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1. Commits on Mar 9, 2016

   • More whitespace fixes

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   • Removing template messages

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   • Remove trailing whitespace globally from .java files

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   • Running addlicense.sh

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2. Commits on Feb 3, 2016

   • Handle symmetry refinement Exceptions

     lafita

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   • Fix bugs in Phylogenetic tree display

     lafita

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   • New feature, show phylogenetic trees for Multiple Structure Alignemnts

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   • FastaWriter was throwing Exception instead of IOException

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3. Commits on Jan 15, 2016

   • Unskip phylo tests

     lafita

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4. Commits on Nov 18, 2015

   • Ignore tests until forester update

     lafita

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   • Tests failing until forester version updated

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5. Commits on Nov 17, 2015

   • More Testing for trees

     lafita

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   • Implement fractional dissimilarity score

     lafita

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   • Create a Test for the distance tree evaluation

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   • Switch phylo and alignment dependencies back

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   • Function to clone forester DistanceMatrix

     lafita

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   • Fix bug in distance matrix calculation

     lafita

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   • Create a Test for Wrapper functions

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6. Commits on Nov 16, 2015

   • Implement the structural distance in phylo

     lafita

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   • Fix bug with the ConcurrencyTools usage

     lafita

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   • Update path to Substitution Matrices (now in core)

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   • Reshape the TreeConstructor class

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   • Create methods for distance matrix calculation

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   • Rename the Tree Evaluator, specific for distance trees

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   • TreeConstructionAlgorithm renamed

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   • Remove unused classes

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   • Create TreeConstructorType (replace TreeType)

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   • The TreeType means the optimization criteria used for tree building

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   • The demo is only for tree construction

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   • Create a Wrapper class for conversion biojava-forester

     lafita

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   • Remove the tree Logger Listeners

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     lafita

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   • Formatting changes to Comparison class

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7. Commits on Nov 10, 2015

   • Improve documentation in phylo module

     lafita

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8. Commits on Nov 9, 2015

   • Fix typo in demo TreeConstructor

     lafita

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   • Port TreeConstructor.main to demo

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