Ultrafast and ultralarge multiple sequence alignments using TWILIGHT.

ABSTRACT:

Motivation

Multiple sequence alignment (MSA) is a fundamental operation in bioinformatics, yet existing MSA tools are struggling to keep up with the speed and volume of incoming data. This is because the runtimes and memory requirements of current MSA tools become untenable when processing large numbers of long input sequences, and they also fail to fully harness the parallelism provided by modern CPUs and GPUs.

Results

We present Tall and Wide Alignments at High Throughput (TWILIGHT), a novel MSA tool optimized for speed, accuracy, scalability, and memory constraints, with both CPU and GPU support. TWILIGHT incorporates innovative parallelization and memory-efficiency strategies that enable it to build ultralarge alignments at high speed even on memory-constrained devices.

SUBMITTER: Tseng YH 

PROVIDER: S-EPMC12261412 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature