Softwares from Sanger Institute
- Alfresco - FRont-End for Sequence COmparison
- Artemis - a free genome viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and also its six-frame translation
- ACT - a DNA sequence comparison viewer written in Java. It is based on the software for Artemis, the genome viewer and annotation tool
- Alien_hunter - an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs)
- DNAPlotter - makes use of the existing circular plot in Jemboss and the Artemis sequence libraries
- Blast - the sequencing projects' Blast Search Services
- CAF - a text format for describing sequence assemblies
- CnD - a copy number variant caller for inbred strains
- DAS - the Institute provides support for the Distributed Annotation Systems via a range of different projects, websites and applications
- Doublescan - a program for comparative ab initio prediction of protein coding genes in mouse and human DNA
- Eponine - a probabilistic method for detecting transcription start sites in mammalian genomic sequence
- Est_DB - a software suite and database system designed to support expressed sequence tag (EST) sequencing projects, and to provide comprehensive bioinformatic analysis of sequenced EST libraries, for gene discovery and other purposes
- GFF - a format for describing genes and other features associated with DNA, RNA and Protein sequences
- GLIDERS - Genome-wide linkage disequilibrium repository and search engine
- Illuminus - a fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology
- Image - a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments
- Logomat-M - a method to graphically visualize all cenral aspects of profile Hidden Markov Models (pHMMs), thus generalizing the concept of sequence logos
- Logomat-P - illustrates the similarities of pairs of protein family profiles in an intuitive way
- Lookseq - a web-based application for alignment visualization, browsing and analysis of genome sequence data
- Margarita - infers genealogies from population genotype data and uses these to map disease loci
- Mascot Percolator - a software package that interfaces the database search algorithm Mascot with Percolator
- NestedMICA - a method for discovering over-represented short motifs in large sets of strings, for example in finding transcription-factor-binding sites in DNA sequences
- NPG - Short read sequencing pipeline
- PEER - A Bayesian framework to account for complex non-genetic factors in high-dimensional phenotype data
- Phusion - a software package for assembling genome sequences from whole genome shotgun(WGS) reads
- Projector - a program for the comparative, homology based prediction of protein coding genes in mouse and human DNA
- Proserver - a very lightweight DAS server written in Perl
- PSILC - Pseudogene inference from loss of constraint
- Quicktree - allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods
- SCOOP - allows the comparison of families of proteins
- SSAHA - a software tool for very fast matching and alignment of DNA sequences
- SSAHA2 - a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences
- SSAHAest - a software tool for very fast matching and alignment of ESTs/cDNAs to genomic DNA sequences
- SSAHAsnp - a polymorphism detection tool, which detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence