Wiki pages
The following pages include content related to BioJava created since the launch of the project. The content has been imported from the legacy mediawiki instance and no new pages have been added.
We did out best to preserve the information, but be aware that some links and content might be outdated or no longer available. We are in the process of organizing and cleaning them up.
- About BioJava
- Algorithm Java port
- Amr AL-HOSSARY
- Andreas Dräger
- Andreas Prlic
- Annotations:List
- Autobuild events
- BOSC2008 Abstract
- BOSC2008 Presentation
- BOSC2009 Presentation
- BioJava3:Coding Conventions
- BioJava3 Design
- BioJava3 Eclipse with SVN
- BioJava3 Feature Requests
- BioJava3:HowTo
- BioJava3 NCBISequenceReader Design
- BioJava3 Proposal
- BioJava3 eclipse
- BioJava3 eclipse template
- BioJava3 license
- BioJava3 logging
- BioJava3 project
- BioJavaKorean:GetStarted
- BioJava:1.5ReleasePlan
- BioJava 3 Use Cases
- BioJava:About
- BioJava:BioJavaInside
- BioJava:BioJavaXDocs
- BioJava:CambridgeDiscussion
- BioJava:Community Portal
- BioJava:CooBook3:HmmerService
- BioJava:CookBook
- BioJava:CookBook1.7
- BioJava:CookBook3.0
- BioJava:CookBook3:AddProtMod
- BioJava:CookBook3:FASTQ
- BioJava:CookBook3:HmmerService
- BioJava:CookBook3:MSA
- BioJava:CookBook3:MSAProfiler
- BioJava:CookBook3:ModFinder
- BioJava:CookBook3:NCBIQBlastService
- BioJava:CookBook3:PSA
- BioJava:CookBook3:PSA DNA
- BioJava:CookBook3:ParsingBlastXMLOutput
- BioJava:CookBook3:ProtMod
- BioJava:CookBook3:ProteinDisorder
- BioJava:CookBook3:ProteinDisorderCLI
- BioJava:CookBook3:Stockholm
- BioJava:CookBook3:SupportedProtMod
- BioJava CookBook
- BioJava:CookBookItaliano
- BioJava:CookBookItaliano:Alphabets
- BioJava:CookBookItaliano:Alphabets:Ambiguous
- BioJava:CookBookItaliano:Alphabets:Canonical
- BioJava:CookBookItaliano:Alphabets:Component
- BioJava:CookBookItaliano:Alphabets:CrossProduct
- BioJava:CookBookItaliano:Alphabets:Custom
- BioJava:CookBookItaliano:Annotations:List
- BioJava:CookBookItaliano:GetStarted
- BioJava:CookBookItaliano:Proteomics
- BioJava:CookBookItaliano:Proteomics:AAindex
- BioJava:CookBookItaliano:SeqIO:GBtoFasta
- BioJava:CookBookItaliano:SeqIO:ReadFasta
- BioJava:CookBookItaliano:SeqIO:ReadGES
- BioJava:CookBookItaliano:SeqIO:WriteInFasta
- BioJava:CookBookItaliano:Sequence
- BioJava:CookBookItaliano:Sequence:ChangeName
- BioJava:CookBookItaliano:Sequence:Edit
- BioJava:CookBookItaliano:Sequence:ExtractGeneRegions
- BioJava:CookBookItaliano:Sequence:Regex
- BioJava:CookBookItaliano:Sequence:Reverse
- BioJava:CookBookItaliano:Sequence:SubSequence
- BioJava:CookBookItaliano:Sequence:Transcribe
- BioJava:CookBookItaliano:Translation
- BioJava:CookBookItaliano:Translation:NonStandart
- BioJava:CookBookItaliano:Translation:OneLetterAmbi
