[med-svn] [iqtree] 03/08: Merge tag 'upstream/1.3.11+dfsg'
Andreas Tille
tille at debian.org
Mon Dec 14 08:24:14 UTC 2015
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tille pushed a commit to branch master
in repository iqtree.
commit 8cc4e6f9dd08499f8777ad025bbd46ba01451d09
Merge: ddc6b1a 073d744
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 14 08:43:35 2015 +0100
Merge tag 'upstream/1.3.11+dfsg'
Upstream version 1.3.11+dfsg
CMakeLists.txt | 125 +-
FindEigen3.cmake | 81 +
LICENSE | 340 ++
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, 4516 insertions(+), 59474 deletions(-)
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