# An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study

## TL;DR

This paper introduces a framework to compare and deploy multiple sequence alignment tools efficiently in high-performance computing environments.

## Contribution

A novel nf-core framework is introduced for systematic evaluation and deployment of MSA tools in HPC settings.

## Key findings

- The framework enables streamlined deployment and comparison of multiple sequence alignment tools.
- It serves as a proof of concept for broader bioinformatics tool evaluation.
- The framework is open-source and available for immediate use by the MSA community.

## Abstract

The computational complexity of many key bioinformatics problems has resulted in numerous alternative heuristic solutions, where no single approach consistently outperforms all others. This creates difficulties for users trying to identify the most suitable tool for their dataset and for developers managing and evaluating alternative methods. As data volumes grow, deploying these methods becomes increasingly difficult, highlighting the need for standardized frameworks for seamless tool deployment and comparison in high-performance computing (HPC) environments. Multiple sequence aligners (MSAs) rank among the most commonly employed modeling techniques in bioinformatics, playing a crucial role in applications such as protein structure prediction, phylogenetic reconstruction, and variant effect prediction. MSAs are NP-hard problems, which makes them a major example of computational challenges where heuristic solutions are essential. Here, we present a pilot design of an nf-core framework for streamlined tool deployment and rigorous performance evaluation focusing on the MSA software ecosystem. While showcased with the integration of popular MSA tools and designed to directly benefit the MSA community, we also present the framework as a proof of principle for the broader bioinformatics community. nf-core/multiplesequencealign is free open-source software available at https://nf-co.re/multiplesequencealign.