1.1

[benfulton]

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)

---

This discussion was created from the release 1.1.

[JiangLab2020]

metazoa_78_cafe.txt
metazoa_78_groupsAllNum.txt
I run the command line: cafe5 -i metazoa_78_groupsAllNum.txt -t metazoa_78_cafe.txt
no result with error: Failed to initialize any reasonable values

[benfulton]

See #132

[JiangLab2020]

What is the maximum size of the tree for cafe5？
Where can I download 'Count' from ?

[JiangLab2020]

plant_25_cafe.txt
plant_25_groupsAllNum.txt
cafe5 -i plant_25_groupsAllNum.txt -t plant_25_cafe.txt -o plant_25
In this case, I only used 25 species in the tree, it still has the error.

[benfulton]

The Count paper is here: https://academic.oup.com/bioinformatics/article/26/15/1910/189891

There is no maximum size of the tree, but if your data is too variable then there will be no sensible lambda value.

[JiangLab2020]

OK，thanks