- BioJava:CookBookItaliano:Translation:Single
- BioJava:CookBookItaliano:Translation:SixFrames
- BioJava:CookBookLegacy
- BioJava:CookBook:AAPROP:AdvancedAminoAcidComposition.xml
- BioJava:CookBook:AAPROP:AdvancedElementMass.xml
- BioJava:CookBook:AAPROP:AminoAcidComposition.xml
- BioJava:CookBook:AAPROP:ElementMass.xml
- BioJava:CookBook:AAPROP:MinAminoAcidComposition.xml
- BioJava:CookBook:AAPROP:MinElementMass.xml
- BioJava:CookBook:AAPROP:absorbanceandextinctioncoefficient
- BioJava:CookBook:AAPROP:aliphaticindex
- BioJava:CookBook:AAPROP:apliphaticindex
- BioJava:CookBook:AAPROP:averagehydropathyvalue
- BioJava:CookBook:AAPROP:commandprompt
- BioJava:CookBook:AAPROP:instabilityindex
- BioJava:CookBook:AAPROP:isoelectricpoint
- BioJava:CookBook:AAPROP:main
- BioJava:CookBook:AAPROP:molecularweight
- BioJava:CookBook:AAPROP:netcharge
- BioJava:CookBook:AAPROP:profeat
- BioJava:CookBook:AAPROP:xmlfiles
- BioJava:CookBook:BioSQL:Manage
- BioJava:CookBook:BioSQL:SetupOracle
- BioJava:CookBook:BioSQL:SetupPostGre
- BioJava:CookBook:Blast:Echo
- BioJava:CookBook:Blast:Extract
- BioJava:CookBook:Blast:Parser
- BioJava:CookBook:Blast:XML
- BioJava:CookBook:Cloud:ec2
- BioJava:CookBook:Core:FastaReadWrite
- BioJava:CookBook:Core:GenbankRead
- BioJava:CookBook:Core:Overview
- BioJava:CookBook:Core:SequenceCompare
- BioJava:CookBook:Core:SequenceFeaturePanel
- BioJava:CookBook:Core:Sequences
- BioJava:CookBook:Count:Frequency
- BioJava:CookBook:Count:Residues
- BioJava:CookBook:Count:ToDistrib
- BioJava:CookBook:DP:HMM
- BioJava:CookBook:DP:PairWise
- BioJava:CookBook:DP:PairWise2
- BioJava:CookBook:DP:WeightMatrix
- BioJava:CookBook:Distribution:Bayes
- BioJava:CookBook:Distribution:Composition
- BioJava:CookBook:Distribution:Custom
- BioJava:CookBook:Distribution:Emission
- BioJava:CookBook:Distribution:Entropy
- BioJava:CookBook:Distribution:Gibbs
- BioJava:CookBook:Distribution:RandomSeqs
- BioJava:CookBook:Distribution:XML
- BioJava:CookBook:ExternalSources:NCBIFetch
- BioJava:CookBook:Fasta:Parser
- BioJava:CookBook:GA
- BioJava:CookBook:Interfaces:Alignments
- BioJava:CookBook:Interfaces:Alignments II
- BioJava:CookBook:Interfaces:Coordinates
- BioJava:CookBook:Interfaces:Features
- BioJava:CookBook:Interfaces:ProteinPeptideFeatures
- BioJava:CookBook:Interfaces:ViewAsTree
- BioJava:CookBook:Interfaces:ViewInGUI
- BioJava:CookBook:Interfaces:ViewInGUI2
- BioJava:CookBook:MSA
- BioJava:CookBook:OBO:parse
- BioJava:CookBook:OBO:visualize
- BioJava:CookBook:PDBP:BerkeleySCOP
- BioJava:CookBook:PDB:BioJava Algorithm
- BioJava:CookBook:PDB:CE Algorithm
- BioJava:CookBook:PDB:FATCAT Algorithm
- BioJava:CookBook:PDB:Jmol
- BioJava:CookBook:PDB:SCOP
- BioJava:CookBook:PDB:aboutalign
- BioJava:CookBook:PDB:align
