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AAINDEX.txt
META-INF/MANIFEST.MF
blosum100.txt
blosum30.txt
blosum35.txt
blosum40.txt
blosum45.txt
blosum50.txt
blosum55.txt
blosum60.txt
blosum62.txt
blosum65.txt
blosum70.txt
blosum75.txt
blosum80.txt
blosum85.txt
blosum90.txt
demo.CookbookMSA.java
demo.DemoLoadSubstMax.java
demo.TestDNANeedlemanWunsch.java
gonnet250.txt
nuc-4_2.txt
nuc-4_4.txt
org.biojava3.alignment.Alignments.java
org.biojava3.alignment.FractionalIdentityInProfileScorer.java
org.biojava3.alignment.FractionalIdentityScorer.java
org.biojava3.alignment.FractionalSimilarityInProfileScorer.java
org.biojava3.alignment.FractionalSimilarityScorer.java
org.biojava3.alignment.GuideTree.java
org.biojava3.alignment.NeedlemanWunsch.java
org.biojava3.alignment.SimpleAlignedSequence.java
org.biojava3.alignment.SimpleGapPenalty.java
org.biojava3.alignment.SimpleProfile.java
org.biojava3.alignment.SimpleProfilePair.java
org.biojava3.alignment.SimpleProfileProfileAligner.java
org.biojava3.alignment.SimpleSequencePair.java
org.biojava3.alignment.SimpleSubstitutionMatrix.java
org.biojava3.alignment.SmithWaterman.java
org.biojava3.alignment.StandardRescoreRefiner.java
org.biojava3.alignment.SubstitutionMatrixHelper.java
org.biojava3.alignment.aaindex.AAIndexFileParser.java
org.biojava3.alignment.aaindex.AAIndexProvider.java
org.biojava3.alignment.aaindex.AAindexFactory.java
org.biojava3.alignment.aaindex.DefaultAAIndexProvider.java
org.biojava3.alignment.aaindex.ScaledSubstitutionMatrix.java
org.biojava3.alignment.io.StockholmConsensusAnnotation.java
org.biojava3.alignment.io.StockholmFileAnnotation.java
org.biojava3.alignment.io.StockholmFileParser.java
org.biojava3.alignment.io.StockholmResidueAnnotation.java
org.biojava3.alignment.io.StockholmSequenceAnnotation.java
org.biojava3.alignment.io.StockholmStructure.java
org.biojava3.alignment.routines.AlignerHelper.java
org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner.java
org.biojava3.alignment.routines.GuanUberbacher.java
org.biojava3.alignment.template.AbstractMatrixAligner.java
org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.java
org.biojava3.alignment.template.AbstractProfileProfileAligner.java
org.biojava3.alignment.template.AbstractScorer.java
org.biojava3.alignment.template.AlignedSequence.java
org.biojava3.alignment.template.Aligner.java
org.biojava3.alignment.template.CallablePairwiseSequenceAligner.java
org.biojava3.alignment.template.CallablePairwiseSequenceScorer.java
org.biojava3.alignment.template.CallableProfileProfileAligner.java
org.biojava3.alignment.template.GapPenalty.java
org.biojava3.alignment.template.GuideTreeNode.java
org.biojava3.alignment.template.HierarchicalClusterer.java
org.biojava3.alignment.template.MatrixAligner.java
org.biojava3.alignment.template.MutableAlignedSequence.java
org.biojava3.alignment.template.MutableProfile.java
org.biojava3.alignment.template.MutableProfilePair.java
org.biojava3.alignment.template.MutableSequencePair.java
org.biojava3.alignment.template.PairInProfileScorer.java
org.biojava3.alignment.template.PairwiseSequenceAligner.java
org.biojava3.alignment.template.PairwiseSequenceScorer.java
org.biojava3.alignment.template.PartitionRefiner.java
org.biojava3.alignment.template.Profile.java
org.biojava3.alignment.template.ProfilePair.java
org.biojava3.alignment.template.ProfileProfileAligner.java
org.biojava3.alignment.template.ProfileProfileScorer.java
org.biojava3.alignment.template.ProfileView.java
org.biojava3.alignment.template.RescoreRefiner.java
org.biojava3.alignment.template.Scorer.java
org.biojava3.alignment.template.SequencePair.java
org.biojava3.alignment.template.SubstitutionMatrix.java
pam250.txt