[med-svn] [Git][med-team/iqtree][debian/unstable] 14 commits: New upstream location for legacy IQ-TREE version 2.x.

Michael R. Crusoe (@crusoe) gitlab at salsa.debian.org
Sat Apr 11 16:59:54 BST 2026 


Michael R. Crusoe pushed to branch debian/unstable at Debian Med / iqtree


Commits:
62495702 by Michael R. Crusoe at 2026-04-11T14:53:10+02:00
New upstream location for legacy IQ-TREE version 2.x.

Updated primary citation as well.

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d6ed65af by Michael R. Crusoe at 2026-04-11T14:55:51+02:00
New upstream version

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84d2d54e by Michael R. Crusoe at 2026-04-11T14:55:52+02:00
New upstream version 2.4.0+dfsg
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b13ded15 by Michael R. Crusoe at 2026-04-11T14:56:04+02:00
Update upstream source from tag 'upstream/2.4.0+dfsg'

Update to upstream version '2.4.0+dfsg'
with Debian dir 48178738441d6fc9eafe90ccc01f85d5faf6de3b
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71396415 by Michael R. Crusoe at 2026-04-11T14:56:05+02:00
Standards-Version: 4.7.4 (routine-update)

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7ce0a9fd by Michael R. Crusoe at 2026-04-11T14:56:11+02:00
Remove trailing whitespace in debian/changelog (routine-update)

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48ce76d6 by Michael R. Crusoe at 2026-04-11T14:56:20+02:00
debputy lint --auto-fix (routine-update)

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b6670245 by Michael R. Crusoe at 2026-04-11T15:00:21+02:00
d/patches: refreshed, dropped 2 no-longer needed: boost1.90 & gcc- 15.

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e871ad21 by Michael R. Crusoe at 2026-04-11T15:32:43+02:00
d/watch: download using git, due to submodules.

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29cc275f by Michael R. Crusoe at 2026-04-11T15:33:43+02:00
New upstream version 2.4.0+dfsg
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421f9fe8 by Michael R. Crusoe at 2026-04-11T15:33:55+02:00
Update upstream source from tag 'upstream/2.4.0+dfsg'

Update to upstream version '2.4.0+dfsg'
with Debian dir f8f2ec89cb9558a4b02e454699d6845a0f250ebe
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2437648c by Michael R. Crusoe at 2026-04-11T15:39:42+02:00
refresh cmake patch

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0c071cb5 by Michael R. Crusoe at 2026-04-11T16:35:23+02:00
Added patch to use googletest, yaml-cpp, & SIMDe packages.

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e951cb72 by Michael R. Crusoe at 2026-04-11T17:02:40+02:00
d/rules: add openmpi include path

- - - - -


512 changed files:

