aphid: an R package for analysis with profile hidden Markov models.

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Hidden Markov Models (HMMs) and profile HMMs are crucial for biological sequence analysis.
• Existing tools may lack comprehensive functionality or efficient implementation.

Purpose of the Study:

• To introduce the 'aphid' R package for HMM and profile HMM manipulation.
• To provide an efficient and user-friendly tool for biological sequence analysis.

Main Methods:

• The 'aphid' R package is implemented in R, with computationally intensive algorithms (Viterbi, forward, backward) in C++.
• Parallelization is used to enhance the speed and efficiency of dynamic programming recursions.

Main Results:

• The package supports deriving, training, plotting, importing, and exporting HMMs and profile HMMs.
• Parallelized C++ implementations ensure efficient computation for complex analyses.

Conclusions:

• The 'aphid' package offers a robust and efficient solution for HMM-based biological sequence analysis within the R environment.
• Its comprehensive features and optimized performance facilitate broader application of HMMs in bioinformatics.