NEFFy: A Versatile Tool for Computing the Number of Effective Sequences.

Bioinformatics (Oxford, England) Pub Date : 2025-06-03 DOI:10.1093/bioinformatics/btaf222

Maryam Haghani, Debswapna Bhattacharya, T M Murali

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Abstract

Motivation: A Multiple Sequence Alignment (MSA) contains fundamental evolutionary information that is useful in the prediction of structure and function of proteins and nucleic acids. The "Number of Effective Sequences" (NEFF) quantifies the diversity of sequences of an MSA. While several tools embed NEFF calculation with various options, none are standalone tools for this purpose, and they do not offer all the available options.

Results: We developed NEFFy, the first software package to integrate all these options and calculate NEFF across diverse MSA formats for proteins, RNAs, and DNAs. It surpasses existing tools in functionality without compromising computational efficiency and scalability. NEFFy also offers per-residue NEFF calculation and supports NEFF computation for MSAs of multimeric proteins, with the capability to be extended to DNAs and RNAs.

Availability and implementation: NEFFy is released as open-source software under the GNU Public License v3.0. The source code in C ++ and a Python wrapper are available at https://github.com/Maryam-Haghani/NEFFy. To ensure users can fully leverage these capabilities, comprehensive documentation and examples are provided at https://Maryam-Haghani.github.io/NEFFy.

Supplementary information: Supplementary data are available at Bioinformatics online.

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NEFFy：一个计算有效序列数的通用工具。

动机：多序列比对（MSA）包含基本的进化信息，在预测蛋白质和核酸的结构和功能方面是有用的。“有效序列数”（Number of Effective Sequences， NEFF）用来量化MSA序列的多样性。虽然有几个工具将NEFF计算嵌入到各种选项中，但没有一个是用于此目的的独立工具，并且它们不提供所有可用的选项。结果：我们开发了NEFFy，这是第一个集成所有这些选项的软件包，并计算蛋白质、rna和dna的不同MSA格式的NEFF。它在功能上超越了现有的工具，而不影响计算效率和可扩展性。NEFFy还提供每个残基的NEFF计算，并支持多聚体蛋白的msa的NEFF计算，具有扩展到dna和rna的能力。可用性和实现：NEFFy在GNU公共许可证v3.0下作为开源软件发布。c++源代码和Python包装器可从https://github.com/Maryam-Haghani/NEFFy获得。为了确保用户能够充分利用这些功能，全面的文档和示例提供在https://Maryam-Haghani.github.io/NEFFy.Supplementary信息：补充数据可在Bioinformatics在线。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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