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