• A Tree Viewer
  • AMAP
  • ANGIS
  • Affymetrix GeneChip Operating Software
  • Arlequin
  • BLAST
  • BLAT (bioinformatics)
  • Beacon designer
  • Bellerophon program
  • BioJava
  • BioPHP
  • BioPerl
  • BioPython
  • BioRuby
  • BioSLAX
  • Bioconductor
  • BioExtract
  • Bioinformatics workflow management systems
  • Biskit
  • CS-BLAST
  • Clone manager
  • Clustal
  • Coot (program)
  • Cytoscape
  • DAVID (bioinformatics tool)
  • DIALIGN-T
  • DIALIGN-TX
  • Dendroscope
  • EMovie
  • ETBLAST
  • FASTA
  • Formatdb
  • Free open source bioinformatics projects
  • GENSCAN
  • GENtle (software)
  • GESS
  • GenMAPP
  • Genedata
  • GenePattern
  • Genevestigator
  • HHpred / HHsearch
  • HYPHY (software)
  • Handel (bioinformatics software package)
  • HMMER
  • Integrated Genome Browser
  • JAligner
  • Jalview
  • Jmol
  • List of RNA structure prediction software
  • List of alignment visualization software
  • List of phylogenetic tree visualization software
  • List of phylogenetics software
  • List of sequence alignment software
  • MAFFT
  • MEGAN
  • MODELLER
  • MUMmer
  • MUSCLE
  • Mascot (software)
  • Mass spectrometry data format
  • MassWiz
  • Morphobank
  • OLIGO Primer Analysis Software
  • PDBREPORT
  • PHYLIP
  • PSI Protein Classifier
  • PSORT
  • Phred base calling
  • PhyloXML
  • Protein Analysis Subcellular Localization Prediction
  • List of protein structure prediction software
  • Proteomics Standards Initiative
  • Protomap (proteomics)
  • PupaSuite
  • PyMOL
  • QuteMol
  • RAPTOR (software)
  • RNA integrity number
  • RasMol
  • SEQUEST
  • STING
  • Simbiosys
  • Sirius visualization software
  • Snagger
  • Soaplab
  • Software for protein model error verification
  • Software for protein structure visualization
  • SplitsTree
  • Stemloc
  • Structural alignment software
  • T-Coffee
  • TaveRNA
  • The Proteolysis Map
  • Treefinder
  • UCSF Chimera
  • UGENE
  • Vector NTI
  • Velvet (algorithm)
  • WHAT IF software
  • Webtag (Software)
  • Xrate
  • Yass (software)