All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- 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.
- 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 application will no longer attempt to compute P-Values or a reconstruction, if the user specifies a lambda and the calculated -lnL is infinite.
- 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)
- Nothing