alterlab-biopython

# Biopython: Computational Molecular Biology in Python ## Overview Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is **Biopython 1.88** (August 2026), which supports Python 3.10–3.14 and requires NumPy. > **Removed / changed APIs to watch for** > > - **Command-line wrappers are gone.** `Bio.Application` and everything built on it — > `Bio.Blast.Applications` (`Ncbiblastn/p/x…Commandline`, `NcbimakeblastdbCommandline`) and > `Bio.Align.Applications` (`ClustalOmegaCommandline`, `MuscleCommandline`) — were > deprecated in 1.78 and **removed in 1.86**. Call the executables through `subprocess` > (see `references/blast.md` and `references/alignment.md`). > - **PairwiseAligner gap scores changed in 1.86.** The default gap score is now **-1** > (was 0), so an aligner left at defaults returns far fewer, non-degenerate alignments. > The gap attributes were also renamed to insertion/deletion forms > (`open_internal_insertion_score`, …); the `*_gap_score` names still work as > meta-attributes. The `alphabet` attribute is deprecated and unused. > - **`Bio.pairwise2` is deprecated** — use `Bio.Align.PairwiseAligner`. > - **`Bio.Blast.NCBIXML` is declared obsolete** as of the 1.89 development line in favour > of the `Bio.Blast` parser added in 1.8...