Bioshape and Data Science Lab

TaxonClassifier is a tool for automatic taxonomy reconstruction via agglomerative clustering.

• Quadrini, Michela; Tesei, Luca; Merelli, Emanuela (2022): Benchmark of 5S, 16S and 23S rRNA Secondary Structures. figshare. Dataset. https://doi.org/10.6084/m9.figshare.20731783.v1
• Quadrini, Michela; Tesei, Luca; Merelli, Emanuela (2022): Automatic Generation of Pseudoknotted RNAs Taxonomy. Submitted, Under Revision. The work introduces the benchmark linked above.

ASPRAlign is a command line tool for Algebraic Structural Pseudoknot RNA Alignment.

• Quadrini, M., Tesei, L. & Merelli, E. An algebraic language for RNA pseudoknots comparison. BMC Bioinformatics 20 (Suppl 4), 161 (2019). https://doi.org/10.1186/s12859-019-2689-5
• Michela Quadrini, Luca Tesei, Emanuela Merelli, ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots, Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3578–3579, https://doi.org/10.1093/bioinformatics/btaa147
• Download the last version of ASPRAlign

jHoles is a tool for topological data analysis.

Dispas 2.0 is an agent-based simulator for fish stock evaluation. It has been implemented focusing on the stock of common sole of the Noerthern and Central Adriatic See.