Miquel Moretó

Theseus: Fast and Optimal Affine-Gap Sequence-to-Graph Alignment

Theseus provides a fast and optimal affine-gap sequence-to-graph alignment algorithm, outperforming existing methods in speed while maintaining optimality.

Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment

Singletrack improves memory efficiency and performance for gap-affine sequence alignment without sacrificing accuracy.

QuickEd: High-performance exact sequence alignment based on bound-and-align

QuickEd improves sequence alignment speed for long reads by using a bound-and-align strategy, achieving faster performance than existing tools while maintaining accuracy.

BIMSA: Accelerating Long Sequence Alignment Using Processing-In-Memory

BIMSA accelerates long sequence alignment using Processing-In-Memory, achieving significant speedups over existing PIM and CPU implementations.

Optimal gap-affine alignment in O(s) space

This paper introduces BiWFA, an algorithm that performs gap-affine sequence alignment in O(s) memory while maintaining O(ns) time complexity, improving memory efficiency for large-scale alignments.

Accurate and efficient constrained molecular dynamics of polymers through Newton's method and special purpose code

This paper introduces ILVES-PC, an algorithm for accurately and efficiently imposing constraints in molecular dynamics simulations, achieving significant speedups and improved accuracy over existing methods.

WFA-GPU: Gap-affine pairwise alignment using GPUs

This paper introduces WFA-GPU, a GPU-accelerated tool for exact gap-affine sequence alignment, showing significant speed improvements over CPU and other GPU implementations.

AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation

AnchorWave improves genome alignment for genomes with high diversity, structural polymorphism, and whole-genome duplication by using a duplication-informed algorithm and gap cost strategy.