[med-svn] [iqtree] branch upstream updated (041fdd6 -> 073d744)
Andreas Tille
tille at debian.org
Mon Dec 14 08:24:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository iqtree.
from 041fdd6 Imported Upstream version 1.3.8+dfsg
new 073d744 Imported Upstream version 1.3.11+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 | 125 +-
FindEigen3.cmake | 81 +
License.txt => LICENSE | 46 +-
README.md | 6 +
alignment.cpp | 20 +-
alignmentpairwise.cpp | 8 +-
bionj.h | 10 +-
eigendecomposition.cpp | 19 +-
example/example.nex | 9 +
example/example.phy | 46 +
{model => example}/models.nex | 0
examples/example.phy | 46 +
gss.cpp | 2 +-
gzstream.h | 3 +-
iqtree.cpp | 662 +-
iqtree.h | 29 +-
iqtree_config.h.in | 4 +-
mexttree.cpp | 22 +
mexttree.h | 9 +
model/modelcodon.cpp | 68 +-
model/modelcodon.h | 3 +-
model/modeldna.cpp | 56 +-
model/modeldna.h | 3 +-
model/modelfactory.cpp | 53 +-
model/modelfactory.h | 3 +-
model/modelgtr.cpp | 160 +-
model/modelgtr.h | 19 +-
model/modelmixture.cpp | 279 +-
model/modelmixture.h | 35 +-
model/modelprotein.cpp | 4 +-
model/modelset.cpp | 6 +-
model/modelset.h | 3 +-
model/modelsubst.h | 13 +-
model/partitionmodel.cpp | 41 +-
model/partitionmodel.h | 13 +
model/ratefree.cpp | 135 +-
model/ratefree.h | 12 +-
model/ratefreeinvar.cpp | 8 +-
model/ratefreeinvar.h | 3 +-
model/rategamma.cpp | 49 +-
model/rategamma.h | 14 +-
model/rategammainvar.cpp | 40 +-
model/rategammainvar.h | 3 +-
model/rateheterogeneity.h | 19 +-
model/rateinvar.cpp | 12 +-
model/rateinvar.h | 21 +-
model/ratekategory.cpp | 22 +-
model/ratekategory.h | 3 +-
msetsblock.cpp | 5 +
mtree.cpp | 103 +-
mtree.h | 20 +
mtreeset.cpp | 29 +
mtreeset.h | 2 +
ncl/nxstoken.h | 6 +-
ngs.cpp | 7 +-
ngs.h | 3 +-
optimization.cpp | 5 +-
optimization.h | 2 +-
pda.cpp | 21 +
pdnetwork.cpp | 4 +-
phyloanalysis.cpp | 164 +-
phylokernel.h | 6 +-
phylokernelmixrate.h | 2 +
phylokernelmixture.h | 2 +
phylolib.h | 26 -
phylonode.cpp | 10 +-
phylosupertree.cpp | 27 +-
phylosupertree.h | 4 +-
phylosupertreeplen.cpp | 351 +-
phylosupertreeplen.h | 43 +-
phylotesting.cpp | 299 +-
phylotesting.h | 4 +-
phylotree.cpp | 556 +-
phylotree.h | 51 +-
phylotreepars.cpp | 2 +
phylotreesse.cpp | 103 +-
pllnni.cpp | 61 +-
pllnni.h | 6 +-
pllrepo/AUTHORS | 0
pllrepo/COPYING | 674 ---
pllrepo/ChangeLog | 0
pllrepo/Doxyfile | 2299 -------
pllrepo/INSTALL | 370 --
pllrepo/Makefile.am | 7 -
pllrepo/NEWS | 0
pllrepo/README | 0
pllrepo/configure.ac | 123 -
pllrepo/sources.am | 2 -
pllrepo/src/CMakeLists.txt | 67 -
pllrepo/src/Makefile.ALL | 54 -
pllrepo/src/Makefile.ARM | 51 -
pllrepo/src/Makefile.AVX | 60 -
pllrepo/src/Makefile.AVX-MPI | 59 -
pllrepo/src/Makefile.AVX-PTHREADS | 61 -
pllrepo/src/Makefile.AVX.clang | 57 -
pllrepo/src/Makefile.AVX.shared | 68 -
pllrepo/src/Makefile.MIC-PTHREADS | 62 -
pllrepo/src/Makefile.SSE3 | 52 -
pllrepo/src/Makefile.SSE3-MPI | 50 -
pllrepo/src/Makefile.SSE3-PTHREADS | 52 -
pllrepo/src/Makefile.am | 53 -
pllrepo/src/alignment.c | 754 ---
pllrepo/src/avxLikelihood.c | 4111 -------------
pllrepo/src/bipartitionList.c | 434 --
pllrepo/src/cycle.h | 516 --
pllrepo/src/errcodes.h | 69 -
pllrepo/src/evaluateGenericSpecial.c | 3321 ----------
pllrepo/src/evaluatePartialGenericSpecial.c | 1378 -----
pllrepo/src/fastDNAparsimony.c | 1941 ------
pllrepo/src/genericParallelization.c | 2283 -------
pllrepo/src/genericParallelization.h | 127 -
