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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)