Programs marked with W can be used with a web browser.

General sequence analysis packages

• EMBOSS  Programs for analysing DNA and amino acid sequence data. W

DNA microarray data analysis

• Chipster Easy-to-use graphical software for DNA microarray data analysis based on R/Bioconductor

• R / Bioconductor A statistical environment with support for genomics

Sequence assembly

• MIRA Whole Genome Shotgun and EST Sequence Assembler
• Velvet assembler for very short reads
• SAMtools utilities for manging SAM/BAM formatted alignmnet files
  

Promoter analysis

• GenomatixSuitePE Databases and tools for promoter and pathway analysis. W

Database searching and sequence alignment

• BLAST Sequence database homology search tool. W

• Exonerate  Generic sequence alignment tool W

• HMMER Sequence database search based on profile-HMM.

• PairsDB  A tool to retrieve pre-calculated BLAST and PSI-BLAST results form the PairsDB database. W
• SSAHA2 Fast hash function based search tool for DNA sequences
  
• Wise2 (GeneWise) comparing protein sequences and HMMs to nucleotide sequences

Multiple sequence alignment

• CD-HIT Sequence clustering and redundancy removal

• ClustalW Multiple sequence alignment W

• Muscle A fast and accurate multiple sequence alignment program W
  
• MAFFT Multiple sequece alignment program W
  

• Seaview A multiple sequence alignment editor

• JalView A multiple sequence alignment editor

Pathway analysis

• Ingenuity Pathways Analysis W

• GenomatixSuitePE Databases and tools for promoter and pathway analysis. W

Phylogenetics

• MrBayes Program for inferring phylogenies using bayesian methods

• PHYLIP Package for inferring phylogenies W

• POY Program for inferring phylogenies

• RAxML Fast program for inferring phylogenies with likelihood

• TNT A fast program for inferring phylogenies with parsimony methods

Structural Biology

• Discovery Studio Molecular modeling package D
  

• Maestro Molecular modeling package

• RasMol Molecular graphics visualisation

• Rosetta Protein structure prediction and protien docking tool
  

• VMD Molecular graphics visualisation

RNA secundary structure prediction

• Vienna Package (within EMBOSS)
  

Gene mapping

• MERLIN A fast program for nonparametric linkage, and haplotyping

• LINKAGE / FASTLINK Parametric linkage analysis

• GENEHUNTER Multi-point linkage calculations for small pedigrees

• SNPHAP Population-based SNP haplotype reconstruction

• SimWalk2 Haplotyping, and non-parametric analysis

• DHSMAP Fine-mapping of qualitative traits by linkage disequilibrium

• SLINK Power simulation tool for linkage studies based

• PedCheck Detects marker typing incompatibilities in pedigree data

• Mega2 Converts Linkage-format files to other formats

• Pseudomarker Joint linkage and LD analysis

Systems biology

• bestim Gene regulatory network inference under the Boolean network model.

• decomptool Decomposition of biochemical networks into subnetworks

• FBAtool A program for flux balance analysis of metabolic networks

• SOSlib Program for running simulations for SBML formatted models.

Other tools

• Bioperl Bioinformatics tools for perl programming

• Jnet Protein secondary structure prediction program

• Primer PCR primer design

• TMHMM Transmembrane helix prediction tool