[med-svn] [iqtree] branch upstream updated (073d744 -> b24d046)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository iqtree.

      from  073d744   Imported Upstream version 1.3.11+dfsg
       new  b24d046   Imported Upstream version 1.3.11.1+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 delete mode 100644 Documents/iqtree-manual-1.0.pdf
 delete mode 100644 examples/example.phy
 create mode 100644 pll/CMakeLists.txt
 create mode 100644 pll/alignment.c
 create mode 100644 pll/avxLikelihood.c
 create mode 100644 pll/bipartitionList.c
 create mode 100644 pll/cycle.h
 create mode 100644 pll/errcodes.h
 create mode 100644 pll/evaluateGenericSpecial.c
 create mode 100644 pll/evaluatePartialGenericSpecial.c
 create mode 100644 pll/fastDNAparsimony.c
 create mode 100644 pll/genericParallelization.c
 create mode 100644 pll/genericParallelization.h
 create mode 100644 pll/globalVariables.h
 create mode 100644 pll/hardware.c
 create mode 100644 pll/hardware.h
 create mode 100644 pll/hash.c
 create mode 100644 pll/hash.h
 create mode 100644 pll/lexer.c
 create mode 100644 pll/lexer.h
 create mode 100644 pll/makenewzGenericSpecial.c
 create mode 100644 pll/mem_alloc.c
 create mode 100644 pll/mem_alloc.h
 create mode 100644 pll/mic_native.h
 create mode 100644 pll/mic_native_aa.c
 create mode 100644 pll/mic_native_dna.c
 create mode 100644 pll/models.c
 create mode 100644 pll/newick.c
 create mode 100644 pll/newick.h
 create mode 100644 pll/newviewGenericSpecial.c
 create mode 100644 pll/optimizeModel.c
 create mode 100644 pll/parsePartition.c
 create mode 100644 pll/parsePartition.h
 create mode 100644 pll/parsimony.c
 create mode 100644 pll/pll.h
 create mode 100644 pll/pllInternal.h
 create mode 100644 pll/pthread.h
 create mode 100644 pll/queue.c
 create mode 100644 pll/queue.h
 create mode 100644 pll/randomTree.c
 create mode 100644 pll/recom.c
 create mode 100644 pll/restartHashTable.c
 create mode 100644 pll/sched.h
 create mode 100644 pll/searchAlgo.c
 create mode 100644 pll/semaphore.h
 create mode 100644 pll/ssort.c
 create mode 100644 pll/stack.c
 create mode 100644 pll/stack.h
 create mode 100644 pll/topologies.c
 create mode 100644 pll/trash.c
 create mode 100644 pll/treeIO.c
 create mode 100644 pll/treeIO.h
 create mode 100644 pll/utils.c

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