pwalign
Bioc currentPerform pairwise sequence alignments
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
46 4 exported
Complexity
7 avg / 27 max
Call network
46 nodes / 30 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
7,051
Files
52
Compiled share
22.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
22
Internal functions
23
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
3
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 11
- Examples that run
- 100%11 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 87%
- Return-value docs
- 67%
- Help pages citing references
- 45%
- No changes in this version.
From NEWS in the release
Repository practices
Checks run against github.com/bioconductor/pwalign on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| BLOSUM100 | matrix | 24 × 24 | 2 packages |
| BLOSUM45 | matrix | 25 × 25 | 2 packages |
| BLOSUM50 | matrix | 24 × 24 | 3 packages |
| BLOSUM62 | matrix | 25 × 25 | 3 packages |
| BLOSUM80 | matrix | 25 × 25 | 2 packages |
| PAM120 | matrix | 24 × 24 | 2 packages |
| PAM250 | matrix | 24 × 24 | 2 packages |
| PAM30 | matrix | 25 × 25 | 2 packages |
| PAM40 | matrix | 24 × 24 | 2 packages |
| PAM70 | matrix | 25 × 25 | 2 packages |
| phiX174Phage | – | – | – |
| quPhiX174 | – | – | – |
| srPhiX174 | – | – | – |
| wtPhiX174 | vector | 1,113 elements | No other package |
Topics
Depended on by (46)
Show 49 packagesHide 49 packages
Bioconductor (36)
CRAN (10)
Suggested by (9)
People
- Hervé Pagès maintainer
- Patrick Aboyoun author
- Robert Gentleman author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("pwalign")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.