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README.md

README.md

Nepal

Neural network Enhanced Profile Alignment Library.

Abstract

Nepal is a profile comparison aligner with optimized scoring function for remote sequence alignment.

Usage

This directory includes several programs, nepal, pssmcompiler and etc.

Nepal

Nepal accepts a pairwise PSSM text file, which is generated by pssmcompiler described below, as an input and outputs an alignment in fasta format.

$ nepal --input [PSSM text file]

Pssmcompiler

The python program, pssmcompiler accepts a pairwise sequence fasta file and outputs Nepal readable profile file. You need to set the correct directory of a binary of deltablast, cdd_delta and a pseudo dataset in advance of use of the program.

Dfnn

Dfnn computes inference of derivative free neural network with CMA-ES. Using the program, the parameters for Nepal was obtained. To compile the program, your computer requires a library "eigen3" installed and C++ compiler.

Reference

Yamada KD, Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment, Algorithms for molecular biology, accepted, 2018