SimCT ( = Similarity Clustering Tree) is a way to visualize relationships between biological objects annotated to an ontology, in the form of a classification tree.

The resulting classification tree is a simplified subgraph of the ontology, allowing easy interpretation of functional annotations.

The tree can be explored and manipulated with a interactive java viewer.

You have the possibility to visualize simultaneously several trees corresponding to different gene groups or ontologies.

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click here for a brief introduction [Click for a 5-step introduction]

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SimCT allows you to input a list of coding SNPs (rs numbers), and cluster them according to the functional annotation of the host gene.


SimCT has been rewritten to allow handling of larger datasets.

Different ways to use it:

[ Use GO annotations ]

[ Use another OBO ontology ]

[ Cluster SNPs ]

If you are interested in using standard Gene Ontology annotations, you need to provide a list of genes, choose the organism among those supported, and one or several GO sub-ontologies to be used. SimCT will automatically associate your genes with their latest annotations. If you want to use a different ontology than GO, or provide your personnal GO annotations, then you must provide a 2-column list of objects|annotations (space or tab separated), and chose the ontology to be considered. You can cluster human coding SNPs according to the Gene Ontology annotations of the host gene, or based on Disease ontology or Phenotype annotations

C. Herrmann, S. BĂ©rard, L. Tichit "SimCT: a generic tool to visualize ontology based relationships for biological objects" Bioinformatics. 2009 Dec 1;25(23):3197-8.