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scikit-bio

What changed in scikit-bio 0.7, from its official release notes, upgrade guides and advisories. Sources checked 2026-10-30.

15 new APIs and options13 performance1 behavior and defaults1 fixes and other

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scikit-bio 0.730 changes

New APIs and options 15

  • Adds an efficient Python implementation of ANCOM-BC2 for differential abundance analysis, including post-hoc tests.

    0.7.4release notes

  • Adds a multiple sequence alignment function using the classical progressive alignment method.

    0.7.4release notes

  • Adds optional Numba acceleration for PCoA.

    0.7.4release notes

  • Adds the inverse robust centered log-ratio transformation.

    0.7.4release notes

  • Adds transition probability matrices for five nucleotide substitution models.

    0.7.4release notes

  • Adds optional Numba acceleration for UniFrac.

    0.7.4release notes

  • Added gamma correction for among-site evolutionary rate heterogeneity for multiple nucleotide substitution models.

    0.7.3release notes

  • Added Microbe-Metabolite Vectors for multiomics co-occurrence analysis and embedding; the implementation is significantly faster than the original program and does not require GPU.

    0.7.3release notes

  • A global mechanism was implemented to support the Python array API standard and GPU computing.

    0.7.3release notes

  • Added robust centered log-ratio transformation of compositional data.

    0.7.3release notes

  • Calculates a distance matrix from a multiple sequence alignment.

    0.7.2release notes

  • A new metric calculates evolutionary distance between aligned sequences.

    0.7.2release notes

  • A new metric calculates evolutionary distance between aligned sequences.

    0.7.2release notes

  • New plotting functionality includes centroids, confidence ellipses, and 2D plotting.

    0.7.2release notes

  • A new format can read PHYLIP formatted distance matrices.

    0.7.2release notes

Performance 13

  • Improves performance of this differential abundance test.

    0.7.4release notes

  • Improves performance of this differential abundance test.

    0.7.4release notes

  • Expands Array API and GPU support, including Numba acceleration on NVIDIA and AMD GPUs.

    0.7.4release notes

  • Adds optional Numba acceleration for Mantel.

    0.7.4release notes

  • Adds optional Numba acceleration for PERMANOVA.

    0.7.4release notes

  • Adds optional Numba acceleration for PERMDISP.

    0.7.4release notes

  • Significantly accelerated the minimum evolution phylogenetics algorithm.

    0.7.3release notes

  • Significantly accelerated the minimum evolution phylogenetics algorithm.

    0.7.3release notes

  • Significantly reduced the time required to import scikit-bio.

    0.7.3release notes

  • Significantly accelerated the minimum evolution phylogenetics algorithm.

    0.7.3release notes

  • Can now operate directly on condensed form DistanceMatrix objects, reducing memory footprint by 50%.

    0.7.2release notes

  • Can now operate directly on condensed form DistanceMatrix objects, reducing memory footprint by 50%.

    0.7.2release notes

  • The method is more efficient and can accept array-like input.

    0.7.2release notes

Behavior and default changes 1

  • The existing format now supports relaxed PHYLIP formatted multiple sequence alignments.

    0.7.2release notes

Fixes and other changes 1

  • Most of scikit-bio is compatible, but users who rely heavily on the metadata module are advised to pin Pandas below 3.0 until a later release.

    0.7.2release notes