- CMakeLists.txt
- + CMakeSettings.json
- + CODE_OF_CONDUCT.md
- README.md
- alignment/CMakeLists.txt
- alignment/alignment.cpp
- alignment/alignment.h
- alignment/alignmentpairwise.cpp
- alignment/alignmentpairwise.h
- + alignment/alignmentsummary.cpp
- + alignment/alignmentsummary.h
- alignment/maalignment.cpp
- alignment/pattern.cpp
- alignment/pattern.h
- + alignment/sequence.cpp
- + alignment/sequence.h
- + alignment/sequencechunkstr.cpp
- + alignment/sequencechunkstr.h
- + alignment/substitution.cpp
- + alignment/substitution.h
- alignment/superalignment.cpp
- alignment/superalignment.h
- alignment/superalignmentpairwise.cpp
- alignment/superalignmentpairwise.h
- alignment/superalignmentpairwiseplen.cpp
- alignment/superalignmentunlinked.cpp
- booster/booster.c
- booster/tree.c
- booster/tree.h
- booster/version.h
- + cmaple/.github/workflows/ci.yaml
- + cmaple/.gitignore
- + cmaple/CMakeLists.txt
- + cmaple/CMakeSettings.json
- + cmaple/CMapleLib.md
- + cmaple/CODE_OF_CONDUCT.md
- + cmaple/CONTRIBUTING.md
- + cmaple/LICENSE
- + cmaple/README.md
- + cmaple/alignment/CMakeLists.txt
- + cmaple/alignment/alignment.cpp
- + cmaple/alignment/alignment.h
- + cmaple/alignment/mutation.cpp
- + cmaple/alignment/mutation.h
- + cmaple/alignment/seqregion.cpp
- + cmaple/alignment/seqregion.h
- + cmaple/alignment/seqregions.cpp
- + cmaple/alignment/seqregions.h
- + cmaple/alignment/sequence.cpp
- + cmaple/alignment/sequence.h
- + cmaple/cmaple.doxy
- + cmaple/cmaple_config.h.in
- + cmaple/example/example.maple
- + cmaple/example/input.fa
- + cmaple/example/input.phy
- + cmaple/example/ref.fa
- + cmaple/example/test_100.maple
- + cmaple/example/test_5K.maple
- + cmaple/example/tree.nwk
- + cmaple/layout.xml
- + cmaple/layout.xml.bak
- + cmaple/libraries/ncl/CMakeLists.txt
- + cmaple/libraries/ncl/ncl.h
- + cmaple/libraries/ncl/nxsblock.cpp
- + cmaple/libraries/ncl/nxsblock.h
- + cmaple/libraries/ncl/nxsdefs.h
- + cmaple/libraries/ncl/nxsexception.cpp
- + cmaple/libraries/ncl/nxsexception.h
- + cmaple/libraries/ncl/nxsindent.h
- + cmaple/libraries/ncl/nxsreader.cpp
- + cmaple/libraries/ncl/nxsreader.h
- + cmaple/libraries/ncl/nxsstring.cpp
- + cmaple/libraries/ncl/nxsstring.h
- + cmaple/libraries/ncl/nxstoken.cpp
- + cmaple/libraries/ncl/nxstoken.h
- + cmaple/libraries/nclextra/CMakeLists.txt
- + cmaple/libraries/nclextra/modelsblock.cpp
- + cmaple/libraries/nclextra/modelsblock.h
- + cmaple/libraries/nclextra/myreader.h
- + cmaple/main/CMakeLists.txt
- + cmaple/main/main.cpp
- + cmaple/maple/CMakeLists.txt
- + cmaple/maple/cmaple.cpp
- + cmaple/maple/cmaple.h
- + cmaple/model/CMakeLists.txt
- + cmaple/model/model.cpp
- + cmaple/model/model.h
- + cmaple/model/model_aa.cpp
- + cmaple/model/model_aa.h
- + cmaple/model/model_aa.nexus
- + cmaple/model/model_dna.cpp
- + cmaple/model/model_dna.h
- + cmaple/model/modelbase.cpp
- + cmaple/model/modelbase.h
- + cmaple/tree/CMakeLists.txt
- + cmaple/tree/altbranch.h
- + cmaple/tree/internal.h
- + cmaple/tree/leaf.h
