Changes in version 2.4.1 (2026-03-26)                  

  - Updates due to BioConductor release.
  - Now requires R >= 4.4 and pwalign (BioC) rather than Biostrings
    (BioC).
  - Swapped RMarkDown URIs for URLs.
  - plot expected occupancies on trees in plotTrees
  - resolveLightChains bug fix

                 Changes in version 2.4.0 (2025-10-14)                  

  - Added getTimeTrees and getTimeTreesIterate and associated functions

                        Changes in version 2.3.2                        

  - Added light chain UCA inference to getTreesAndUCAs and addressed
    minor bugs

                        Changes in version 2.3.1                        

  - Added a UCA inference function called getTreesAndUCAs

                  Changes in version 2.3 (2024-10-22)                   

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

                        Changes in version 2.2.1                        

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

                 Changes in version 2.2.0 (2024-05-09)                  

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

                 Changes in version 2.1.0 (2023-12-22)                  

  - 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

                        Changes in version 2.0.1                        

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

                 Changes in version 2.0.0 (2023-09-27)                  

  - 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

                 Changes in version 1.2.0 (2023-05-30)                  

  - 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.

                 Changes in version 1.1.0 (2022-10-04)                  

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

                 Changes in version 1.0.0 (2022-04-13)                  

  - 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")

                 Changes in version 0.1.0 (2021-07-22)                  

  - Initial CRAN release.

                        Changes in version 0.0.3                        

  - Correlation test added.
  - Additional vignettes added.

                        Changes in version 0.0.2                        

  - Integration with new Alakazam lineage functions

                      Changes in version 0.0.0.999                      

  - Base functions getTrees, bootstrapTrees, and plotTrees