NEFFy

NEFFy integrates all available options to calculate the Number of Effective Sequences (NEFF) across diverse multiple sequence alignment (MSA) formats for proteins, RNAs, and DNAs.

Key Features:

• Cross-molecule support: NEFFy calculates NEFF for MSAs of proteins, RNA, and DNA.
• Format compatibility: NEFFy supports various MSA formats.
• Per-residue NEFF calculation: NEFFy computes NEFF values for individual residues within an alignment.
• Multimeric protein support: NEFFy supports NEFF computation for MSAs of multimeric proteins.
• Computational efficiency and scalability: NEFFy surpasses existing tools in functionality without compromising computational efficiency and scalability.

Scientific Applications:

• Evolutionary diversity quantification: NEFFy quantifies the diversity of sequences in an MSA, which contains fundamental evolutionary information useful in the prediction of structure and function of proteins and nucleic acids.

Methodology:

NEFFy is implemented in C++ with a Python wrapper.