CAFE 5.1 pre-release now available

[benfulton]

We will be releasing a new version of CAFE 5 soon. The pre-release is available for testing if you would like to try it out. Please report any issues on the Issues tab. Changes include:

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)