Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
software [2019/04/30 17:42]
luca [ASPRAlign]
software [2022/12/13 17:07] (current)
luca [Github Repository]
Line 1: Line 1:
-====== ​jHoles ​======+====== ​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. 
 + 
 + 
  
-[[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 
 + 
 +====== jHoles ====== 
 + 
 +[[https://​www.jholes.eu/​|jHoles]] is a tool for topological data analysis.
  
 ====== DISPAS 2.0 ====== ====== DISPAS 2.0 ======