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Commits on Mar 9, 2016

• More whitespace fixes

  sbliven

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• Removing template messages

  sbliven

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• Remove trailing whitespace globally from .java files

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  sbliven

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• Running addlicense.sh

  sbliven

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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
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• FastaWriter was throwing Exception instead of IOException

  lafita

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Commits on Jan 15, 2016

• Unskip phylo tests

  lafita

  committed
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Commits on Nov 18, 2015

• Tests failing until forester version updated

  lafita

  committed
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Commits on Nov 17, 2015

• Implement fractional dissimilarity score

  lafita

  committed
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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

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Commits on Nov 16, 2015

• Implement the structural distance in phylo

  lafita

  committed
  2a8487d

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• Fix bug with the ConcurrencyTools usage

  lafita

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  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

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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

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• TreeConstructionAlgorithm renamed

  lafita

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• Remove unused classes

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  lafita

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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

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  571ebb0

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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

  lafita

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Commits on Nov 10, 2015

• Improve documentation in phylo module

  lafita

  committed
  0073740

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Commits on Nov 9, 2015

• Fix typo in demo TreeConstructor

  lafita

  committed
  37ae6c2

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• Port TreeConstructor.main to demo

  lafita

  committed
  4485ea6

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• Fix bug with TreeConstructor indices to MSA

  lafita

  committed
  04a9adb

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• Add CookBook demo for creating a phylogenetic tree from MSA

  lafita

  committed
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Commits on Jan 30, 2015

• Refactoring of all package names according to #245 #242 #240

  andreasprlic

  committed
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