.aligners | |
| jebl.evolution.alignments | |
| jebl.evolution.io | |
| jebl.evolution.parsimony | |
| jebl.evolution.sequences | |
| jebl.evolution.substmodel |
| Class | Description |
|---|---|
| Sequence |
A biomolecular sequence.
|
| Class | Description |
|---|---|
| Sequence |
A biomolecular sequence.
|
| Class | Description |
|---|---|
| Sequence |
A biomolecular sequence.
|
| Sequences |
A set of sequence objects.
|
| SequenceType |
Interface for sequences data types.
|
| State |
| Class | Description |
|---|---|
| Sequence |
A biomolecular sequence.
|
| SequenceType |
Interface for sequences data types.
|
| Class | Description |
|---|---|
| State |
| Class | Description |
|---|---|
| AminoAcidState | |
| CodonState |
As of 2007-07-30, instances of this class are only constructed for non-ambigous
nucleotide triplets - see
Codons. |
| FilteredSequence | |
| GeneticCode |
A set of standard genetic codes.
|
| NucleotideState | |
| Sequence |
A biomolecular sequence.
|
| SequenceType |
Interface for sequences data types.
|
| State | |
| StateClassification |
| Class | Description |
|---|---|
| SequenceType |
Interface for sequences data types.
|
http://code.google.com/p/jebl2/