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Commits on Mar 9, 2016

• More whitespace fixes

  sbliven

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  af59f90

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• Removing template messages

  sbliven

  committed
  2bb0271

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• Remove trailing whitespace globally from .java files

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  sbliven

  committed
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• Running addlicense.sh

  sbliven

  committed
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Commits on Feb 3, 2016

• Handle symmetry refinement Exceptions

  lafita

  committed
  d66cc12

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• Fix bugs in Phylogenetic tree display

  lafita

  committed
  36b9bf2

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• New feature, show phylogenetic trees for Multiple Structure Alignemnts

  lafita

  committed
  b7f2ea9

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• FastaWriter was throwing Exception instead of IOException

  lafita

  committed
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Commits on Jan 26, 2016

• Making demos compile but not package into jar #387

  josemduarte

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Commits on Jan 15, 2016

• Unskip phylo tests

  lafita

  committed
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Commits on Jan 14, 2016

• Merge branch 'master' into phylo

  lafita

  committed
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Commits on Jan 12, 2016

• Adding license to sub-poms

  sbliven

  committed
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Commits on Dec 1, 2015

• Unifying forester version to main pom.xml

  sbliven

  committed
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Commits on Nov 18, 2015

• Ignore tests until forester update

  lafita

  committed
  4cac1d5

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• Tests failing until forester version updated

  lafita

  committed
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Commits on Nov 17, 2015

• More Testing for trees

  lafita

  committed
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• Implement fractional dissimilarity score

  lafita

  committed
  4a4c06d

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• Create a Test for the distance tree evaluation

  lafita

  committed
  85578cc

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• Switch phylo and alignment dependencies back

  lafita

  committed
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• Function to clone forester DistanceMatrix

  lafita

  committed
  8a0da08

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• Fix bug in distance matrix calculation

  lafita

  committed
  9cabf41

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• Create a Test for Wrapper functions

  lafita

  committed
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Commits on Nov 16, 2015

• Implement the structural distance in phylo

  lafita

  committed
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• Fix bug with the ConcurrencyTools usage

  lafita

  committed
  fea2b4c

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• Update path to Substitution Matrices (now in core)

  lafita

  committed
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• Reshape the TreeConstructor class

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  lafita

  committed
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• Create methods for distance matrix calculation

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  lafita

  committed
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• Rename the Tree Evaluator, specific for distance trees

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  lafita

  committed
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• TreeConstructionAlgorithm renamed

  lafita

  committed
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• Remove unused classes

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  lafita

  committed
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• Create TreeConstructorType (replace TreeType)

  lafita

  committed
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• The TreeType means the optimization criteria used for tree building

  lafita

  committed
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• The demo is only for tree construction

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  lafita

  committed
  571ebb0

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• Create a Wrapper class for conversion biojava-forester

  lafita

  committed
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• Remove the tree Logger Listeners

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  lafita

  committed
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