Announcements

March 15, 2019

CAFE v4.2.1 is out!

Changed

Fixed a memory leak in situations where branch lengths were almost identical to each other
Improved error messages when there is an error in the family file
Fixed bug where the tree was printed twice in the report

CAFE v4.2 is out!

Added

tree: a -i parameter is now supported to load a tree from a file.
A wider variety of compiler/operating system combinations are now tested before releasing
lambda: a -score parameter has been added which logs the calculated log-likelihood for the given set of lambdas.
The PGI compiler will now be autodetected and used if available.

Changed

Fixed bug where running the optimizer could change the initial values passed to the optimizer. (This did not seem to have an effect on the final values but made the optimizer less predictable)
load: Fixed occasional crash if the log file specified with the -l parameter is invalid
report: Fixed occasional crash if multiple threads were specified in the load command
lambda: Fixed crash if there is a species in the family file that does not appear in the tree
tree: A warning is now emitted if the tree is not ultrametric (to within 0.01% of the max root-to-leaf length)

CAFE v4.1 is out!

Added

seed: new command that sets the random seed so commands with randomness can be replicated

Changed

CAFE v4.0.2 is out!

Added

load: max_size parameter added that filters out any families with family sizes larger than the value
lambda: warning added when calculated posterior probability for a family is 0
Use Intel compiler and MKL library for calculations if they are available

Changed

- Fixes to allow compilation with gcc 4.9
Errormodel command no longer fails if model has fewer lines than the expected maximum family size

CAFE v4.0.1 is out!

Added

report: "json" flag added to output data in that format;
load: Files with "CSV" extension will now be interpreted as comma-separated values;

Changed