genoaligner

Pairwise sequence alignment for R, from one portable C++17 core.

genoaligner provides edit-distance (Levenshtein / WFA-equivalent) and Smith-Waterman local alignment, both with score and CIGAR reconstruction, from a self-contained C++17 core that needs no GPU toolchain — so it builds and runs on CRAN and anywhere R runs.

The two entry points are designed to slot straight into a data.frame/tibble pipeline:

align(c("AAAACCC", "ACGT"), c("AAAATCC", "ACCT"), smax = 8)
align_sw(c("ACGTACGT", "GGGG"), "ACGTTCGT", scoring = c(2, -3, 5, 2))

Install

From GitHub (development head):

remotes::install_github("alrobles/genoaligner-r")

What is this?

A pairwise aligner — not a multiple aligner (it does not replace MAFFT or MACSE) and not a search tool. It aligns two sequences you already have:

• align() — edit distance with CIGAR, bounded by smax. Pairs whose true distance exceeds smax are reported unresolved (never silently wrong).
• align_sw() — local Smith-Waterman (affine gaps) with CIGAR and the aligned span’s coordinates.

The wavefront/GPU backend (ROCm/CUDA) that computes the same results with acceleration lives in the sibling C++ repository.

Documentation

See the package vignette and function reference in the site.