| AggloDel (Unraveling overlapping deletions by agglomerative clustering) This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping deletion predictions. The method does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity, polyploidy, etc. Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of a deletion into account.
| Inferring Candidate Somatic Deletions using Short-Reads Combined from Normal and Mixed Samples Software and Data used in: Wittler R, Chauve C. Consistency-based detection of potential tumor-specfic deletions in matched normal/tumor genomes. In: BMC Bioinformatics.; 2011.
| rococo (Reconstruction of Conserved Optimal Clusters of Orthologs) I have developed this program as part of my Ph.D. project. Rococo reconstructs ancestral gene clusters. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates sets of gene clusters for the inner nodes. In contrast to roci (see below), this method provides a well defined optimization criterion and is not restricted to a specific gene cluster model.
| roci (Reconstruction of Conserved Intervals) I have developed this program during my diploma theses. Roci reconstructs ancestral gene orders of a phylogenetic tree. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates sets of gene orders for the inner nodes, represented by conserved intervals.