[med-svn] [iqtree] 02/05: Merge tag 'upstream/1.5.2+dfsg'
Kevin Murray
daube-guest at moszumanska.debian.org
Sun Dec 4 01:29:03 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository iqtree.
commit ddcc25e7d065654eb85a59769ac507fce6709ea0
Merge: b5cfc5f 80d3582
Author: Kevin Murray <kdmfoss at gmail.com>
Date: Sun Dec 4 11:25:35 2016 +1100
Merge tag 'upstream/1.5.2+dfsg'
Upstream version 1.5.2+dfsg
CMakeLists.txt | 416 ++++--
MPIHelper.cpp | 560 +++++++
MPIHelper.h | 305 ++++
ObjectStream.cpp | 113 ++
ObjectStream.h | 82 ++
README.md | 71 +-
TreeCollection.cpp | 56 +
TreeCollection.h | 63 +
alignment.cpp | 21 +-
alignment.h | 7 +-
candidateset.cpp | 584 +++++---
candidateset.h | 260 ++--
checkpoint.cpp | 120 +-
checkpoint.h | 20 +-
constrainttree.cpp | 211 +++
constrainttree.h | 81 ++
example/example.nex | 6 +-
example/example.phy | 64 +-
gsl/gauss.cpp | 12 +
hashsplitset.h | 19 +-
iqtree.cpp | 2064 +++++++++++++++++---------
iqtree.h | 378 +++--
iqtree_config.h.in | 3 +
lpwrapper.c | 2 +-
memslot.cpp | 254 ++++
memslot.h | 111 ++
mexttree.cpp | 73 +-
mexttree.h | 10 +
model/modelcodon.cpp | 8 +
model/modelfactory.cpp | 34 +-
model/modelmixture.cpp | 26 +-
model/modelmixture.h | 11 +
model/modelpomo.cpp | 3 +-
model/modelset.cpp | 136 +-
model/modelset.h | 7 +-
model/modelsubst.h | 6 +
model/partitionmodel.cpp | 6 +-
model/ratefree.cpp | 23 +-
model/rategamma.cpp | 8 +-
model/rategamma.h | 8 +-
model/rategammainvar.cpp | 3 +-
model/rateheterogeneity.h | 12 +-
model/rateinvar.cpp | 11 +-
model/rateinvar.h | 2 +-
mtree.cpp | 391 +++--
mtree.h | 123 +-
mtreeset.cpp | 1 +
ngs.cpp | 2 +-
node.cpp | 6 +-
node.h | 20 +-
optimization.cpp | 29 +-
pda.cpp | 196 ++-
pdtree.cpp | 5 +-
phyloanalysis.cpp | 369 +++--
phyloanalysis.h | 6 +-
phylokernel.h | 904 +++++++-----
phylokernelavx512.cpp | 120 ++
phylokernelfma.cpp | 164 +++
phylokernelmixrate.h | 2 +-
phylokernelmixture.h | 2 +-
phylokernelnew.h | 2802 ++++++++++++++++++++++++++++++++++++
phylokernel.h => phylokernelsafe.h | 1155 +++++++++------
phylokernelsitemodel.cpp | 6 +-
phylokernelsse.cpp | 169 +++
phylonode.cpp | 49 +-
phylonode.h | 22 +-
phylosupertree.cpp | 76 +-
phylosupertree.h | 7 +-
phylosupertreeplen.cpp | 164 ++-
phylosupertreeplen.h | 9 +-
phylotesting.cpp | 316 +++-
phylotesting.h | 21 +-
phylotree.cpp | 874 ++++++-----
phylotree.h | 400 +++--
phylotreeavx.cpp | 203 +--
phylotreepars.cpp | 354 +++--
phylotreesse.cpp | 2647 ++++++++++------------------------
pllnni.cpp | 53 +-
pllnni.h | 22 +-
quartet.cpp | 2 +-
split.cpp | 6 +-
split.h | 7 +-
splitgraph.cpp | 2 +-
splitgraph.h | 2 +-
splitset.cpp | 6 +-
splitset.h | 6 +-
stoprule.cpp | 44 +-
stoprule.h | 19 +-
superalignment.cpp | 66 +-
superalignment.h | 19 +
test_scripts/README | 22 +-
test_scripts/compile.sh | 113 +-
test_scripts/gen_test_standard.py | 34 +-
test_scripts/generate_test_cmds.py | 97 --
test_scripts/run_tests.sh | 50 +
test_scripts/submit_jobs.sh | 8 +-
test_scripts/submitjob.sh | 2 -
test_scripts/test_configs.txt | 18 +-
test_scripts/test_data/d59_8.nex | 2 -
tools.cpp | 339 ++++-
tools.h | 180 ++-
vectorclass/changelog.txt | 32 +-
vectorclass/dispatch_example.cpp | 12 +-
vectorclass/instrset.h | 60 +-
vectorclass/instrset_detect.cpp | 18 +-
vectorclass/special.zip | Bin 34477 -> 34897 bytes
vectorclass/vectorclass.h | 10 +-
vectorclass/vectorclass.pdf | Bin 476370 -> 431608 bytes
vectorclass/vectorf128.h | 46 +-
vectorclass/vectorf256.h | 14 +-
vectorclass/vectorf256e.h | 13 +-
vectorclass/vectorf512.h | 22 +-
vectorclass/vectorf512e.h | 13 +-
vectorclass/vectori128.h | 140 +-
vectorclass/vectori256.h | 28 +-
vectorclass/vectori256e.h | 21 +-
vectorclass/vectori512.h | 31 +-
vectorclass/vectori512e.h | 25 +-
vectorclass/vectormath_common.h | 93 +-
vectorclass/vectormath_exp.h | 27 +-
vectorclass/vectormath_hyp.h | 9 +-
vectorclass/vectormath_lib.h | 103 +-
vectorclass/vectormath_trig.h | 204 +--
vectorf64.h | 377 +++++
124 files changed, 14411 insertions(+), 5890 deletions(-)
--
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