- + cmaple/tree/phylonode.cpp
- + cmaple/tree/phylonode.h
- + cmaple/tree/rootcandidate.h
- + cmaple/tree/traversingnode.cpp
- + cmaple/tree/traversingnode.h
- + cmaple/tree/tree.cpp
- + cmaple/tree/tree.h
- + cmaple/tree/updatingnode.cpp
- + cmaple/tree/updatingnode.h
- + cmaple/unittest/CMakeLists.txt
- + cmaple/unittest/alignment_test.cpp
- + cmaple/unittest/cmaple_test.cpp
- + cmaple/unittest/matrix_test.cpp
- + cmaple/unittest/model_test.cpp
- + cmaple/unittest/mutation_test.cpp
- + cmaple/unittest/phylonode_test.cpp
- + cmaple/unittest/seqregion_test.cpp
- + cmaple/unittest/seqregions_test.cpp
- + cmaple/unittest/sequence_test.cpp
- + cmaple/utils/CMakeLists.txt
- + cmaple/utils/gzstream.cpp
- + cmaple/utils/gzstream.h
- + cmaple/utils/logstream.cpp
- + cmaple/utils/logstream.h
- + cmaple/utils/matrix.h
- + cmaple/utils/operatingsystem.cpp
- + cmaple/utils/operatingsystem.h
- + cmaple/utils/timeutil.h
- + cmaple/utils/tools.cpp
- + cmaple/utils/tools.h
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/boost1.90.patch
- debian/patches/cmake-4.patch
- + debian/patches/find-libs
- − debian/patches/gcc-15.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
- debian/watch
- + example/custom_distributions.txt
- + example/tree.nwk
- + flake.lock
- + flake.nix
- + iqtree.doxy
- + lsd2/CMakeLists.txt
- + lsd2/LICENSE
- + lsd2/NEWS
- + lsd2/README.md
- + lsd2/examples/fig/ex.png
- + lsd2/examples/rooted_tree/h1n1.date
- + lsd2/examples/rooted_tree/h1n1_flexible.date
- + lsd2/examples/rooted_tree/h1n1_partition
- + lsd2/examples/rooted_tree/h1n1_phyml.tree
- + lsd2/examples/rooted_tree/h1n1_phyml.tree.result
- + lsd2/examples/unrooted_tree_with_outgroups/h1n1.date
- + lsd2/examples/unrooted_tree_with_outgroups/h1n1_outgroup.txt
- + lsd2/examples/unrooted_tree_with_outgroups/h1n1_phyml.tree
- + lsd2/examples/unrooted_tree_without_outgroups/Dengue.date
- + lsd2/examples/unrooted_tree_without_outgroups/Dengue.phy_phyml_tree.txt
- + lsd2/src/confidence_interval.cpp
- + lsd2/src/confidence_interval.h
- + lsd2/src/date.h
- + lsd2/src/dating.cpp
- + lsd2/src/dating.h
- + lsd2/src/estimate_root.cpp
- + lsd2/src/estimate_root.h
- + lsd2/src/lsd.cpp
- + lsd2/src/lsd.h
- + lsd2/src/makefile
- + lsd2/src/node.h
- + lsd2/src/options.cpp
- + lsd2/src/options.h
- + lsd2/src/outliers.cpp
- + lsd2/src/outliers.h
- + lsd2/src/pair.h
- + lsd2/src/part.h
- + lsd2/src/pr.h
- + lsd2/src/readData.cpp
- + lsd2/src/readData.h
- + lsd2/src/subtree.h
- + lsd2/src/utils.cpp
- + lsd2/src/utils.h
- main/CMakeLists.txt
- + main/alisim.cpp
- + main/alisim.h
- main/main.cpp
- main/phyloanalysis.cpp
- main/phyloanalysis.h
- main/phylotesting.cpp
- main/phylotesting.h
- + main/terraceanalysis.cpp
- + main/terraceanalysis.h
- main/timetree.cpp
- main/treetesting.cpp
- main/treetesting.h
- model/CMakeLists.txt
- model/modelbin.cpp
- model/modelbin.h
- model/modelcodon.cpp
- model/modelcodon.h
- model/modeldna.cpp
- model/modeldna.h
- + model/modeldnaerror.cpp
- + model/modeldnaerror.h
- model/modelfactory.cpp
