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Version 2.4.0 October 14, 2025

• Added getTimeTrees and getTimeTreesIterate and associated functions

Version 2.3.1 March 13, 2025

• Added a UCA inference function called getTreesAndUCAs

Version 2.3 October 18, 2024

• Fixed bugs in and added features to buildRAxML
• Fixed bugs in resolveLightChains
• Added trimming option to createGermlines

Version 2.2.1 May 23, 2024

• Updated correlationTest
• Fixed bugs in buildRAxML
• Added ASR check for version changes in phangorn

Version 2.2.0 May 7, 2024

• added suggestion for pwalign dependency
• set filter_stop=FALSE in formatClones for better speed

Version 2.1.0 December 21, 2023

• plotTrees uses palette instead of tip_palette/node_palette
• palette options deprecated in getTrees and sub-functions
• getPalette colors Germline as black by default
• ambiguous nodes are now grey by default

Version 2.0.1: October 25, 2023

• Fixed bugs in buildRAxML and getTrees
• Added an option to formatClones to consider light chain traits

Version 2.0.0: September 8, 2023

• Added paired heavy and light chain single cell integration into formatClones
• Added lone light chain integration into formatClones
• Added resolveLightChains, a function that assigned clones ‘clonal_subgroups’
• Added a vignette about how to create H+L trees

Version 1.2.0: May 30, 2023

• Fixed bugs in createGermlines, plotTrees, and getTrees
• Added getBootstraps, a bootstrapping function separate from findSwitches
• Added RAxML build option
• Added partitioned IgPhyML and RAxML build options (experimental)
• Added calcRF for RF distance calculations.

Version 1.1.0: October 4, 2022

• createGermlines now works on all loci simultaneously
• Vignettes for measurable evolution and discrete trait analysis
• Corrected bugs in createGermlines and findSwitches

Version 1.0.0: April 8, 2022

• Deprecated bootstrapTrees in favor of findSwitches
• Deprecated getSeq in favor of getNodeSeq
• Added vignettes for discrete trait analysis and measurable evolution
• Changed permutation to perm_type in correlationTest
• Added common_scale to plotTrees
• Removed trace and warning printouts from getTrees(build=“pml”)

Version 0.1.0: July 13, 2021

• Initial CRAN release.

Version 0.0.3: December 12, 2020

• Correlation test added.
• Additional vignettes added.

Version 0.0.2: August 28, 2020

• Integration with new Alakazam lineage functions

Version 0.0.0.999: April 14, 2020

• Base functions getTrees, bootstrapTrees, and plotTrees

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.