bio-alignment-multiple skillA
bio-alignment-multiple is agent-read markdown (skill) from pku-yuangroup/openai4s: Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies..
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What the file says
## Version Compatibility Reference examples tested with: MAFFT 7.520+, MUSCLE 5.1+, ClustalOmega 1.2.4+, T-Coffee 13+, PAL2NAL 14+, BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `mafft --version`, `muscle -version`, `clustalo --version` - Python: `pip show biopython` then `help(module.function)` to check signatures If code throws errors, introspect the installed tool and adapt the example to match the actual CLI flags rather than retrying. # Multiple Sequence Alignment **"Align multiple sequences"** -> Compute an optimal alignment of three or more homologous sequences using progressive, iterative, or consistency-based methods. - CLI: `mafft` (most versatile), `muscle` (highest accuracy), `clustalo` (scales well), `t_coffee` (consistency-based) - Python: `subprocess.run()` wrapping CLI tools; BioPython `Bio.Align.Applications` was removed in BioPython 1.86 (verify with `pip show biopython`); use `subprocess` directly ## MSA Algorithm Taxonomy When a tool is failing on a dataset, switch to a tool from a different algorithmic family rather than tuning flags. The six families and their characteristic failure modes: …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-multiple@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-multiple@sha256:ff8a8f6274ce33f1Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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