- BioJava:CookBook:PDB:alignGUI
- BioJava:CookBook:PDB:atoms
- BioJava:CookBook:PDB:atomsCalc
- BioJava:CookBook:PDB:bioassembly
- BioJava:CookBook:PDB:datamodel
- BioJava:CookBook:PDB:groups
- BioJava:CookBook:PDB:header
- BioJava:CookBook:PDB:hibernate
- BioJava:CookBook:PDB:ligands
- BioJava:CookBook:PDB:mmcif
- BioJava:CookBook:PDB:mutate
- BioJava:CookBook:PDB:read
- BioJava:CookBook:PDB:read3.0
- BioJava:CookBook:PDB:residuerange
- BioJava:CookBook:PDB:restful
- BioJava:CookBook:PDB:seqres
- BioJava:CookBook:PSA
- BioJava:CookBook:Phylo:Overview
- BioJava:CookBook:Phylo:ProfileToMSA
- BioJava:CookBook:Services:Qblast
- BioJava:CookBook:genome:Overview
- BioJava:CookBool:PDB:mmcif
- BioJava:CookbookFR
- BioJava:CookbookFrench
- BioJava:CookbookFrenchAlphabets
- BioJava:CookbookFrench:Alphabets
- BioJava:CookbookFrench:Alphabets:Ambiguity
- BioJava:CookbookFrench:Alphabets:Canonical
- BioJava:CookbookFrench:Alphabets:Component
- BioJava:CookbookFrench:Alphabets:CrossProduct
- BioJava:CookbookFrench:Alphabets:CustomAlphabets
- BioJava:CookbookFrench:Annotations:Filter
- BioJava:CookbookFrench:Annotations:List
- BioJava:CookbookFrench:BioSQL:Manage
- BioJava:CookbookFrench:Blast:Echo
- BioJava:CookbookFrench:Blast:Extract
- BioJava:CookbookFrench:Blast:Parser
- BioJava:CookbookFrench:Count:Frequency
- BioJava:CookbookFrench:Count:Residues
- BioJava:CookbookFrench:Count:ToDistrib
- BioJava:CookbookFrench:DP:HMM
- BioJava:CookbookFrench:DP:PairWise
- BioJava:CookbookFrench:DP:PairWise2
- BioJava:CookbookFrench:DP:WeightMatrix
- BioJava:CookbookFrench:Distirbution:Custom
- BioJava:CookbookFrench:Distirbution:Emission
- BioJava:CookbookFrench:Distirbution:Entropy
- BioJava:CookbookFrench:Distribution:Bayes
- BioJava:CookbookFrench:Distribution:Composition
- BioJava:CookbookFrench:Distribution:Custom
- BioJava:CookbookFrench:Distribution:Gibbs
- BioJava:CookbookFrench:Distribution:RandomSeqs
- BioJava:CookbookFrench:Distribution:XML
- BioJava:CookbookFrench:ExternalSources:NCBIFetch
- BioJava:CookbookFrench:Fasta:Parser
- BioJava:CookbookFrench:GA
- BioJava:CookbookFrench:Interfaces:Coordinates
- BioJava:CookbookFrench:Interfaces:Features
- BioJava:CookbookFrench:Interfaces:ProteinPeptideFeatures
- BioJava:CookbookFrench:Interfaces:ViewAsTree
- BioJava:CookbookFrench:Interfaces:ViewInGUI
- BioJava:CookbookFrench:Locations:Circular
- BioJava:CookbookFrench:Locations:Feature
- BioJava:CookbookFrench:Locations:Filter
- BioJava:CookbookFrench:Locations:Point
- BioJava:CookbookFrench:Locations:Range
- BioJava:CookbookFrench:Locations:Remove
- BioJava:CookbookFrench:Ontology:OBO
- BioJava:CookbookFrench:PDB:Align
- BioJava:CookbookFrench:PDB:Atom
- BioJava:CookbookFrench:PDB:AtomCalc
- BioJava:CookbookFrench:PDB:Group
- BioJava:CookbookFrench:PDB:Header
