EvoPhylo News and Updates

Development: EvoPhylo 0.3.5

(August 26th, 2025) * Function combine_log now also reads and combine log files from BEAST2 and MCMCTREE * Added Z-transformation for functions plot_back_rates and plot_treerates_sgn * New function write_partitioned_alignments2 write alignment partitions as separate alignment files for various data types * New function clade_membershipdesignates clade membership for each tip for downstream analyses summarizing rates for each clade

Development: EvoPhylo 0.3.3

(July 21st, 2023)

• Function plot_back_rates corrected for MrBayes.
• New warnings and import of MrBayes single {all} clock partition for plot_treerates_sgn.

Development: EvoPhylo 0.3.2

(October 31st, 2022)

• New function plot_back_rates and updates on vignettes.

Development: EvoPhylo 0.3.1

(OCtober 20th, 2022)

• Bug fixes and adjustment of selection functions for BEAST2: old 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.

Development: EvoPhylo 0.3

(August 1st, 2022)

Implementation of functions for BEAST2 data now complete!

• Added function (write_partitioned_alignments) to write partitioned alignments based on the inferred clusters.
• Added BEAST2 support for clock rate table import - old get_clockrate_table function exists now in two versions, get_clockrate_table_MrBayes and get_clockrate_table_BEAST2

Development: EvoPhylo 0.2.1

(July 8th, 2022)

• Added function (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).

Development: EvoPhylo 0.2.0

(June 27th, 2022)

• Added functions (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 clades
• FBD functions can now handle BEAST2 log files produced by several packages (SA, BDSKY)
• plot_treerates_sgn() function update: outputs chosen thresholds and estimated rate values for each threshold.

EvoPhylo 0.1.0

(May 12th, 2022)

• First version!