# Upstream helpers for biopython

The files listed below were recovered from [K-Dense-AI/scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills) at commit `0936740e52033a6256085be5fc81e5e56d606110`. The repository ID is `1079456184`.

They retain the upstream **MIT** license reproduced in [UPSTREAM-LICENSE.txt](UPSTREAM-LICENSE.txt). This notice applies to the listed support files; it does not replace the license metadata of other catalog files. Preserve the upstream license and this attribution when redistributing them.

License wording is unchanged; text-only trailing whitespace and EOF blank lines are normalized. Original license: https://github.com/K-Dense-AI/scientific-agent-skills/blob/0936740e52033a6256085be5fc81e5e56d606110/LICENSE.md

| Local file | Original upstream path | Original Git blob SHA | Import changes |
| --- | --- | --- | --- |
| `references/sequence_io.md` | `skills/biopython/references/sequence_io.md` | `a6a5e31df6f7d3cec2ab776d4cf67e7a8bb7ee2d` | text-only trailing whitespace and EOF blank lines normalized |
| `references/alignment.md` | `skills/biopython/references/alignment.md` | `2a45961ef8ebb429bb0ef55df42d0cb862072c82` | text-only trailing whitespace and EOF blank lines normalized |
| `references/databases.md` | `skills/biopython/references/databases.md` | `75c271e9d0e7c6d4eb1da46b221e6a194d40a058` | text-only trailing whitespace and EOF blank lines normalized |
| `references/blast.md` | `skills/biopython/references/blast.md` | `634cc6291333ec3a612580a4024592a2ffb5b463` | text-only trailing whitespace and EOF blank lines normalized |
| `references/structure.md` | `skills/biopython/references/structure.md` | `5a5d301f37e66f6106415aa808e6856d93e521cf` | text-only trailing whitespace and EOF blank lines normalized |
| `references/phylogenetics.md` | `skills/biopython/references/phylogenetics.md` | `3f570115e901be429fcab94d4ce2d84e25546096` | text-only trailing whitespace and EOF blank lines normalized |
| `references/advanced.md` | `skills/biopython/references/advanced.md` | `02fef358c87ba40b88ff82485e5279c1e1ecec0e` | text-only trailing whitespace and EOF blank lines normalized |

## Local review amendments

The original blob identifiers above describe imported provenance, not the current edited bytes. The2026-10-23 individual review repaired API examples, compressed I/O, external command invocation, sequence/structure/tree calculations, service limits and privacy boundaries. Preserve original attribution and MIT license; do not infer that upstream endorsed these local changes. Root licensing metadata remains distinct.