[med-svn] [jmodeltest] 09/14: Merge tag 'upstream/2.1.10+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository jmodeltest.

commit 0a0e7334b0a80c718b63be8134cb0ee58996cd73
Merge: 3fcbb6e 4cee886
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 10 13:49:43 2016 +0200

    Merge tag 'upstream/2.1.10+dfsg'
    
    Upstream version 2.1.10+dfsg

 Manifest                                           |   2 +-
 README.md                                          |   6 +-
 manual/changelog.tex                               | 141 ++++
 manual/manual.tex                                  | 171 +----
 .../java/es/uvigo/darwin/jmodeltest/ModelTest.java |   6 +-
 .../darwin/jmodeltest/ModelTestConfiguration.java  |  28 +-
 .../jmodeltest/exception/InternalException.java    |   6 +-
 .../jmodeltest/exe/ExternalExecutionManager.java   | 108 ++++
 .../darwin/jmodeltest/exe/MultipleDistributor.java |   3 -
 .../uvigo/darwin/jmodeltest/exe/RunConsense.java   |  20 +-
 .../es/uvigo/darwin/jmodeltest/exe/RunPhyml.java   |   5 +-
 .../darwin/jmodeltest/gui/Frame_Progress.java      |   2 +-
 .../darwin/jmodeltest/io/AlignmentReader.java      |  24 +-
 .../uvigo/darwin/jmodeltest/io/HtmlReporter.java   |  11 +-
 .../es/uvigo/darwin/jmodeltest/io/RFHistogram.java |   4 +-
 .../es/uvigo/darwin/jmodeltest/tree/Consensus.java | 717 +++++++++++++++++++++
 .../darwin/jmodeltest/tree/TreeUtilities.java      | 196 +++++-
 .../uvigo/darwin/jmodeltest/tree/WeightedTree.java |  60 ++
 .../darwin/jmodeltest/utilities/FixedBitSet.java   | 268 ++++++++
 .../jmodeltest/utilities/MyFormattedOutput.java    | 181 ++++++
 src/main/resources/CHANGELOG                       |   6 +
 src/main/resources/README                          |   2 +-
 src/main/resources/resources/template/index.html   |   8 +-
 23 files changed, 1776 insertions(+), 199 deletions(-)

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