align() renamed to align_edit() — the generic name
collides with Biostrings/IRanges exports in mixed sessions. align()
remains as a deprecated alias returning identical results.msa_align(seqs, mode = "dna" | "protein") — progressive
profile-profile MSA with a deterministic NJ guide tree.msa_codon(seqs, gc = 1 | 2, refine = FALSE) — MACSE-class codon-aware
MSA: whole-codon indels preserve the reading frame; refine = TRUE
runs a frameshift-refinement pass producing a nucleotide MSA.genoaligner_msa ($aligned character
matrix, $qc per-sequence QC — frame / stop codons / partial codons in
codon mode —, $params), with print/as.matrix/as.character methods
and optional ape::DNAbin coercion via as_dnabin().msa_align()/msa_codon() gain iterative refinement and FFT anchors
(MAFFT FFT-NS-i class): iter_refine = k realigns the two induced
profiles of every guide-tree edge and keeps a candidate only when the
sum-of-pairs score strictly improves; fft_band > 0 restricts each
realignment DP to a band around Fourier-detected homology anchors
(faster, exact-rescored, falls back to the full DP on weak signal).
On 37 real Lepus cytb sequences two rounds improve the SP objective
620,764 → 628,384 at ~30% less refinement time with fft_band = 32.devin/msa-iter-refine @ 2b15a7a
(PR #13) — see inst/VENDORED.txt.lepus_cytb: 37 real NCBI cytochrome b records for three hare
species plus an Oryctolagus outgroup (mixed lengths, includes two
mislabelled records used as a QC teaching case).lepus-cytb (real-data case study: locus QC, common-window
cropping, barcode gap, smax semantics) and simulated-use-cases
(bounded off-target scoring, adapter scan, read dereplication).Initial release.
align() and align_sw() over
data.frame/tibble pair columns; smax-bounded resolution that reports
unresolved pairs rather than returning silently wrong scores.R CMD check clean.containers/) to reproduce the build in a pinned cluster
environment; verified on a KU HPC Q6000 node with --gres + --nv.