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NEFFy: a versatile tool for computing the number of effective sequences
Maryam Haghani1, Debswapna Bhattacharya1, T M Murali1
1Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States.
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.
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