pllrepo/src/globalVariables.h | 170 -
pllrepo/src/hardware.c | 165 -
pllrepo/src/hardware.h | 48 -
pllrepo/src/hash.c | 219 -
pllrepo/src/hash.h | 50 -
pllrepo/src/lexer.c | 299 -
pllrepo/src/lexer.h | 88 -
pllrepo/src/makenewzGenericSpecial.c | 3145 ----------
pllrepo/src/mem_alloc.c | 228 -
pllrepo/src/mem_alloc.h | 70 -
pllrepo/src/mic_native.h | 56 -
pllrepo/src/mic_native_aa.c | 1254 ----
pllrepo/src/mic_native_dna.c | 676 ---
pllrepo/src/models.c | 4377 --------------
pllrepo/src/newick.c | 583 --
pllrepo/src/newick.h | 61 -
pllrepo/src/newviewGenericSpecial.c | 8736 ---------------------------
pllrepo/src/optimizeModel.c | 3145 ----------
pllrepo/src/parsePartition.c | 388 --
pllrepo/src/parsePartition.h | 51 -
pllrepo/src/parsimony.c | 865 ---
pllrepo/src/pll.h | 1692 ------
pllrepo/src/pllInternal.h | 313 -
pllrepo/src/pthread.h | 1368 -----
pllrepo/src/queue.c | 96 -
pllrepo/src/queue.h | 48 -
pllrepo/src/randomTree.c | 177 -
pllrepo/src/recom.c | 689 ---
pllrepo/src/restartHashTable.c | 357 --
pllrepo/src/sched.h | 183 -
pllrepo/src/searchAlgo.c | 3310 ----------
pllrepo/src/semaphore.h | 169 -
pllrepo/src/ssort.c | 121 -
pllrepo/src/stack.c | 85 -
pllrepo/src/stack.h | 48 -
pllrepo/src/topologies.c | 778 ---
pllrepo/src/trash.c | 129 -
pllrepo/src/treeIO.c | 236 -
pllrepo/src/treeIO.h | 23 -
pllrepo/src/utils.c | 3734 ------------
stoprule.cpp | 4 +-
test_scripts/README | 19 +
test_scripts/compile.sh | 120 +
test_scripts/gen_test_standard.py | 92 +
test_scripts/gen_test_webserver.py | 85 +
test_scripts/generate_test_cmds.py | 97 +
test_scripts/jobmanager.py | 102 +
test_scripts/submit_jobs.sh | 45 +
test_scripts/submitjob.sh | 2 +
test_scripts/test_configs.txt | 27 +
test_scripts/test_data/d59_8.nex | 13 +
test_scripts/test_data/d59_8.phy | 60 +
test_scripts/test_data/example.nex | 5 +
test_scripts/test_data/example.phy | 46 +
test_scripts/test_data/prot_M126_27_269.phy | 28 +
tools.cpp | 193 +-
tools.h | 68 +-
vectorclass/changelog.txt | 25 +-
vectorclass/special.zip | Bin 34472 -> 34477 bytes
vectorclass/vectorclass.h | 6 +-
vectorclass/vectorclass.pdf | Bin 466946 -> 476370 bytes
vectorclass/vectorf128.h | 32 +-
vectorclass/vectorf256.h | 30 +-
vectorclass/vectorf256e.h | 8 +-
vectorclass/vectorf512.h | 29 +-
vectorclass/vectori128.h | 103 +-
vectorclass/vectori256.h | 529 +-
vectorclass/vectori256e.h | 68 +-
vectorclass/vectori512.h | 4 +-
vectorclass/vectormath_exp.h | 94 +-
vectorclass/vectormath_hyp.h | 120 +-
vectorclass/vectormath_trig.h | 86 +-
183 files changed, 4199 insertions(+), 59497 deletions(-)
create mode 100644 FindEigen3.cmake
copy License.txt => LICENSE (95%)
create mode 100644 README.md
create mode 100644 example/example.nex
create mode 100644 example/example.phy
rename {model => example}/models.nex (100%)
create mode 100644 examples/example.phy
delete mode 100755 phylolib.h
delete mode 100644 pllrepo/AUTHORS
delete mode 100644 pllrepo/COPYING
delete mode 100644 pllrepo/ChangeLog
delete mode 100644 pllrepo/Doxyfile
delete mode 100644 pllrepo/INSTALL
delete mode 100644 pllrepo/Makefile.am
delete mode 100644 pllrepo/NEWS
delete mode 100644 pllrepo/README
delete mode 100644 pllrepo/configure.ac
delete mode 100644 pllrepo/sources.am
delete mode 100644 pllrepo/src/CMakeLists.txt
delete mode 100644 pllrepo/src/Makefile.ALL
delete mode 100644 pllrepo/src/Makefile.ARM
delete mode 100644 pllrepo/src/Makefile.AVX
