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Pull requests: biopython/biopython

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Pull requests list

Add an example to Bio.codonalign docstring using the newer CodonAligner in Bio.Align
#5285 opened Aug 16, 2026 by mdehoon Contributor Loading…
3 tasks done
1
Handle empty QUAL title line without raising IndexError
#5283 opened Aug 10, 2026 by eeshsaxena Loading…
3 tasks
4
Fix comparison of atom's element/pqr_charge/radius etc
#5282 opened Aug 7, 2026 by peterjc Member Loading…
3 tasks done
1
Add radius of gyration to Bio.PDB Entity (#5257)
#5279 opened Aug 5, 2026 by yiyabo Loading…
2 of 3 tasks
1
4
Fix Nexus TRANSLATE block rejecting unquoted taxon names with hyphens (#1022)
#5278 opened Aug 5, 2026 by yiyabo Loading…
2 of 3 tasks
1
3
Fix ArrayCore initialization reference handling
#5276 opened Aug 4, 2026 by stanbot8 Contributor Loading…
3 tasks done
1
8
Remove long deprecated Bio.pairwise2 code
#5273 opened Aug 3, 2026 by peterjc Member Loading…
3 tasks done
4
1
Fix PDBList access to EBI and other mirrors (#3987)
#5268 opened Jul 30, 2026 by lilibai338431 Loading…
3 tasks
3
Fix obsolete move logic in PDBList.update_pdb for mmCIF/mmtf and assemblies
#5256 opened Jul 3, 2026 by SID-6921 Loading…
7
Update KEGG API
#5255 opened Jul 1, 2026 by synqa • Draft
3 tasks done
1
7
Bump actions/cache from 5 to 6 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#5253 opened Jun 29, 2026 by dependabot Bot Loading…
Fix 5235 - Endian issue with binary CIF
#5252 opened Jun 27, 2026 by Will-Tyler Contributor Loading…
3 tasks done
1
9
Atom comparison of element, pqr_charge, and radius was broken
#5249 opened Jun 25, 2026 by peterjc Member Loading…
3 tasks done
1
Calculate TLEN when writing SAM alignments
#5244 opened Jun 23, 2026 by GeneratedScript-RL Contributor Loading…
3 tasks done
1
11
First draft of no-AI policy.
#5241 opened Jun 22, 2026 by peterjc Member Loading…
3 tasks done
17
Add docstrings to SequenceDataAbstractBaseClass magic methods
#5240 opened Jun 19, 2026 by LuciPengu Loading…
3 tasks done
7
Add PDB and PAE downloads to Bio.PDB.alphafold_db
#5236 opened Jun 15, 2026 by jam-sudo Loading…
3 tasks done
4
Bump codecov/codecov-action from 6 to 7 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#5234 opened Jun 8, 2026 by dependabot Bot Loading…
1
Add pymysql driver support to BioSQL
#5233 opened Jun 5, 2026 by yiyabo Loading…
3 tasks done
1
9
fix(PDB): extend obsolete file handling to mmCIF and XML formats
#5231 opened Jun 2, 2026 by mayank-dev-15 Loading…
1
4
Feature/alphafold proteome bulk download
#5221 opened May 27, 2026 by gabufle Loading…
3 tasks done
1
Percent to f-strings using flynt v1.0.6
#5219 opened May 22, 2026 by peterjc Member Loading…
3 tasks done
1
SeqUtils: Improve GC123 robustness and modernize SearchIO repr
#5214 opened May 16, 2026 by Amnotreallyfunny Loading…
1
Tests: add tests for six_frame_translations and nt_search in Bio.SeqUtils
#5211 opened May 11, 2026 by amitsjc Loading…
1
Add fasta-ncbi format for NCBI FASTA header dbxref parsing
#5201 opened Apr 17, 2026 by mmokrejs Loading…
2
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