ArticleBioinformatics (Oxford, England)2026
NEFFy: a versatile tool for computing the number of effective sequences.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- DeorphaNN: Virtual screening of GPCR peptide agonists using AlphaFold-predicted active-state complexes and deep learning embeddings.Molecular cell · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- MAKA-Map: Real-Valued Distance Prediction for Protein Folding Mechanisms via a Hybrid Neural Framework Integrating the Mamba and Kolmogorov-Arnold Networks.Biomolecules · 2026Article
- Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.Nucleic acids research · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- CASP16 Protein Monomer Structure Prediction Assessment.Proteins · 2026Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- Article
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Assessment of Protein Complex Predictions in CASP16: Are we making progress?bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationA 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.
resultsWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.