March 15, 2019
CAFE v4.2.1 is out!
- 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
July 1, 2018
CAFE v4.2 is out!
- 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.
- 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)
November 1, 2017
CAFE v4.1 is out!
- seed: new command that sets the random seed so commands with randomness can be replicated
- report: fixed bug where viterbi values were showing incorrect data
- load: fixed bug in handling trees with more than about 100 species
August 21, 2017
CAFE v4.0.2 is out!
- 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
- - Fixes to allow compilation with gcc 4.9
- Errormodel command no longer fails if model has fewer lines than the expected maximum family size
May 15, 2017
CAFE v4.0.1 is out!
- report: "json" flag added to output data in that format;
- load: Files with "CSV" extension will now be interpreted as comma-separated values;
- Buffer overflow error when setting random family sizes fixed