1.1

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 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)

Version 5.1 Beta

[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)

Initial Version 5 Release

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.

CAFE5 Initial Release (beta 2)

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.

Beta 2:

• Fixes an issue with the optimizer when including an error model
• Fixes an issue incorrectly assigning significance to some branches of the tree

CAFE5 Initial Release (beta)

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.