[med-svn] [Git][med-team/iqtree][upstream] New upstream version 3.0.1+dfsg

Fri Sep 5 16:20:06 BST 2025

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

Commits:
47062497 by Michael R. Crusoe at 2025-09-05T17:18:10+02:00
New upstream version 3.0.1+dfsg
- - - - -

459 changed files:

- CMakeLists.txt
- README.md
- alignment/alignment.cpp
- alignment/alignment.h
- alignment/pattern.cpp
- alignment/pattern.h
- alignment/superalignment.cpp
- booster/booster.c
- booster/tree.c
- + 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/doc/html/alignment_8h_source.html
- + cmaple/doc/html/annotated.html
- + cmaple/doc/html/bc_s.png
- + cmaple/doc/html/bc_sd.png
- + cmaple/doc/html/classcmaple_1_1_alignment-members.html
- + cmaple/doc/html/classcmaple_1_1_alignment.html
- + cmaple/doc/html/classcmaple_1_1_model-members.html
- + cmaple/doc/html/classcmaple_1_1_model.html
- + cmaple/doc/html/classcmaple_1_1_params-members.html
- + cmaple/doc/html/classcmaple_1_1_params.html
- + cmaple/doc/html/classcmaple_1_1_tree-members.html
- + cmaple/doc/html/classcmaple_1_1_tree.html
- + cmaple/doc/html/classes.html
- + cmaple/doc/html/closed.png
- + cmaple/doc/html/dir_0aa59dc4e14f78a2ec16bea9baba3f8e.html
- + cmaple/doc/html/dir_3f14f6767c31cb4a1d22c13c18cc6fc3.html
- + cmaple/doc/html/dir_70093cb3a9d1f8840af4e997fde867c3.html
- + cmaple/doc/html/dir_cbdb8362360e11eafe2fa3bc74cf0ffd.html
- + cmaple/doc/html/doc.svg
- + cmaple/doc/html/docd.svg
- + cmaple/doc/html/doxygen.css
- + cmaple/doc/html/doxygen.svg
- + cmaple/doc/html/dynsections.js
- + cmaple/doc/html/files.html
- + cmaple/doc/html/folderclosed.svg
- + cmaple/doc/html/folderclosedd.svg
- + cmaple/doc/html/folderopen.svg
- + cmaple/doc/html/folderopend.svg
- + cmaple/doc/html/functions.html
- + cmaple/doc/html/functions_func.html
- + cmaple/doc/html/functions_vars.html
- + cmaple/doc/html/index.html
- + cmaple/doc/html/jquery.js
- + cmaple/doc/html/menu.js
- + cmaple/doc/html/menudata.js
- + cmaple/doc/html/model_8h_source.html
- + cmaple/doc/html/nav_f.png
- + cmaple/doc/html/nav_fd.png
- + cmaple/doc/html/nav_g.png
- + cmaple/doc/html/nav_h.png
- + cmaple/doc/html/nav_hd.png
- + cmaple/doc/html/open.png
- + cmaple/doc/html/search/all_0.js
- + cmaple/doc/html/search/all_1.js
- + cmaple/doc/html/search/all_10.js
- + cmaple/doc/html/search/all_2.js
- + cmaple/doc/html/search/all_3.js
- + cmaple/doc/html/search/all_4.js
- + cmaple/doc/html/search/all_5.js
- + cmaple/doc/html/search/all_6.js
- + cmaple/doc/html/search/all_7.js
- + cmaple/doc/html/search/all_8.js
- + cmaple/doc/html/search/all_9.js
- + cmaple/doc/html/search/all_a.js
- + cmaple/doc/html/search/all_b.js
- + cmaple/doc/html/search/all_c.js
- + cmaple/doc/html/search/all_d.js
- + cmaple/doc/html/search/all_e.js
- + cmaple/doc/html/search/all_f.js
- + cmaple/doc/html/search/classes_0.js
- + cmaple/doc/html/search/classes_1.js
- + cmaple/doc/html/search/classes_2.js
- + cmaple/doc/html/search/classes_3.js
- + cmaple/doc/html/search/classes_4.js
- + cmaple/doc/html/search/classes_5.js
- + cmaple/doc/html/search/close.svg
- + cmaple/doc/html/search/functions_0.js
- + cmaple/doc/html/search/functions_1.js
- + cmaple/doc/html/search/functions_2.js
- + cmaple/doc/html/search/functions_3.js
- + cmaple/doc/html/search/functions_4.js
- + cmaple/doc/html/search/functions_5.js
- + cmaple/doc/html/search/functions_6.js
- + cmaple/doc/html/search/functions_7.js
- + cmaple/doc/html/search/functions_8.js
- + cmaple/doc/html/search/functions_9.js
- + cmaple/doc/html/search/functions_a.js
- + cmaple/doc/html/search/functions_b.js
- + cmaple/doc/html/search/mag.svg
- + cmaple/doc/html/search/mag_d.svg
- + cmaple/doc/html/search/mag_sel.svg
- + cmaple/doc/html/search/mag_seld.svg
- + cmaple/doc/html/search/pages_0.js
- + cmaple/doc/html/search/search.css
- + cmaple/doc/html/search/search.js
- + cmaple/doc/html/search/searchdata.js
- + cmaple/doc/html/search/variables_0.js
- + cmaple/doc/html/search/variables_1.js
- + cmaple/doc/html/search/variables_2.js
- + cmaple/doc/html/search/variables_3.js
- + cmaple/doc/html/search/variables_4.js
- + cmaple/doc/html/search/variables_5.js
