Published March 19, 2026
| Version v1.0.1
Software
Open
OrensteinLab/SWOffinder: v1.0.1
Authors/Creators
Description
- Added support for IUPAC nucleotide codes.
- Added a command-line interface (CLI).
- Enabled user control over the Smith–Waterman DP window size, allowing trade-offs between runtime and memory usage.
- Optimized alignment reconstruction by eliminating repeated string copying during recursive backtracking. Replaced per-call StringBuilder cloning with in-place updates and backtracking, reducing memory allocations and improving runtime performance, particularly for large edit distances during post-processing. This optimization was adapted from AutoFFinder.
Files
OrensteinLab/SWOffinder-v1.0.1.zip
Files
(14.4 kB)
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md5:18d3b15dff3ce431d8472ddbed59d261
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Additional details
Related works
- Is supplement to
- Software: https://github.com/OrensteinLab/SWOffinder/tree/v1.0.1 (URL)
Software
- Repository URL
- https://github.com/OrensteinLab/SWOffinder