2.5.86

[spond]

New Features & Enhancements:

• Ancestral Sequence Reconstruction in RELAX: The RELAX analysis script now includes ancestral sequence reconstruction, providing deeper insights into selection pressures by mapping
  substitutions on the phylogeny.
• Enhanced Tree Manipulation:
  • The trees.ParentMap function now correctly identifies the root of the tree.
  • It's now possible to remove multiple nodes from a tree in a single operation, improving efficiency for large tree manipulations.
• New Genetic Code Function: A new function, genetic_code.ComputeStringToInteger, has been added to map codon strings to their corresponding integer representations.

Bug Fixes & Stability:

• FMA3 Build Fix: A compilation bug affecting systems with FMA3 support has been resolved, ensuring wider compatibility.
• Improved Path Handling: HyPhy now more gracefully handles long directory paths, preventing crashes when the current working directory path exceeds the buffer size.
• RELAX Analysis Updates: The RELAX script has received several patches to improve the reliability and clarity of its JSON output and progress messages.

[sonarqubecloud]

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