- + cmaple/doc/html/splitbar.png
- + cmaple/doc/html/splitbard.png
- + cmaple/doc/html/sync_off.png
- + cmaple/doc/html/sync_on.png
- + cmaple/doc/html/tab_a.png
- + cmaple/doc/html/tab_ad.png
- + cmaple/doc/html/tab_b.png
- + cmaple/doc/html/tab_bd.png
- + cmaple/doc/html/tab_h.png
- + cmaple/doc/html/tab_hd.png
- + cmaple/doc/html/tab_s.png
- + cmaple/doc/html/tab_sd.png
- + cmaple/doc/html/tabs.css
- + cmaple/doc/html/tools_8h_source.html
- + cmaple/doc/html/tree_8h_source.html
- + cmaple/doc/latex/Makefile
- + cmaple/doc/latex/alignment_8h_source.tex
- + cmaple/doc/latex/annotated.tex
- + cmaple/doc/latex/classcmaple_1_1_alignment.tex
- + cmaple/doc/latex/classcmaple_1_1_model.tex
- + cmaple/doc/latex/classcmaple_1_1_params.tex
- + cmaple/doc/latex/classcmaple_1_1_tree.tex
- + cmaple/doc/latex/doxygen.sty
- + cmaple/doc/latex/etoc_doxygen.sty
- + cmaple/doc/latex/files.tex
- + cmaple/doc/latex/index.tex
- + cmaple/doc/latex/longtable_doxygen.sty
- + cmaple/doc/latex/model_8h_source.tex
- + cmaple/doc/latex/refman.tex
- + cmaple/doc/latex/tabu_doxygen.sty
- + cmaple/doc/latex/tools_8h_source.tex
- + cmaple/doc/latex/tree_8h_source.tex
- + 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/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
- doc/html/md__r_e_a_d_m_e.html
- doc/latex/md__r_e_a_d_m_e.tex
- + flake.lock
- + flake.nix
- + lsd2/CMakeLists.txt
- + lsd2/LICENSE
- + lsd2/NEWS
- + lsd2/README.md
- + 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/main.cpp
- main/phyloanalysis.cpp
- main/phyloanalysis.h
- main/phylotesting.cpp
- main/phylotesting.h
- main/timetree.cpp
- main/treetesting.cpp
- main/treetesting.h
- model/CMakeLists.txt
- model/modelcodon.cpp
- model/modelcodon.h
- + model/modelcodonmixture.cpp
- + model/modelcodonmixture.h
- model/modeldna.cpp
- model/modeldna.h
- model/modelfactory.cpp
- model/modelfactory.h
- model/modelmarkov.cpp
- model/modelmarkov.h
- model/modelmixture.cpp
- model/modelmixture.h
- model/modelmorphology.cpp
- model/modelmorphology.h
- model/modelprotein.cpp
- model/modelprotein.h
- model/modelsubst.cpp
- model/modelsubst.h
- model/modelunrest.cpp
- model/modelunrest.h
- model/partitionmodel.cpp
- model/partitionmodel.h
- model/ratefree.cpp
- model/ratefree.h
- model/rateheterogeneity.h
- ncl/nxscharactersblock.cpp
- ncl/nxsstring.cpp
- ncl/nxsstring.h
- nclextra/myreader.h
- + nn/CMakeLists.txt
- + nn/neuralnetwork.cpp
- + nn/neuralnetwork.h
- + onnxruntimeConfig.cmake
- pda/circularnetwork.cpp
- pda/pdnetwork.cpp
- pda/split.cpp
- pll/avxLikelihood.c
- pll/evaluateGenericSpecial.c
- pll/evaluatePartialGenericSpecial.c
- pll/fastDNAparsimony.c
- pll/hardware.c
- pll/makenewzGenericSpecial.c
- pll/newviewGenericSpecial.c
- pll/pll.h
- pll/treeIO.c
- pll/utils.c
- simulator/alisimulator.cpp
- simulator/alisimulator.h
- simulator/alisimulatorheterogeneity.cpp
- terrace/terrace.cpp
- terraphast/CMakeLists.txt
- + test_scripts/iqtree2.h
- + test_scripts/linux_universal.sh
- + test_scripts/make_linux_universal.sh
- + test_scripts/make_universal.sh
- + test_scripts/unify-static-libs.sh
- tree/CMakeLists.txt
- tree/discordance.cpp
- tree/iqtree.cpp
- tree/iqtree.h
- tree/iqtreemix.cpp
- tree/iqtreemix.h
- tree/iqtreemixhmm.cpp
- tree/iqtreemixhmm.h
- tree/mtree.cpp
- tree/mtree.h
- tree/node.cpp
- tree/phylohmm.cpp
- tree/phylohmm.h
- tree/phylokernelnew.h
- + tree/phylosuperhmm.cpp
- + tree/phylosuperhmm.h
- tree/phylosupertree.cpp
- tree/phylosupertree.h
- tree/phylosupertreeplen.cpp
- tree/phylosupertreeplen.h
- tree/phylotree.cpp
- tree/phylotree.h
- tree/phylotreemixlen.cpp
- tree/phylotreemixlen.h
- tree/quartet.cpp
- utils/CMakeLists.txt
- utils/MPIHelper.cpp
- utils/bionj.cpp
- utils/checkpoint.cpp
- utils/checkpoint.h
- utils/optimization.cpp
- utils/pllnni.cpp
- utils/progress.cpp
- utils/progress.h
- sse2neon.h → utils/sse2neon.h
- utils/timeutil.h
- utils/tools.cpp
- utils/tools.h
- vectorclass/instrset.h
- vectorclass/vectori128.h
- whtest/weisslambda_sub.h
- 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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