NEWS

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dowser 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

dowser 2.4.0 (2025-10-14)

• Added getTimeTrees and getTimeTreesIterate and associated functions

dowser 2.3.2

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

dowser 2.3.1

• Added a UCA inference function called getTreesAndUCAs

dowser 2.3 (2024-10-22)

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

dowser 2.2.1

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

dowser 2.2.0 (2024-05-09)

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

dowser 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

dowser 2.0.1

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

dowser 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

dowser 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.

dowser 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

dowser 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")

dowser 0.1.0 (2021-07-22)

• Initial CRAN release.

dowser 0.0.3

• Correlation test added.
• Additional vignettes added.

dowser 0.0.2

• Integration with new Alakazam lineage functions

dowser 0.0.0.999

• Base functions getTrees, bootstrapTrees, and plotTrees