BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

biojava3-alignment.jar is the Alignment module of BioJava 3.

JAR File Size and Download Location:

File name: biojava3-alignment.jar, biojava3-alignment-3.0.2.jar
File size: 158408 bytes
Date modified: 02-Sep-2011
Download: BioJava 3.0 - Alignment

JAR File Size and Download Location:

File name: biojava3-alignment-3.0.2.jar
File size: 158408 bytes
Date modified: 02-Sep-2011
Download: 

Manifest of the JAR:

Archiver-Version: Plexus Archiver
Built-By: andreas
Build-Jdk: 1.7.0

List of Classes in the JAR:

org/biojava3/alignment/Alignments
org/biojava3/alignment/routines/AlignerHelper
org/biojava3/alignment/routines/AnchoredPairwiseSequenceAligner
org/biojava3/alignment/routines/GuanUberbacher
org/biojava3/alignment/SimpleProfile
org/biojava3/alignment/aaindex/DefaultAAIndexProvider
org/biojava3/alignment/aaindex/AAIndexProvider
org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix
org/biojava3/alignment/aaindex/AAIndexFileParser
org/biojava3/alignment/aaindex/AAindexFactory
org/biojava3/alignment/NeedlemanWunsch
org/biojava3/alignment/StandardRescoreRefiner
org/biojava3/alignment/SimpleGapPenalty
org/biojava3/alignment/FractionalSimilarityInProfileScorer
org/biojava3/alignment/SimpleProfileProfileAligner
org/biojava3/alignment/GuideTree
org/biojava3/alignment/SimpleProfilePair
org/biojava3/alignment/SimpleSubstitutionMatrix
org/biojava3/alignment/FractionalIdentityScorer
org/biojava3/alignment/FractionalSimilarityScorer
org/biojava3/alignment/SimpleSequencePair
org/biojava3/alignment/FractionalIdentityInProfileScorer
org/biojava3/alignment/SmithWaterman
org/biojava3/alignment/SubstitutionMatrixHelper
org/biojava3/alignment/SimpleAlignedSequence
org/biojava3/alignment/template/AbstractScorer
org/biojava3/alignment/template/ProfileProfileScorer
org/biojava3/alignment/template/PartitionRefiner
org/biojava3/alignment/template/HierarchicalClusterer
org/biojava3/alignment/template/Scorer
org/biojava3/alignment/template/Aligner
org/biojava3/alignment/template/ProfileView
org/biojava3/alignment/template/PairInProfileScorer
org/biojava3/alignment/template/ProfilePair
org/biojava3/alignment/template/ProfileProfileAligner
org/biojava3/alignment/template/GuideTreeNode
org/biojava3/alignment/template/MutableSequencePair
org/biojava3/alignment/template/SubstitutionMatrix
org/biojava3/alignment/template/AlignedSequence
org/biojava3/alignment/template/MatrixAligner
org/biojava3/alignment/template/PairwiseSequenceAligner
org/biojava3/alignment/template/RescoreRefiner
org/biojava3/alignment/template/SequencePair
org/biojava3/alignment/template/PairwiseSequenceScorer
org/biojava3/alignment/template/AbstractMatrixAligner
org/biojava3/alignment/template/MutableProfilePair
org/biojava3/alignment/template/CallablePairwiseSequenceScorer
org/biojava3/alignment/template/CallablePairwiseSequenceAligner
org/biojava3/alignment/template/MutableAlignedSequence
org/biojava3/alignment/template/AbstractProfileProfileAligner
org/biojava3/alignment/template/CallableProfileProfileAligner
org/biojava3/alignment/template/MutableProfile
org/biojava3/alignment/template/AbstractPairwiseSequenceAligner
org/biojava3/alignment/template/Profile
org/biojava3/alignment/template/GapPenalty