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2010-08-11	Ben Blackburne	Clean up ReadTree	commit \| commitdiff \| tree
2010-08-11	Ben Blackburne	Merge branch 'newaln'	commit \| commitdiff \| tree
2010-08-11	Ben Blackburne	Passing Unit Tests	commit \| commitdiff \| tree
2010-08-11	Ben Blackburne	Fix some warnings	commit \| commitdiff \| tree
2010-08-11	Ben Blackburne	Don't assume we always want WAG	commit \| commitdiff \| tree
2010-08-09	Ben Blackburne	Don't assume we always want WAG	commit \| commitdiff \| tree
2010-08-09	Ben Blackburne	Fixing up alignment code	commit \| commitdiff \| tree
2010-07-14	Ben Blackburne	Update to 2.8.0 final!	commit \| commitdiff \| tree
2010-06-22	Ben Blackburne	Update to RC6	commit \| commitdiff \| tree
2010-06-21	Ben Blackburne	Add eclipsify plugin	commit \| commitdiff \| tree
2010-06-21	Ben Blackburne	Try and throttle computations on Param thread pool	commit \| commitdiff \| tree
2010-06-16	Ben Blackburne	Update to scala 2.8.0.RC5	commit \| commitdiff \| tree
2010-06-15	Ben Blackburne	Merge branch 'scala28c'	commit \| commitdiff \| tree
2010-06-15	Ben Blackburne	Fixes for 2.8	commit \| commitdiff \| tree
2010-06-01	Ben Blackburne	Version bump	commit \| commitdiff \| tree
2010-06-01	Ben Blackburne	Additional optimisation options	commit \| commitdiff \| tree
2010-05-28	Ben Blackburne	Switch ActorModel actors to separate thread pool	commit \| commitdiff \| tree
2010-05-27	Ben Blackburne	Fix error message on bad alignment	commit \| commitdiff \| tree
2010-05-27	Ben Blackburne	Fix error message on bad alignment	commit \| commitdiff \| tree
2010-05-26	Ben Blackburne	Finish update to 2.8.0.RC2	commit \| commitdiff \| tree
2010-05-26	Ben Blackburne	Parsing of PAML alignments	commit \| commitdiff \| tree
2010-05-20	Ben Blackburne	Extra niceties in DSL	commit \| commitdiff \| tree
2010-05-18	Ben Blackburne	Further "inner loop" optimisations	commit \| commitdiff \| tree
2010-05-18	Ben Blackburne	Optimise matrix access in lkl calc	commit \| commitdiff \| tree
2010-05-13	Ben Blackburne	Added Randomisation to OptSetters	commit \| commitdiff \| tree
2010-05-13	Ben Blackburne	fix toLabelledString	commit \| commitdiff \| tree
2010-05-13	Ben Blackburne	Fixed bug with branch length parameter ordering	commit \| commitdiff \| tree
2010-05-11	Ben Blackburne	generics in ActorModel	commit \| commitdiff \| tree
2010-05-05	Ben Blackburne	Test for new tree code	commit \| commitdiff \| tree
2010-05-05	Ben Blackburne	Add optional labels to tree	commit \| commitdiff \| tree
2010-03-24	Ben Blackburne	Bump ScalaTest version	commit \| commitdiff \| tree
2010-03-23	Ben Blackburne	Bump sbt to 0.7.1	commit \| commitdiff \| tree
2010-03-08	Ben Blackburne	Yet more old code removed	commit \| commitdiff \| tree
2010-03-07	Ben Blackburne	More removal of dead code	commit \| commitdiff \| tree
2010-03-07	Ben Blackburne	Remove old cruft from Opt	commit \| commitdiff \| tree
2010-03-05	Ben Blackburne	SwitchingTree printout fix	commit \| commitdiff \| tree
2010-03-04	Ben Blackburne	Useful outputting features	commit \| commitdiff \| tree
2010-03-03	Ben Blackburne	Switch to single normalisation step	commit \| commitdiff \| tree
2010-03-03	Ben Blackburne	Fixed important bug with normalisation	commit \| commitdiff \| tree
2010-03-03	Ben Blackburne	Allow printing of Q Matrix	commit \| commitdiff \| tree
2010-03-03	Ben Blackburne	Extension of Parameters to allow more flexibility	commit \| commitdiff \| tree
2010-03-02	Ben Blackburne	Fixed race condition from multiple .start()s	commit \| commitdiff \| tree
2010-02-28	Ben Blackburne	More refactoring by extending SimpleActor...	commit \| commitdiff \| tree
2010-02-27	Ben Blackburne	Simplification of ActorModelComponents	commit \| commitdiff \| tree
2010-02-26	Ben Blackburne	Handle unseen amino acids in getF	commit \| commitdiff \| tree
2010-02-26	Ben Blackburne	Fixed Type system for models	commit \| commitdiff \| tree
2010-02-25	Ben Blackburne	Bugfixes	commit \| commitdiff \| tree
2010-02-25	Ben Blackburne	Hacked/worked around bugs	commit \| commitdiff \| tree
2010-02-24	Ben Blackburne	Try 2	commit \| commitdiff \| tree
2010-02-24	Ben Blackburne	Some bugfixes but model initialization still trouble	commit \| commitdiff \| tree
2010-02-24	Ben Blackburne	Remove debugging println	commit \| commitdiff \| tree
