JustClust is a tool for analysing biological data with cluster analysis. JustClust can handle many formats of data and cluster the data with many state-of-the-art techniques. The aim of JustClust is to provide an easy-to-use application which can perform any analysis on any data.
GEMS is a suit of softweares for entropy-scaling searching of massive biological data.
Ammolite is production-quality software designed to do a Tanimoto distance similarity search over chemical graphs for small molecules.
MICA (Metagenomic Inquiry Compressive Acceleration) is a full drop-in replacement for BLASTX and DIAMOND supporting all command-line options that is 3.5x faster than DIAMOND (and over 3000x faster than BLASTX) with no loss in specificity and less than 5% loss in sensitivity.
esFragBag (entropy-scaling FragBag) is prototype software that applies entropy-scaling to accelerate only the all r-nearest neighbor search functionality of FragBag by a factor of ~10 with no loss in specificity and less than 0.2% loss in sensitivity.
NYoSh (Not your ordinary Shell) Analysis Workbench is a data analysis workbench built on top of MPS. Takes advantage of composable languages to create a platform intermediate between command line flexibility and user-friendly custom interfaces.
BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.
BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494.
MOBY (Model Organism Bring Your) system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach.