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ADHoRe (Automatic Detection of Homologous Regions) is a software tool that automatically detects genomic regions with statistically significant conserved gene content and order.

The ADHoRe software is freely available for academic users. Commercial users need to register for a commercial license. Please contact V.I.B license manager Chris De Jonghe for further details.

It should be noted however that have recently published an extension of ADHoRe called i-ADHoRe. As this package also provides the same functionality as ADHoRe but is easier to use and provides clearer output you might want to consider this package instead. Click here to go to the i-ADHoRe download page.

Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12(11):1792-801.

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AFLPinSilico performs AFLP simulations with different combinations of restriction enzymes or selective nucleotides, on organisms or data sets for which DNA sequences are available.

Rombauts, S., Van de Peer, Y., Rouzé, P. (2003) AFLPInsilico, simulating AFLP fingerprints. Bioinformatics 19(6):776-7.

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We have developed a Java application called ASaturA that discriminates amino acid substitutions with high and low probabilities of occurrence.

Van de Peer, Y., Frickey, T., Taylor, J.S., Meyer, A. (2002) Dealing with saturation at the amino acid level: A case study involving anciently duplicated zebrafish genes. Gene 295(2):205-11.

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The ATCOECIS resource makes it possible to query coexpression data, GO and cis-regulatory elements annotations, submit user-defined gene sets for motif analysis and provides an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis.

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CyClus3D is a Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.

* Audenaert, P., * Van Parys, T., Brondel, F., Pickavet, M., Demeester, P., Van de Peer, Y., Michoel, T. (2011) CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinformatics 27(11):1587-8. *contributed equally

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DASS-GUI is a stand-alone program written in C++ that calculates all significant closed sets of a given dataset containing the host sets. Some of the used algorithms are taken from Hollunder et al. (2007).

* Hollunder, J., * Friedel, M., Kuiper, M., Wilhelm, T. (2010) DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics 26(7):987-9. *contributed equally

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Diffany is an open-source toolbox for calculating and visualizing differential networks. It is packaged in three separate modules: the algorithms as the core library, a commandline interface to generate Diffany networks through the console, and a cytoscape plugin for generation, visualisation and easy manipulation of the input and output networks.

Van Landeghem, S., Van Parys, T., Dubois, M., Inzé, D., Van de Peer, Y. (2016) Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinformatics 17(1):18.

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Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model.

Michoel, T., Van de Peer, Y. (2006) A helicoidal transfer matrix model for inhomogeneous DNA melting. Physical Review E. 73(1 Pt 1):011908.

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ENIGMA is a software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating GO annotation and transcription factor binding information and by learning tentative regulation programs.

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EP3 is a tool for the identification of the core region of a eukaryotic gene promoter. It uses universal properties of the promoter to detect those regions in a whole genome context. EP3 has been tested on several eukaryotes ranging from protists to human. On human it is, at the moment, the best performing tool to identify regions that are associated with transcription initiation.

Abeel, T., Van de Peer, Y., Saeys, Y. (2009) Towards a gold standard for promoter prediction evaluation. Bioinformatics 25(12):i313-20.

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An open source gene finder to annotate eukaryotic sequences

Foissac, S., Gouzy, J.P., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van de Peer, Y., Rouzé, P., Schiex, T. (2008) Genome Annotation in Plants and Fungi: EuGene as a model platform. Curr. Bioinform. 3(2):87-97.

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EVEX is a large-scale text mining resource containing millions of biomolecular events extracted from PubMed abstracts and PubMed Central full-text articles. The data in EVEX can be accessed by pubmed ID, gene/protein symbol, Entrez Gene ID, UniProt ID or through gene families. This rich resource is distributed as a MySQL database, can be browsed via an online web application, and is accessible through an API.

Van Landeghem, S., Hakala, K., Rönnqvist, S., Salakoski, T., Van de Peer, Y., Ginter, F. (2012) Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology and Indirect Associations. Advances in Bioinformatics 2012:582765.

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ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments.

Raes, J., Van de Peer, Y. (1999) ForCon : a software tool for the conversion of sequence alignments. Embnet. News 6, 10-12..

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FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA

Van Bel, M., Saeys, Y., Van de Peer, Y. (2008) FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. Bioinformatics 24(13):1532-3.

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GaneSh - a software to cluster expression data by Gibbs sampling procedure

Joshi, A., Van de Peer, Y., Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24(2):176-83.

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GenomeView is a stand-alone sequence browser specifically designed to visualize and manipulate a multitude of genomics data interactively.

Abeel, T., Van Parys, T., Saeys, Y., Galagan, J., Van de Peer, Y. (2012) GenomeView: a next-generation genome browser. Nucleic Acids Res. 40(2):e12.

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Xie, G.-C., Tzfadia, O., Levy, AA., Weithorn, E., Peled-Zehavi, H., Van Parys, T., Van de Peer, Y., Galili, G. (2016) hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms. Autophagy 12(5):876-87.

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HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures. Both an online and offline version is available.

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i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

The i-ADHoRe software is freely available for academic users. Commercial users need to register for a commercial license. Please contact Yves Van de Peer for further details.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008) i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24(1):127-8.

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The latest version of i-ADHoRe, a highly sensitive tool to detect degenerated homology relations within and between different genomes.

* Proost, S., * Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., Van de Peer, Y., Vandepoele, K. (2012) i-ADHoRe 3.0 - Fast and Sensitive Detection of Genomic Homology in Extremely Large Data Sets. Nucleic Acids Res. 40(2):e11. *contributed equally

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Java package for learning module networks from gene expression data.

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MatrixClust is a Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network. The algorithm is an improved version of the fuzzy clustering algorithm described in

Joshi, A., Van de Peer, Y., Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24(2):176-83.

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MORPH (“MOdule guided Ranking of candidate PatHway genes”) is an algorithm to associate candidate genes with a given target pathway. Unlike any other algorithm in plant sciences, MORPH tests multiple combinations by learning how to choose among various forms of evidence (large scale data sets) to link genes to a specific target pathway.

Tzfadia, O., Amar, M., Bradbury, LMT., Wurtzel, ET., Shamir, R. (2012) The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana pathways. The Plant Cell 24,4389-406.

Network Motif Clustering Toolbox
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The Network Notif Clustering Toolbox is a toolbox for clustering topological network motifs in large-scale, integrated networks.

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The Cytoscape plug-in ‘Pathicular’ identifies path motifs in integrated networks and arranges them in a modular structure. After the integrated network and the source network (deletion or overexpression in this case) are loaded into Cytoscape, Pathicular can be used to find all the paths of a given type in the source network using the integrated network. A p-value is provided to check the overrepresentation of the path of interest.

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We present a large-scale benchmarking study of 17 state-of-the-art PPPs.

Abeel, T., Van de Peer, Y., Saeys, Y. (2009) Towards a gold standard for promoter prediction evaluation. Bioinformatics 25(12):i313-20.

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ProNet is a tool to search a module network inferred with the LeMoNe algorithm using prostate cancer expression data.

Bonnet, E., Michoel, T., Van de Peer, Y. (2010) Prediction of a regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 26(18):i638-44.

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ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.

Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y. (2008) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 24(13):i24-31.

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This is RANDFOLD version 2. The software compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

* Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20(17):2911-7. *contributed equally

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SPADS (Specific Primer and Amplicon Design Software) is a tool for the design of specific GSTs (Gene Specific Tags).

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A splice site prediction tool named SpliceMachine that
  • shows state-of-the-art prediction performance on Arabidopsis thaliana and human sequences,
  • performs a computationally fast annotation and
  • can be trained by the user on its own data.

Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005) Predicting splice sites from high-dimensional local context representations. Bioinformatics 21(8):1332-8.

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StartScan is a tool to detect translation initiation sites (TIS) in genomic sequences. Due to its efficient design, StartScan shows state-of-the-art performance on genome wide TIS detection, while at the same time being a fast annotation tool. So far, the model only works for Human, but models for other organisms can be trained upon request.

Saeys, Y., Abeel, T., Degroeve, S., Van de Peer, Y. (2007) Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics 23(13):i418-23.

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TAPIR is a web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA - target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA - target duplex having a large loop, making them undetectable by traditional tools.

Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26(12):1566-8.

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TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.

Van de Peer, Y., De Wachter, Y. (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10(5):569-70.

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This package contains 3 small programs to convert phylogenetic trees between NH, NHX and Treecon formats.

These 3 programs are implemented as TCL ( scripts. TCL is installed by default on most Unix systems (Linux, MacOS X, Solaris,...). Windows users will first need to install TCL.

Venn Diagrams
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A simple but fast tool to calculate the intersection(s) of list of elements. It produces textual and graphical output

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ZT is a free software tool which performs simple and partial Mantel tests.

Van de Peer, Y. (2002) ZT: a software tool for simple and partial Mantel tests. J. Stat. Softw. 7, 1-12..



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