- BioJava:CookbookFrench:PDB:Jmol
- BioJava:CookbookFrench:PDB:Mmcif
- BioJava:CookbookFrench:PDB:Mutate
- BioJava:CookbookFrench:PDB:Read
- BioJava:CookbookFrench:PDB:Seqres
- BioJava:CookbookFrench:Proteomics
- BioJava:CookbookFrench:Proteomics:AAindex
- BioJava:CookbookFrench:SeqIO:ABItoSequence
- BioJava:CookbookFrench:SeqIO:Echo
- BioJava:CookbookFrench:SeqIO:GBToFasta
- BioJava:CookbookFrench:SeqIO:ReadFasta
- BioJava:CookbookFrench:SeqIO:ReadGES
- BioJava:CookbookFrench:SeqIO:ReadGESBiojavax
- BioJava:CookbookFrench:SeqIO:WriteInFasta
- BioJava:CookbookFrench:Sequence
- BioJava:CookbookFrench:Sequence:ChangeName
- BioJava:CookbookFrench:Sequence:Edit
- BioJava:CookbookFrench:Sequence:Regex
- BioJava:CookbookFrench:Sequence:Reverse
- BioJava:CookbookFrench:Sequence:SubSequence
- BioJava:CookbookFrench:Sequence:Transcribe
- BioJava:CookbookFrench:Services:Qblast
- BioJava:CookbookFrench:Translation
- BioJava:CookbookFrench:Translation:NonStandard
- BioJava:CookbookFrench:Translation:OneLetterAmbi
- BioJava:CookbookFrench:Translation:Single
- BioJava:CookbookFrench:Translation:SixFrame
- BioJava:CookbookKorean
- BioJava:CookbookPortuguese
- BioJava:CookbookPortuguese:Alphabets
- BioJava:CookbookPortuguese:Alphabets:CrossProduct
- BioJava:CookbookPortuguese:Alphabets:Custom
- BioJava:CookbookPortuguese:Blast:Parser
- BioJava:CookbookPortuguese:Count:Frequency
- BioJava:CookbookPortuguese:Count:Residues
- BioJava:CookbookPortuguese:Interfaces:ViewAsTree
- BioJava:CookbookPortuguese:PDB:mutate
- BioJava:CookbookPortuguese:PDB:read
- BioJava:CookbookPortuguese:Proteomics
- BioJava:CookbookPortuguese:SeqIO:WriteInFasta
- BioJava:CookbookPortuguese:Sequence
- BioJava:CookbookPortuguese:Translation
- BioJava:Cookbook:Alphabets
- BioJava:Cookbook:Alphabets:Ambiguous
- BioJava:Cookbook:Alphabets:Component
- BioJava:Cookbook:Alphabets:Cononical
- BioJava:Cookbook:Alphabets:CrossProduct
- BioJava:Cookbook:Alphabets:Custom
- BioJava:Cookbook:Annotations:Filter
- BioJava:Cookbook:Annotations:List
- BioJava:Cookbook:Annotations:List2
- BioJava:Cookbook:Locations:Circular
- BioJava:Cookbook:Locations:Feature
- BioJava:Cookbook:Locations:Filter
- BioJava:Cookbook:Locations:Point
- BioJava:Cookbook:Locations:Range
- BioJava:Cookbook:Locations:Remove
- BioJava:Cookbook:Proteomics
- BioJava:Cookbook:Proteomics:AAindex
- BioJava:Cookbook:SeqIO:ABItoSequence
- BioJava:Cookbook:SeqIO:Echo
- BioJava:Cookbook:SeqIO:FASTQ
- BioJava:Cookbook:SeqIO:GBtoFasta
- BioJava:Cookbook:SeqIO:ReadFasta
- BioJava:Cookbook:SeqIO:ReadGES
- BioJava:Cookbook:SeqIO:ReadGESBiojavax
- BioJava:Cookbook:SeqIO:WriteInFasta
- BioJava:Cookbook:Sequence
- BioJava:Cookbook:Sequence:ChangeName
- BioJava:Cookbook:Sequence:Edit
- BioJava:Cookbook:Sequence:ExtractGeneRegions
