Package: genoaligner 2.0.0.9000

genoaligner: GPU-Portable Pairwise and Codon-Aware Multiple Sequence Alignment

Sequence alignment from one portable C++17 core: edit-distance (Levenshtein / WFA-equivalent) and Smith-Waterman local pairwise alignment with score and CIGAR reconstruction, plus multiple sequence alignment in DNA, protein and codon-aware modes (MACSE-class: whole-codon indels that preserve the reading frame, optional frameshift refinement). The core builds and runs anywhere (it is the CPU backend, so it needs no GPU toolchain); the wavefront/GPU backend (ROCm/CUDA) computes the same results with acceleration and is tracked in the sibling C++ repository. A batch API aligns many pairs in one call and reports how many were resolved, so silent under-serving is impossible. Designed to slot into data.frame/tibble pipelines.

Authors:Angel Robles-Fernandez [aut, cre]

genoaligner_2.0.0.9000.tar.gz
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genoaligner_2.0.0.9000.tgz(r-4.6-x86_64)genoaligner_2.0.0.9000.tgz(r-4.6-arm64)genoaligner_2.0.0.9000.tgz(r-4.5-x86_64)genoaligner_2.0.0.9000.tgz(r-4.5-arm64)
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genoaligner_1.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genoaligner/json (API)

# Install 'genoaligner' in R:
install.packages('genoaligner', repos = c('https://alrobles.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alrobles/genoaligner-r/issues

Pkgdown/docs site:https://alrobles.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • lepus_cytb - Cytochrome b sequences from four leporid species

On CRAN:

Conda:

cpp

4.88 score 7 scripts 337 downloads 6 exports 1 dependencies

Last updated from:d7a0767e86. Checks:13 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE130
linux-devel-x86_64NOTE118
source / vignettesOK183
linux-release-arm64NOTE88
linux-release-x86_64NOTE118
macos-release-arm64NOTE104
macos-release-x86_64NOTE221
macos-oldrel-arm64NOTE102
macos-oldrel-x86_64NOTE303
windows-devel-arm64NOTE195
windows-devel-x86_64NOTE150
windows-release-arm64NOTE211
windows-release-x86_64NOTE114
windows-oldrel-x86_64NOTE107
wasm-releaseFAIL99

Exports:alignalign_editalign_swas_dnabinmsa_alignmsa_codon

Dependencies:Rcpp

Aligning sequences with genoaligner
Edit distance | Smith-Waterman local alignment | The CIGAR convention | GPU backend
Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-13

Case study: hare cytochrome b fragments
QC pass: which records actually are cytb? | A common window, honestly chosen | Edit distance recovers the species | smax is a claim about relatedness | Takeaway
Rendered fromlepus-cytb.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-24

Codon-aware MSA: hare cytochrome b
The alignment | What the QC already knows | Frame integrity: codon mode vs plain DNA mode | Frameshift refinement | Interoperability | Where this engine lives
Rendered frommsa-codon-lepus.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-27

Reproducing the build with Apptainer
What you get | The recipe
Rendered fromapptainer.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-13

Three pipeline use cases
1. Off-target candidate scoring (bounded edit distance) | 2. Adapter contamination scan (local alignment) | 3. Read dereplication into haplotypes | Why these three?
Rendered fromsimulated-use-cases.Rmdusingknitr::rmarkdown

Last update: 2026-09-27
Started: 2026-09-24