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 - 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+ 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 The diff was not included because it is too large. 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