Version 5.1 Beta
Pre-release
Pre-release
[1.1.0] - 2023-03-30
Added
- The output file Base_report.cafe or Gamma_report.cafe has been added. This file has a
format roughly the same as the CAFE 4 output, so tools and scripts that work with this
format should run properly. - The tutorial now includes a cafe5_draw_tree.py script, demonstrating how to use BioPython
to create a tree.
Changed
- Ordering of nodes has changed. The order should now be the same, relative to the source Newick
tree, as in the R package Ape. - The model_change.tab file no longer includes a "+" sign before positive change counts.
- The simulator handles different max family and max root sizes correctly.
- The DocTest unit tester has been updated to v2.4.9.
- The configure script now checks for the existence of mkl.h before attempting to use it.
- Building the application should no longer fail if OpenMP is missing. (It will probably run
much slower, however)