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Bioinformatics Tools

Programs marked with W can be used with a web browser and programs marked with C or E can be used with Chipster and Embster graphical user interfaces.

General sequence analysis packages

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

  • Embster A graphical user inteface for EMBOSS, BLAST, MAFFT and Phylip programs

Next generation sequencing data analysis

  • Chipster v2.0 User-friendly analysis software for ChIP-seq, RNA-seq, miRNA-seq and methyl-seq data. Contains a built-in genome browser and workflow functionality.

Microarray data analysis

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

  • R / Bioconductor A statistical environment with support for genomics


Sequence assembly and mapping

  • ABySS Assembler for very short reads
  • Bowtie short read aligner C
  • BWA Burrows-Wheeler aligner for aligning short nucleotide sequences against a reference genome C
  • Maq short read aligner
  • MIRA Whole genome shotgun and EST sequence Assembler
  • SAMtools Utilities for managing SAM/BAM formatted alignment files C
  • SHRiMP short read aligner
  • SOAPdenovo Assembler for very short reads
  • TopHat Splice junction mapper for RNA-Seq reads C
  • Velvet Assembler for very short reads

Proteomics

  • Chipster Easy-to-use graphical software based on R/Bioconductor. Chipster is a generic platform which was originally developed for microarray data analysis, but it has also tools and workflows for proteomics data i.e. from LC-MS and iTRAQ experiments. C

Promoter analysis

Database searching and sequence alignment

  • BLAST Sequence database homology search tool. E

  • CUDASW++ GPGPU accelerated Smith-Waterman search tool for protein sequences
  • Exonerate  Generic sequence alignment tool

  • HMMER Sequence database search based on profile-HMM. E

  • 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 E

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

  • Seaview A multiple sequence alignment editor

  • JalView A multiple sequence alignment editor

Pathway analysis

Phylogenetics

  • BEAST Program for Bayesian MCMC analysis of molecular sequences
  • MrBayes Program for inferring phylogenies using bayesian methods

  • PHYLIP Package for inferring phylogenies E

  • 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

  • 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


Other tools