- model/modelfactory.h
- model/modelfactorymixlen.cpp
- + model/modelhmm.cpp
- + model/modelhmm.h
- + model/modelhmmgm.cpp
- + model/modelhmmgm.h
- + model/modelhmmtm.cpp
- + model/modelhmmtm.h
- model/modelliemarkov.cpp
- model/modelliemarkov.h
- model/modelmarkov.cpp
- model/modelmarkov.h
- model/modelmixture.cpp
- model/modelmixture.h
- model/modelmorphology.cpp
- model/modelmorphology.h
- model/modelpomo.cpp
- model/modelpomo.h
- model/modelpomomixture.cpp
- model/modelpomomixture.h
- model/modelprotein.cpp
- model/modelprotein.h
- model/modelset.cpp
- model/modelset.h
- model/modelsubst.cpp
- model/modelsubst.h
- model/modelunrest.cpp
- model/modelunrest.h
- model/partitionmodel.cpp
- model/partitionmodel.h
- model/partitionmodelplen.cpp
- + model/ratecontinuousgamma.cpp
- + model/ratecontinuousgamma.h
- + model/ratecontinuousgammainvar.cpp
- + model/ratecontinuousgammainvar.h
- model/ratefree.cpp
- model/ratefree.h
- model/ratefreeinvar.cpp
- model/ratefreeinvar.h
- model/rategamma.cpp
- model/rategammainvar.cpp
- model/rateheterogeneity.h
- model/rateheterotachy.cpp
- model/rateinvar.cpp
- model/rateinvar.h
- model/ratekategory.cpp
- model/ratemeyerdiscrete.cpp
- model/ratemeyerhaeseler.cpp
- ncl/ncl.h
- ncl/nxsblock.h
- ncl/nxscharactersblock.cpp
- ncl/nxscharactersblock.h
- ncl/nxsdefs.h
- ncl/nxsexception.cpp
- ncl/nxsexception.h
- ncl/nxsindent.h
- ncl/nxsstring.cpp
- ncl/nxsstring.h
- ncl/nxstaxablock.h
- ncl/nxstoken.h
- nclextra/msetsblock.h
- nclextra/myreader.h
- pda/ecopd.cpp
- pda/pdnetwork.cpp
- pda/splitgraph.h
- phylo-yaml/statespace.cpp
- phylo-yaml/statespace.h
- pll/avxLikelihood.c
- pll/bipartitionList.c
- pll/cycle.h
- pll/evaluateGenericSpecial.c
- pll/evaluatePartialGenericSpecial.c
- pll/fastDNAparsimony.c
- pll/genericParallelization.c
- pll/genericParallelization.h
- pll/hardware.c
- pll/makenewzGenericSpecial.c
- pll/mem_alloc.h
- pll/mic_native_aa.c
- pll/mic_native_dna.c
- pll/models.c
- pll/newviewGenericSpecial.c
- pll/optimizeModel.c
- pll/parsimony.c
- pll/pll.h
- pll/pllInternal.h
- pll/recom.c
- pll/restartHashTable.c
- pll/searchAlgo.c
- + pll/systypes.h
- pll/topologies.c
- pll/trash.c
- pll/treeIO.c
- pll/utils.c
- + simulator/CMakeLists.txt
- + simulator/alisimulator.cpp
- + simulator/alisimulator.h
- + simulator/alisimulatorheterogeneity.cpp
- + simulator/alisimulatorheterogeneity.h
- + simulator/alisimulatorheterogeneityinvar.cpp
- + simulator/alisimulatorheterogeneityinvar.h
- + simulator/alisimulatorinvar.cpp
- + simulator/alisimulatorinvar.h
- sprng/lcg64.c
- terrace/CMakeLists.txt
- + terrace/README.md
- + terrace/presenceabsencematrix.cpp
- + terrace/presenceabsencematrix.hpp
- terrace/terrace.cpp
- + terrace/terrace.hpp
- + terrace/terracenode.cpp
- + terrace/terracenode.hpp
- + terrace/terracetree.cpp
- + terrace/terracetree.hpp
- + terracetphast/CMakeLists.txt
- + terracetphast/terracetphast.cpp
- terrace/terrace.h → terracetphast/terracetphast.h
- + terraphast/.gitattributes
- + terraphast/.gitignore
