Published January 13, 2025 | Version 0.6.3
Software Open

scikit-bio/scikit-bio: scikit-bio 0.6.3

Description

We are excited to announce scikit-bio 0.6.3!

This is a massive upgrade, despite minor version change. Release highlights include:

  • Significantly improved the tree and phylogenetics module (skbio.tree), with:
    • Optimized the TreeNode class such that it can efficiently handle very large phylogenetic trees.
    • Added, extended and/or optimized many methods of TreeNode. It now features a standard, flexible and scalable API to perform various common tasks in phylogenetics and data science.
    • Refined and expanded tree comparison metrics, including original, weighted, and variants of Robinson-Foulds distances, path / cophenetic distance and variants. Also added driver functions for computing distances between multiple trees.
    • Added and/or optimized minimum evolution (ME) algorithms for phylogenetic reconstruction and rearrangement, including GME (gme), BME (bme), FastNNI, and BNNI (nni).
    • Optimized the canonical neighbor joining (NJ) algorithm (nj) for phylogenetic reconstruction.
  • Refined the I/O system (skbio.io) to improve its efficiency, maintainability and expansibility. Also expanded the tutorial of I/O in scikit-bio.
  • Allowed the user to specify a random seed or random generator for all stochastic algorithms in scikit-bio to ensure reproducibilty.
  • Allowed the user to specify a desired fractional cumulative variance for pcoa.
  • Added support for Python 3.13. Dropped support for Python 3.8.
  • Multiple bug fixes and miscellaneous improvements.

Review the changelog for a complete list of the changes. Browse the documentation to learn about what you can do with scikit-bio. Follow @scikitbio for project updates. Thanks for your interest in scikit-bio!

Files

scikit-bio/scikit-bio-0.6.3.zip

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