delete mode 100644 pllrepo/src/Makefile.AVX-MPI
delete mode 100644 pllrepo/src/Makefile.AVX-PTHREADS
delete mode 100644 pllrepo/src/Makefile.AVX.clang
delete mode 100644 pllrepo/src/Makefile.AVX.shared
delete mode 100644 pllrepo/src/Makefile.MIC-PTHREADS
delete mode 100644 pllrepo/src/Makefile.SSE3
delete mode 100644 pllrepo/src/Makefile.SSE3-MPI
delete mode 100644 pllrepo/src/Makefile.SSE3-PTHREADS
delete mode 100644 pllrepo/src/Makefile.am
delete mode 100644 pllrepo/src/alignment.c
delete mode 100644 pllrepo/src/avxLikelihood.c
delete mode 100644 pllrepo/src/bipartitionList.c
delete mode 100644 pllrepo/src/cycle.h
delete mode 100644 pllrepo/src/errcodes.h
delete mode 100644 pllrepo/src/evaluateGenericSpecial.c
delete mode 100644 pllrepo/src/evaluatePartialGenericSpecial.c
delete mode 100644 pllrepo/src/fastDNAparsimony.c
delete mode 100644 pllrepo/src/genericParallelization.c
delete mode 100644 pllrepo/src/genericParallelization.h
delete mode 100644 pllrepo/src/globalVariables.h
delete mode 100644 pllrepo/src/hardware.c
delete mode 100644 pllrepo/src/hardware.h
delete mode 100644 pllrepo/src/hash.c
delete mode 100644 pllrepo/src/hash.h
delete mode 100644 pllrepo/src/lexer.c
delete mode 100644 pllrepo/src/lexer.h
delete mode 100644 pllrepo/src/makenewzGenericSpecial.c
delete mode 100644 pllrepo/src/mem_alloc.c
delete mode 100644 pllrepo/src/mem_alloc.h
delete mode 100644 pllrepo/src/mic_native.h
delete mode 100644 pllrepo/src/mic_native_aa.c
delete mode 100644 pllrepo/src/mic_native_dna.c
delete mode 100644 pllrepo/src/models.c
delete mode 100644 pllrepo/src/newick.c
delete mode 100644 pllrepo/src/newick.h
delete mode 100644 pllrepo/src/newviewGenericSpecial.c
delete mode 100644 pllrepo/src/optimizeModel.c
delete mode 100644 pllrepo/src/parsePartition.c
delete mode 100644 pllrepo/src/parsePartition.h
delete mode 100644 pllrepo/src/parsimony.c
delete mode 100644 pllrepo/src/pll.h
delete mode 100644 pllrepo/src/pllInternal.h
delete mode 100644 pllrepo/src/pthread.h
delete mode 100644 pllrepo/src/queue.c
delete mode 100644 pllrepo/src/queue.h
delete mode 100644 pllrepo/src/randomTree.c
delete mode 100644 pllrepo/src/recom.c
delete mode 100644 pllrepo/src/restartHashTable.c
delete mode 100644 pllrepo/src/sched.h
delete mode 100644 pllrepo/src/searchAlgo.c
delete mode 100644 pllrepo/src/semaphore.h
delete mode 100644 pllrepo/src/ssort.c
delete mode 100644 pllrepo/src/stack.c
delete mode 100644 pllrepo/src/stack.h
delete mode 100644 pllrepo/src/topologies.c
delete mode 100644 pllrepo/src/trash.c
delete mode 100644 pllrepo/src/treeIO.c
delete mode 100644 pllrepo/src/treeIO.h
delete mode 100644 pllrepo/src/utils.c
create mode 100644 test_scripts/README
create mode 100755 test_scripts/compile.sh
create mode 100755 test_scripts/gen_test_standard.py
create mode 100755 test_scripts/gen_test_webserver.py
create mode 100755 test_scripts/generate_test_cmds.py
create mode 100755 test_scripts/jobmanager.py
create mode 100755 test_scripts/submit_jobs.sh
create mode 100755 test_scripts/submitjob.sh
create mode 100644 test_scripts/test_configs.txt
create mode 100644 test_scripts/test_data/d59_8.nex
create mode 100644 test_scripts/test_data/d59_8.phy
create mode 100644 test_scripts/test_data/example.nex
create mode 100644 test_scripts/test_data/example.phy
create mode 100644 test_scripts/test_data/prot_M126_27_269.phy
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