Tootfinder

Practical colinear chaining on sequences revisited
Nicola Rizzo, Manuel C\'aceres, Veli M\"akinen
https://arxiv.org/abs/2506.11750 https://…

Practical colinear chaining on sequences revisited
Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an $O(n \log^3 n)$ time algorithm to chain a set of $n$ anchors so that the chaining cost matches the edit distance of the input sequences, when anchors are maximal exact matches. Moreover, assuming a uniform and sparse distribution of anchors, they provided a practical solution ($\mathtt{ChainX}$) working in $O(n \cdot \mathsf{SOL} + n …

BWT for string collections
Davide Cenzato, Zsuzsanna Lipt\'ak, Nadia Pisanti, Giovanna Rosone, Marinella Sciortino
https://arxiv.org/abs/2506.01092 htt…

BWT for string collections
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with resp…

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