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software [2019/04/30 17:42] luca [ASPRAlign] |
software [2022/12/13 17:06] luca |
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| - | ====== jHoles ====== | + | ====== Github Repository ====== |
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| + | [[https://github.com/bdslab|Bioshape and Data Science Lab]] | ||
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| + | ====== TaxonClassifier ====== | ||
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| + | [[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. | ||
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| - | [[https://www.jholes.eu/|jHoles]] is a tool for topological data analysis. | ||
| ====== ASPRAlign ====== | ====== ASPRAlign ====== | ||
| [[https://github.com/bdslab/aspralign|ASPRAlign]] is a command line tool for Algebraic Structural Pseudoknot RNA Alignment. | [[https://github.com/bdslab/aspralign|ASPRAlign]] is a command line tool for Algebraic Structural Pseudoknot RNA Alignment. | ||
| - | * {{ :aspralign-0.91.zip |Download}} the last version of ASPRAlign | + | * 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]] |
| - | * [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2689-5|Paper]] about Algebraic and Structural RNA Trees and computation of ASPRA distance among RNA secondary structures with arbitrary pseudoknots. | + | * 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 | ||
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| + | ====== jHoles ====== | ||
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| + | [[https://www.jholes.eu/|jHoles]] is a tool for topological data analysis. | ||
| ====== DISPAS 2.0 ====== | ====== DISPAS 2.0 ====== | ||