GEPAS: A web-based tool for microarray data analysis and interpretation
GEPAS was one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 10 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. In 2013 GEPAS was discontinued and all its functionality was implemented in Babelomics.
GEPAS offered diverse analysis options that included well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression wer included in subsequent versions.
An extensive re-engineering of GEPAS was carried out which included the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS has been the most quoted web tool in its field and it has been extensively used by researchers of many countries. GEPAS statistics indicate an average usage rate of 500 experiments per day.
All the functionality of GEPAS, is now available within Babelomics http://www.babelomics.org.
Tools no longer supported
Pupasuite: SNP prioritization for large scale genotyping and functional characterization of SNPs in next generation sequencing experiments
PupaSuite is a web tool for the selection of SNPs with potential phenotypic effect, oriented to help in the design of large-scale genotyping projects and to the characterization of new SNPs from next generation technologies.
PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included.
PupaSuite 2 can input lists of SNPs, genes, or chromosomal regions and produce lists of SNPs with their possible phenotypic effect. Moreover, it can also calculate haplotypes and estimate the possible functionality of the corresponding combinations of SNPs.
PupaSuite can also produce graphic interactive analyses of single genes. There, a filter allows displaying SNPs potentially causing different types (structural, regulatory, splicing, etc.) and degrees of alterations.
Phylemon: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypothesis testing
Phylemon 2.0 is the second release of the suite of web-tools for molecular evolution, phylogenetics and phylogenomics. It is conceived as a natural response to the increasing demand of data analysis of experimental scientists seeking to add molecular evolution and phylogenetic insight into their research.
Phylemon 2.0 has several features that differentiate it from other web resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, format conversions, the storage and edition of projects and results,(ii) Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save pipelines for specific phylogenetic analysis to be used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics).
The new web server integrates a suite of more than 30 different tools such as sequence alignment of long genomic regions, alignment refinement, tree reconstruction by distances using the best DNA model explaining the data, DNA model selection and averaging using the jModelTest and HyPhy tools to test for molecular adaptation considering synonymous rate variation across sites. Phylemon 2.0 has been completely re-engineered improving job submission, project, file, and task management.
more info at: http://phylemon.bioinfo.cipf.es