[med-svn] [iqtree] branch master updated (a2e119e -> 3e4ff49)
Andreas Tille
tille at debian.org
Thu Dec 17 16:18:52 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository iqtree.
from a2e119e Manual source is under debian/* so specify this separatel
new b24d046 Imported Upstream version 1.3.11.1+dfsg
new 903f7a7 Merge tag 'upstream/1.3.11.1+dfsg'
new 501bea5 Patches not needed for new upstream version
new e608e13 Renamed dir
new 7fac079 Remove new files in unusual dir
new 36ac723 New upstream version
new 820aeb0 Fix spelling
new 3e4ff49 Upload to new
The 8 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
debian/changelog | 4 +-
debian/copyright | 2 +-
debian/patches/debian_packaged_sprng.patch | 55 -
debian/patches/series | 3 +-
debian/patches/spelling.patch | 15 +
debian/patches/use_debian_packaged_libs.patch | 82 -
debian/patches/work_around_missing_example.patch | 15 -
debian/rules | 11 +-
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 +-
65 files changed, 53276 insertions(+), 219 deletions(-)
delete mode 100644 Documents/iqtree-manual-1.0.pdf
delete mode 100644 debian/patches/debian_packaged_sprng.patch
create mode 100644 debian/patches/spelling.patch
delete mode 100644 debian/patches/use_debian_packaged_libs.patch
delete mode 100644 debian/patches/work_around_missing_example.patch
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
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