[med-svn] [iqtree] 02/08: Merge tag 'upstream/1.3.11.1+dfsg'

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository iqtree.

commit 903f7a708bec15550bc378eb9882c22d5098d28b
Merge: a2e119e b24d046
Author: Andreas Tille <tille at debian.org>
Date:   Thu Dec 17 14:15:27 2015 +0100

    Merge tag 'upstream/1.3.11.1+dfsg'
    
    Upstream version 1.3.11.1+dfsg

 CMakeLists.txt                      |   11 +-
 Documents/iqtree-manual-1.0.pdf     |  Bin 158099 -> 0 bytes
 examples/example.phy                |   46 -
 iqtree.cpp                          |    3 +-
 phylotree.h                         |    2 +-
 pll/CMakeLists.txt                  |   67 +
 pll/alignment.c                     |  754 +++
 pll/avxLikelihood.c                 | 4111 ++++++++++++++++
 pll/bipartitionList.c               |  434 ++
 pll/cycle.h                         |  516 +++
 pll/errcodes.h                      |   69 +
 pll/evaluateGenericSpecial.c        | 3321 +++++++++++++
 pll/evaluatePartialGenericSpecial.c | 1378 ++++++
 pll/fastDNAparsimony.c              | 1942 ++++++++
 pll/genericParallelization.c        | 2283 +++++++++
 pll/genericParallelization.h        |  127 +
 pll/globalVariables.h               |  170 +
 pll/hardware.c                      |  165 +
 pll/hardware.h                      |   48 +
 pll/hash.c                          |  219 +
 pll/hash.h                          |   50 +
 pll/lexer.c                         |  299 ++
 pll/lexer.h                         |   88 +
 pll/makenewzGenericSpecial.c        | 3145 +++++++++++++
 pll/mem_alloc.c                     |  228 +
 pll/mem_alloc.h                     |   77 +
 pll/mic_native.h                    |   56 +
 pll/mic_native_aa.c                 | 1254 +++++
 pll/mic_native_dna.c                |  676 +++
 pll/models.c                        | 4377 ++++++++++++++++++
 pll/newick.c                        |  583 +++
 pll/newick.h                        |   61 +
 pll/newviewGenericSpecial.c         | 8736 +++++++++++++++++++++++++++++++++++
 pll/optimizeModel.c                 | 3149 +++++++++++++
 pll/parsePartition.c                |  388 ++
 pll/parsePartition.h                |   51 +
 pll/parsimony.c                     |  865 ++++
 pll/pll.h                           | 1692 +++++++
 pll/pllInternal.h                   |  313 ++
 pll/pthread.h                       | 1368 ++++++
 pll/queue.c                         |   96 +
 pll/queue.h                         |   48 +
 pll/randomTree.c                    |  177 +
 pll/recom.c                         |  689 +++
 pll/restartHashTable.c              |  357 ++
 pll/sched.h                         |  183 +
 pll/searchAlgo.c                    | 3310 +++++++++++++
 pll/semaphore.h                     |  169 +
 pll/ssort.c                         |  121 +
 pll/stack.c                         |   85 +
 pll/stack.h                         |   48 +
 pll/topologies.c                    |  778 ++++
 pll/trash.c                         |  129 +
 pll/treeIO.c                        |  236 +
 pll/treeIO.h                        |   23 +
 pll/utils.c                         | 3735 +++++++++++++++
 pllnni.h                            |    2 +-
 57 files changed, 53252 insertions(+), 56 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iqtree.git