====== GitHub Repository ======

[[https://github.com/bdslab|Bioshape and Data Science Lab]]


====== TaxonClassifier ======

[[https://github.com/bdslab/TaxonClassifier|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 ======

[[https://github.com/bdslab/aspralign|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]]
  * [[https://github.com/bdslab/aspralign/tree/master/download|Download]] the last version of ASPRAlign

====== jHoles ======

[[https://www.jholes.eu/|jHoles]] is a tool for topological data analysis.

====== DISPAS 2.0 ======

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.