[med-svn] [Git][med-team/iqtree][upstream] Deleted 1 commit: New upstream version 2.3.4+dfsg

Fri Apr 10 14:58:39 BST 2026

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

WARNING: The push did not contain any new commits, but force pushed to delete the commits and changes below.

Deleted commits:
9105938f by Michael R. Crusoe at 2024-05-10T17:47:11+02:00
New upstream version 2.3.4+dfsg
- - - - -

298 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
- + doc/html/bc_s.png
- + doc/html/bdwn.png
- + doc/html/closed.png
- + doc/html/doc.png
- + doc/html/doxygen.css
- + doc/html/doxygen.svg
- + doc/html/dynsections.js
- + doc/html/folderclosed.png
- + doc/html/folderopen.png
- + doc/html/index.html
- + doc/html/jquery.js
- + doc/html/md__r_e_a_d_m_e.html
- + doc/html/menu.js
- + doc/html/menudata.js
- + doc/html/nav_f.png
- + doc/html/nav_g.png
- + doc/html/nav_h.png
- + doc/html/open.png
- + doc/html/pages.html
- + doc/html/search/all_0.html
- + doc/html/search/all_0.js
- + doc/html/search/close.svg
- + doc/html/search/mag_sel.svg
- + doc/html/search/nomatches.html
- + doc/html/search/pages_0.html
- + doc/html/search/pages_0.js
- + doc/html/search/search.css
- + doc/html/search/search.js
- + doc/html/search/search_l.png
- + doc/html/search/search_m.png
- + doc/html/search/search_r.png
- + doc/html/search/searchdata.js
- + doc/html/splitbar.png
- + doc/html/sync_off.png
- + doc/html/sync_on.png
- + doc/html/tab_a.png
- + doc/html/tab_b.png
- + doc/html/tab_h.png
- + doc/html/tab_s.png
- + doc/html/tabs.css
- + doc/latex/Makefile
- + doc/latex/doxygen.sty
- + doc/latex/longtable_doxygen.sty
- + doc/latex/md__r_e_a_d_m_e.tex
- + doc/latex/refman.tex
- + doc/latex/tabu_doxygen.sty
- + example/custom_distributions.txt
- + example/tree.nwk
- + iqtree.doxy
- 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
- pda/ecopd.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
- + sse2neon.h
- 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/CMakeLists.txt
- terraphast/include/terraces/constraints.hpp
- terraphast/include/terraces/definitions.hpp
- terraphast/lib/multitree_iterator.cpp
- terraphast/lib/multitree_iterator.hpp
- 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/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

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/iqtree/-/commit/9105938f00ec6f5282a700e9759a4b6b2885be3c

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