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Commits on Aug 10, 2015

• added modified makefiles that will do a clean build (i.e. remove all .o and the corresponding executable prior to compiling)

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Commits on Mar 19, 2014

• fixed some typos in the printouts, made the makefiles debian compliant

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Commits on Dec 13, 2013

• -put eigenvalue/eigenvector decomposition into separate file that is compiled without any

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Commits on Nov 22, 2013

• integrated david dao's faster implementation of the plausibility checker algorithm (-f R option)

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Commits on Jun 24, 2013

• -fixed some minor compiler issues with the Makefiles and source files

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Commits on Mar 14, 2013

• -fully implemented optimized support for LG4 model

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Commits on Sep 2, 2012

• -removed code for mesh-based likelihood calculations

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Commits on Jun 1, 2012

• -added full AVX support for DNA and PROTEIN likelihood function implementations

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Commits on Sep 16, 2011

• -added ancestralStates.c

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Commits on Jul 17, 2011

• completely reorganized and simplified the way in which memory for likelihood vectors is allocated at inner

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