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Bio.Align.chain AlignmentIterator fails on chain files with metadata.

Status: Open.

#5122 In biopython/biopython;

· diekhans opened on Dec 19, 2025

Why does read_PIC_seq give different distances and angles for each residue?

Status: Open.

#5119 In biopython/biopython;

· HakonOnco opened on Dec 8, 2025

Proposal: Optional ProteinSeq class for protein sequences

Status: Open.

#5115 In biopython/biopython;

· harisj739 opened on Nov 30, 2025

IC_residue's get_angle function gives different results for psi and "N:CA:C:1N"

Status: Open.

#5113 In biopython/biopython;

· HakonOnco opened on Nov 28, 2025

[CVE-2025-68463] <code>Bio.Entrez.DataHandler</code>, <code>Bio.Entrez.read</code>, <code>Bio.Entrez.parse</code> are vulnerable to XXE and SSRF

Status: Open.

#5109 In biopython/biopython;

· hartwork opened on Nov 25, 2025

GenBank multi-line qualifier value parsed incorrectly in specific cases

Status: Open.

#5101 In biopython/biopython;

· BioGavin opened on Nov 14, 2025

Proposal: Integrate advanced peptide descriptors into Bio.SeqUtils

Status: Open.

#5100 In biopython/biopython;

· flyfir248 opened on Nov 7, 2025

FoldX PositionScan: "Specified residue not found"

Status: Open.

#5096 In biopython/biopython;

· LLG00 opened on Oct 29, 2025

Warning: Package 'Bio.Align.substitution_matrices' is absent from the <code>packages</code> configuration.

Status: Open.

#5092 In biopython/biopython;

· peterjc opened on Oct 28, 2025

Combining PWAs and MSAs

Status: Open.

#5075 In biopython/biopython;

· Cassiebastress opened on Oct 3, 2025

[Bio.Blast.qblast] The username and password parameters seem useless

Status: Open.

#5059 In biopython/biopython;

· PlatonB opened on Sep 8, 2025

Proposal to Add <code>aligned_tuples_to_MSA()</code> Class Method

Status: Open.

#5052 In biopython/biopython;

· Cassiebastress opened on Sep 1, 2025