Galaxy is "an open, web-based platform for performing accessible, reproducible, and transparent genomic science."
Galaxy provides a way to generate scientific workflows including data integration, and analysis persistence. It could be considered as a publishing platform making computational biology accessible to research scientists that do not have computer programming skills. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
http://galaxy.sb-roscoff.fr: the generalist Galaxy instance with different thematics
NGS: DNASeq, RNASeq, ChipSeq, SNP/Variant calling...
similary search : Blast
Phylogeny: Alignment, Maximum-Likelihood, Distance, Parsimony, Bayesian methods, ...
Population genetics: RADSeq, …
And one instance without account needed:
http://webtools.sb-roscoff.fr: Galaxy instance that hosts tools developped at the Station Biologique de Roscoff in collaboration with ABiMS
Cyanorak Blast: Blast query sequences on Synechococcus and Prochlorococcus strains (blastn, blastp, blastx, tblastn, tblastx). [webpage]
Hectar: Predict subcellular targeting for heterokont proteins.
MicRhoDE workflow: places query sequences into MicRhoDE tree (type-1 rhodopsin phylogeny). [webpage]
Renkan BLAST: blast query sequences to 18S and 28S radiolaria databases (blastn). [webpage]
WiseScaffolder: genome scaffolding of pre-assembled contigs using mate-pair data. [webpage]
ABiMS is also part of the project Workflow4Metabolomics which proposes a dedicated Galaxy instance to analyse LC-MS, GS-MS and NMR data.
analytical drift correction
uni- and multivariate analysis
Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy: a platform for interactive large-scale genome analysis." Genome Research. 2005 Oct; 15(10):1451-5.