- BioJava:Cookbook:Sequence:Regex
- BioJava:Cookbook:Sequence:Reverse
- BioJava:Cookbook:Sequence:SubSequence
- BioJava:Cookbook:Sequence:Transcribe
- BioJava:Cookbook:Translation
- BioJava:Cookbook:Translation:NonStandart
- BioJava:Cookbook:Translation:OneLetterAmbi
- BioJava:Cookbook:Translation:Single
- BioJava:Cookbook:Translation:SixFrames
- BioJava:Current events
- BioJava:Download
- BioJava:Download 1.3
- BioJava:Download 1.4
- BioJava:Download 1.5
- BioJava:Download 1.6
- BioJava:Download 1.7.1
- BioJava:Download 1.7
- BioJava:Download 1.8.1
- BioJava:Download 1.8.2
- BioJava:Download 1.8.4
- BioJava:Download 1.8.5
- BioJava:Download 1.8
- BioJava:Download 1.9.0
- BioJava:Download 1.9.1
- BioJava:Download 3.0.1
- BioJava:Download 3.0.2
- BioJava:Download 3.0.3
- BioJava:Download 3.0.4
- BioJava:Download 3.0.5
- BioJava:Download 3.0.6
- BioJava:Download 3.0.7
- BioJava:Download 3.0.8
- BioJava:Download 3.0
- BioJava:Download 3.1.0
- BioJava:Download 4.0.0
- BioJava:Download 4.1.0
- BioJava:Download 4.2.0
- BioJava:EnsureCopyrightHeader
- BioJava:Forum
- Get Started
- BioJava:GetStartedLegacy
- BioJava:Hackathon2010
- BioJava:Hackaton2010
- BioJava:Hackers Guide
- BioJava:License
- BioJava:Logo
- BioJava:MailingLists
- BioJava:Make release
- BioJava:MavenMigration
- BioJava:Modules
- BioJava:My build biojava
- BioJava:Performance
- BioJava:Performance:AlignMyoHemo
- BioJava:Performance:AlignSW
- BioJava:Performance:ReadDrosophila
- BioJava:Performance:ReverseComplement
- BioJava:PhyloSOC07
- BioJava:PhyloSOC07 doc
- BioJava:Site support
- BioJava:SocialNetworking
- BioJava:ToDo
- BioJava:Tutorial
- BioJava:Tutorial:Blast-like Parsing Cook Book
- BioJava:Tutorial:Blast2HTML
- BioJava:Tutorial:Blast2HTML Example Application
- BioJava:Tutorial:ChangeEvent example using Distribution objects
- BioJava:Tutorial:ChangeEvent overview
- BioJava:Tutorial:Changeability, Mutability and Events
- BioJava:Tutorial:Changeability examples
- BioJava:Tutorial:Dynamic programming examples
- BioJava:Tutorial:Implementing Changeable
- BioJava:Tutorial:Installing BioSQL
- BioJava:Tutorial:Installing and using BioSQL
- BioJava:Tutorial:MultiAlignClustalW
- BioJava:Tutorial:Sequence IO basics
- BioJava:Tutorial:Sequences and Features
- BioJava:Tutorial:Simple HMMs with BioJava
- BioJava:Tutorial:Symbols and SymbolLists
- BioJava talk:About
- BioJava talk:BioJavaXDocs
- BioJava talk:CookBook
- BioJava talk:CookBook1.7
- BioJava talk:CookBook3:NCBIQBlastService
- BioJava talk:CookBook3:PSA DNA
- BioJava talk:CookBook:Blast:Parser
- BioJava talk:CookBook:Blast:XML
- BioJava talk:CookBook:Interfaces:ViewInGUI2
- BioJava talk:CookBook:PDB:ligands
- BioJava talk:CookBook:PDB:mutate
- BioJava talk:CookbookPortuguese
- BioJava talk:Cookbook:SeqIO:ReadGES
