(August 26th, 2025)
combine_log now also reads and combine log files from BEAST2 and MCMCTREEplot_back_rates and plot_treerates_sgnwrite_partitioned_alignments2 write alignment partitions as separate alignment files for various data typesclade_membershipdesignates clade membership for each tip for downstream analyses summarizing rates for each clade(July 21st, 2023)
plot_back_rates corrected for MrBayes.plot_treerates_sgn.(October 31st, 2022)
plot_back_rates and updates on vignettes.(OCtober 20th, 2022)
get_pwt_rates function exists now in two versionsget_pwt_rates_MrBayes and get_pwt_rates_BEAST2, and updates on plot_treerates_sgn to handle BEAST2.(August 1st, 2022)
Implementation of functions for BEAST2 data now complete!
write_partitioned_alignments) to write partitioned alignments based on the inferred clusters.get_clockrate_table function exists now in two versions, get_clockrate_table_MrBayes and get_clockrate_table_BEAST2(July 8th, 2022)
drop.dummy.mb) to remove "dummy" tip from Mr. Bayes summary trees and export tree accounting for metadata on the tips (for fully extinct clades).(June 27th, 2022)
drop.dummy.beast, offset.to.dummy, write.beast.treedata, offset.to.dummy.metadata) to handle trees with offsets as produced by the BEAST2 SA package for fully extinct cladesplot_treerates_sgn() function update: outputs chosen thresholds and estimated rate values for each threshold.(May 12th, 2022)