- terraphast/CMakeLists.txt
- terraphast/appveyor.yml
- terraphast/include/terraces/constraints.hpp
- terraphast/include/terraces/definitions.hpp
- terraphast/lib/multitree_iterator.cpp
- terraphast/lib/multitree_iterator.hpp
- + test_scripts/iqtree2.h
- + test_scripts/unify-static-libs.sh
- tree/CMakeLists.txt
- tree/candidateset.cpp
- tree/discordance.cpp
- + tree/genomenode.cpp
- + tree/genomenode.h
- + tree/genometree.cpp
- + tree/genometree.h
- tree/iqtree.cpp
- tree/iqtree.h
- + tree/iqtreemix.cpp
- + tree/iqtreemix.h
- + tree/iqtreemixhmm.cpp
- + tree/iqtreemixhmm.h
- tree/mexttree.cpp
- tree/mexttree.h
- tree/mtree.cpp
- tree/mtree.h
- tree/mtreeset.cpp
- tree/node.cpp
- tree/node.h
- + tree/phylohmm.cpp
- + tree/phylohmm.h
- tree/phylokernel.h
- tree/phylokernelfma.cpp
- tree/phylokernelnew.h
- tree/phylokernelnonrev.h
- tree/phylokernelsse.cpp
- tree/phylonode.cpp
- tree/phylosupertree.cpp
- tree/phylosupertree.h
- tree/phylosupertreeplen.cpp
- tree/phylosupertreeplen.h
- tree/phylotree.cpp
- tree/phylotree.h
- tree/phylotreeavx.cpp
- tree/phylotreemixlen.cpp
- tree/phylotreemixlen.h
- tree/phylotreepars.cpp
- tree/phylotreesse.cpp
- tree/quartet.cpp
- tree/tinatree.cpp
- utils/CMakeLists.txt
- utils/MPIHelper.cpp
- utils/MPIHelper.h
- utils/bionj.h → utils/bionj.cpp
- + utils/bionj2.cpp
- + utils/bionj2.h
- utils/checkpoint.cpp
- utils/checkpoint.h
- + utils/decenttree.cpp
- utils/eigendecomposition.cpp
- utils/gzstream.cpp
- utils/gzstream.h
- + utils/hammingdistance.h
- + utils/heapsort.h
- + utils/operatingsystem.cpp
- + utils/operatingsystem.h
- utils/optimization.cpp
- utils/pllnni.cpp
- + utils/progress.cpp
- + utils/progress.h
- + utils/sse2neon.h
- + utils/starttree.cpp
- + utils/starttree.h
- utils/stoprule.cpp
- utils/timeutil.h
- utils/tools.cpp
- utils/tools.h
- vectorclass/instrset.h
- vectorclass/instrset_detect.cpp
- vectorclass/vectorf128.h
- vectorclass/vectori128.h
- whtest/eigen.c
- whtest/weisslambda_sub.h
- whtest/whtest.c
- whtest/whtest_wrapper.cpp
- − yaml-cpp/CMakeLists.txt
- − yaml-cpp/CONTRIBUTING.md
- − yaml-cpp/LICENSE
- − yaml-cpp/README.md
- − yaml-cpp/include/yaml-cpp/anchor.h
- − yaml-cpp/include/yaml-cpp/binary.h
- − yaml-cpp/include/yaml-cpp/contrib/anchordict.h
- − yaml-cpp/include/yaml-cpp/contrib/graphbuilder.h
- − yaml-cpp/include/yaml-cpp/dll.h
- − yaml-cpp/include/yaml-cpp/emitfromevents.h
- − yaml-cpp/include/yaml-cpp/emitter.h
- − yaml-cpp/include/yaml-cpp/emitterdef.h
- − yaml-cpp/include/yaml-cpp/emittermanip.h
- − yaml-cpp/include/yaml-cpp/emitterstyle.h
- − yaml-cpp/include/yaml-cpp/eventhandler.h
- − yaml-cpp/include/yaml-cpp/exceptions.h
- − yaml-cpp/include/yaml-cpp/mark.h
- − yaml-cpp/include/yaml-cpp/node/convert.h
- − yaml-cpp/include/yaml-cpp/node/detail/bool_type.h
- − yaml-cpp/include/yaml-cpp/node/detail/impl.h
- − yaml-cpp/include/yaml-cpp/node/detail/iterator.h
- − yaml-cpp/include/yaml-cpp/node/detail/iterator_fwd.h
- − yaml-cpp/include/yaml-cpp/node/detail/memory.h