- BioJava talk:Cookbook:Sequence:ExtractGeneRegions
- BioJava talk:Forum
- BioJava talk:MailingLists
- BioJava talk:ToDo
- BioJava talk:Tutorial:Blast-like Parsing Cook Book
- BioJava talk:Tutorial:Installing and using BioSQL
- BioJava talk:Tutorial:Simple HMMs with BioJava
- BioJava talk:Tutorial:Symbols and SymbolLists
- BioLit
- BiojavaKorean:Cookbook:Alphabets
- BiojavaKorean:Cookbook:Alphabets:Custom
- CE-CP
- CECP
- CVS to SVN Migration
- Category:People
- Category:Tutorial
- Chuan Hock Koh
- Coding exercise
- Combinatorial Extension with Circular Permutations
- Core Team
- Current events
- Czar
- David Huen
- Dazzle
- DazzleQuickStartGuide
- Dazzle:Ensembl
- Dazzle:deployment
- Dazzle:deployment google app engine
- Dazzle:eclipse
- Dazzle:examplePlugin
- Dazzle:plugins
- Dazzle:writeplugin
- Developer Code Access
- Dickson Guedes
- Dickson S. Guedes
- Frequently Asked Questions
- File talk:Biojava logo.gif
- Francois Pepin
- GSoC:AAPropertiesComputation
- GSoC:MSA
- GSoC:MSA Design
- GSoC:PTM
- Get involved
- Get source
- Git workflow
- Google Summer of Code
- Google Summer of Code 2010
- Google Summer of Code 2011
- Google Summer of Code 2012
- Google Summer of Code 2013
- Google Summer of Code 2014
- Help talk:Contents
- How are Physico-Chemical Properties Computed?
- How to integrate BioJava in NetBeans IDE
- Jianjiong Gao
- Keith James
- MBTOpen:About
- MSA skype 20100608
- MSA skype 20100615
- MSA skype 20100622
- MSA skype 20100629
- MSA skype 20100721
- MSA skype 20100727
- MSA skype 20100810
- MSA skype 20100817
- Main Page
- Maintainers wanted
- Mark Chapman
- Mark Schreiber
- Martin Szugat
- Matthew Pocock
- MediaWiki talk:Sidebar
- Michael Heuer
- RCSB Viewers:About
- RCSB Viewers:Architectural Overview
- RCSB Viewers:Developer Environment
- RCSB Viewers:MBT Libs:Bonds and Nucleic Acid Identification^Classification
- RCSB Viewers:MBT Libs:Fragment (Secondary Structure) Definition
- RCSB Viewers:MBT Libs:PDBToNdbConverter
- RCSB Viewers:Projects Overview
- RCSB Viewers:Source Division
- RCSB Viewers:Viewer Framework:General Rendering
- RCSB Viewers:Viewer Framework:Picking
- Richard Holland
- SVN to GIT Migration
- SVNmigrationHistory
- Sandbox
- Scala
- Short coding exercise
- Sitesupport-url
- Sylvain Foisy
- Test.fasta
- Test Jmol with PDB file
- Test Jmol with XYZ file
- Thomas Down
- To know folllow this link
- Tutorial:Footer
- UsageAnalysis
- User talk:Ammad
- User talk:Biki proteomics
- User talk:Eye glasses
- User talk:Foisys
- User talk:HomeWork Solver
- User talk:John Ting
- User talk:Johnwall7144
- User talk:Lily Joey
- User talk:Mauricio
- User talk:S Khadar
- User talk:Seeker
- User talk:Sibel Karabulut
- User talk:Suji
- User talk:Sulaman
- User talk:Wy666
- User talk:Yasset.perez
- Documentation