2010-02-24	Ben Blackburne	Splitting Alignments for greater parallelization	commit \| commitdiff \| tree
2010-02-24	Ben Blackburne	Likelihood ratio test	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	README looking outdated	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Version bump to 0.9.0	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Logging rather then spamming with printlns	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Further fix to fasta parsing	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Fix fasta name parsing	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Formatting output fix	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	More bugfixes	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Bugfix	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Bugfixes	commit \| commitdiff \| tree
2010-02-23	Ben Blackburne	Addded optimiser bounds checking	commit \| commitdiff \| tree
2010-02-22	Ben Blackburne	Optimiser bugfix	commit \| commitdiff \| tree
2010-02-22	Ben Blackburne	More features, passing basic tests	commit \| commitdiff \| tree
2010-02-22	Ben Blackburne	Branch Length Optimisation passes basic test	commit \| commitdiff \| tree
2010-02-22	Ben Blackburne	ForkParam allowing branch-specific models	commit \| commitdiff \| tree
2010-02-21	Ben Blackburne	Moving to actor based model and tree	commit \| commitdiff \| tree
2010-02-19	Ben Blackburne	Fixed 'bug' where pi values were normalised	commit \| commitdiff \| tree
2010-02-17	Ben Blackburne	SBT 0.7.0 compliant	commit \| commitdiff \| tree
2010-02-11	Ben Blackburne	Allow returning of small values rather than NaN	commit \| commitdiff \| tree
2010-02-10	Ben Blackburne	Allow splitting of Alignments and Tree Datasets	commit \| commitdiff \| tree
2010-02-09	Ben Blackburne	Added optimisation from Beast	commit \| commitdiff \| tree
2010-02-06	Ben Blackburne	Using new optimisation routines	commit \| commitdiff \| tree
2010-02-06	Ben Blackburne	Add Beast dependency for optimisation routines	commit \| commitdiff \| tree
2010-02-03	Ben Blackburne	New THMM abilities	commit \| commitdiff \| tree
2010-01-29	Ben Blackburne	Remove some obnoxious printlns	commit \| commitdiff \| tree
2010-01-29	Ben Blackburne	Fixed +F model	commit \| commitdiff \| tree
2010-01-22	Ben Blackburne	MixtureModel implementation	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Version bump to 0.3.0	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Added tests vs Leaphy	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Bugfixes	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Remove a lot of old-style Model classes	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Missing Gamma Opt in THMMInvar	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Initial version of Param unit tests	commit \| commitdiff \| tree
2010-01-21	Ben Blackburne	Bugfix in FirstPiParam	commit \| commitdiff \| tree
2010-01-20	Ben Blackburne	Fixed bug in Invariant Model	commit \| commitdiff \| tree
2010-01-20	Ben Blackburne	Param Names	commit \| commitdiff \| tree
2010-01-20	Ben Blackburne	Added branch length optimisations to new Model code	commit \| commitdiff \| tree
2010-01-20	Ben Blackburne	Added Invariant model	commit \| commitdiff \| tree
2010-01-18	Ben Blackburne	Further tests and fixes	commit \| commitdiff \| tree
2010-01-17	Ben Blackburne	Don't need to recreate the same object	commit \| commitdiff \| tree
2010-01-17	Ben Blackburne	Use Colt functions rather than loops	commit \| commitdiff \| tree
2010-01-17	Ben Blackburne	Added some new tests to compare with PAML results	commit \| commitdiff \| tree
2010-01-17	Ben Blackburne	Remove PAL dependency	commit \| commitdiff \| tree
2010-01-16	Ben Blackburne	Changing Model implementation	commit \| commitdiff \| tree
2010-01-14	Ben Blackburne	Added getParamName	commit \| commitdiff \| tree
2010-01-14	Ben Blackburne	Corrected README	commit \| commitdiff \| tree
2010-01-14	Ben Blackburne	THMM models	commit \| commitdiff \| tree
2010-01-13	Ben Blackburne	Allow optimisation of a chosen subset of parameters	commit \| commitdiff \| tree
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Flexible Scala Library for hypothesis testing using phylogenetic models

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