- − yaml-cpp/include/yaml-cpp/node/detail/node.h
- − yaml-cpp/include/yaml-cpp/node/detail/node_data.h
- − yaml-cpp/include/yaml-cpp/node/detail/node_iterator.h
- − yaml-cpp/include/yaml-cpp/node/detail/node_ref.h
- − yaml-cpp/include/yaml-cpp/node/emit.h
- − yaml-cpp/include/yaml-cpp/node/impl.h
- − yaml-cpp/include/yaml-cpp/node/iterator.h
- − yaml-cpp/include/yaml-cpp/node/node.h
- − yaml-cpp/include/yaml-cpp/node/parse.h
- − yaml-cpp/include/yaml-cpp/node/ptr.h
- − yaml-cpp/include/yaml-cpp/node/type.h
- − yaml-cpp/include/yaml-cpp/noncopyable.h
- − yaml-cpp/include/yaml-cpp/null.h
- − yaml-cpp/include/yaml-cpp/ostream_wrapper.h
- − yaml-cpp/include/yaml-cpp/parser.h
- − yaml-cpp/include/yaml-cpp/stlemitter.h
- − yaml-cpp/include/yaml-cpp/traits.h
- − yaml-cpp/include/yaml-cpp/yaml.h
- − yaml-cpp/install.txt
- − yaml-cpp/src/binary.cpp
- − yaml-cpp/src/collectionstack.h
- − yaml-cpp/src/contrib/graphbuilder.cpp
- − yaml-cpp/src/contrib/graphbuilderadapter.cpp
- − yaml-cpp/src/contrib/graphbuilderadapter.h
- − yaml-cpp/src/contrib/yaml-cpp.natvis
- − yaml-cpp/src/contrib/yaml-cpp.natvis.md
- − yaml-cpp/src/convert.cpp
- − yaml-cpp/src/directives.cpp
- − yaml-cpp/src/directives.h
- − yaml-cpp/src/emit.cpp
- − yaml-cpp/src/emitfromevents.cpp
- − yaml-cpp/src/emitter.cpp
- − yaml-cpp/src/emitterstate.cpp
- − yaml-cpp/src/emitterstate.h
- − yaml-cpp/src/emitterutils.cpp
- − yaml-cpp/src/emitterutils.h
- − yaml-cpp/src/exceptions.cpp
- − yaml-cpp/src/exp.cpp
- − yaml-cpp/src/exp.h
- − yaml-cpp/src/indentation.h
- − yaml-cpp/src/memory.cpp
- − yaml-cpp/src/node.cpp
- − yaml-cpp/src/node_data.cpp
- − yaml-cpp/src/nodebuilder.cpp
- − yaml-cpp/src/nodebuilder.h
- − yaml-cpp/src/nodeevents.cpp
- − yaml-cpp/src/nodeevents.h
- − yaml-cpp/src/null.cpp
- − yaml-cpp/src/ostream_wrapper.cpp
- − yaml-cpp/src/parse.cpp
- − yaml-cpp/src/parser.cpp
- − yaml-cpp/src/ptr_vector.h
- − yaml-cpp/src/regex_yaml.cpp
- − yaml-cpp/src/regex_yaml.h
- − yaml-cpp/src/regeximpl.h
- − yaml-cpp/src/scanner.cpp
- − yaml-cpp/src/scanner.h
- − yaml-cpp/src/scanscalar.cpp
- − yaml-cpp/src/scanscalar.h
- − yaml-cpp/src/scantag.cpp
- − yaml-cpp/src/scantag.h
- − yaml-cpp/src/scantoken.cpp
- − yaml-cpp/src/setting.h
- − yaml-cpp/src/simplekey.cpp
- − yaml-cpp/src/singledocparser.cpp
- − yaml-cpp/src/singledocparser.h
- − yaml-cpp/src/stream.cpp
- − yaml-cpp/src/stream.h
- − yaml-cpp/src/streamcharsource.h
- − yaml-cpp/src/stringsource.h
- − yaml-cpp/src/tag.cpp
- − yaml-cpp/src/tag.h
- − yaml-cpp/src/token.h
- − yaml-cpp/util/CMakeLists.txt
- − yaml-cpp/util/api.cpp
- − yaml-cpp/util/parse.cpp
- − yaml-cpp/util/read.cpp
- − yaml-cpp/util/sandbox.cpp
- − yaml-cpp/yaml-cpp-config-version.cmake.in
- − yaml-cpp/yaml-cpp-config.cmake.in
- − yaml-cpp/yaml-cpp.pc.cmake


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View it on GitLab: https://salsa.debian.org/med-team/iqtree/-/compare/07dc39a888e8cab024bfa59555009cb83c4603a1...e951cb727403b5909d816ef8fd1cbfe8f7407773

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