Changelog

Source: NEWS.md

ScrambledTreeBuilder 1.3.0

• Expand recordClades() to work on taxon tables (one genome per line).
• New removeAssemblies() function for on-the-fly filtering.

ScrambledTreeBuilder 1.2.0

• Fix diagonal values in Halo_PercentDiff.
• Fix detection of YAML files.
• Make formatStats() robust to the presence of character values.
• Stop dropping zero-valued columns in formatStats().
• New residualBootstrapTree() function.
• makeMatrix() now warns and returns NULL if a column is not found.
• makeValueTibble() returns the original tree if NULL is passed instead of a matrix.
• Added treeHeatMap() to visualise distance matrices with their values sorted like the branches of a phylogenetic tree, and optional focal clade highlighting.

ScrambledTreeBuilder 1.1.0

• Add oikData 2025_02_25 that uses the experimental windowed scrambling index.

ScrambledTreeBuilder 1.0.2

• Make formatStats() more robust when computing percent_aligned

ScrambledTreeBuilder 1.0.1

• Fix error messages in subMatrix() and document that it also works with focal clades.

ScrambledTreeBuilder 1.0.0

• First release with semantic versioning.

ScrambledTreeBuilder 0.0.0.9001

• Versions used before June 2025.