TreeSearch
Phylogenetic Analysis with Discrete Character Data

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Phylogenetic Analysis with Discrete Character Data

MD5
NEWS.md
NAMESPACE
DESCRIPTION
R/AdditionTree.R R/RcppExports.R R/Concordance.R R/PolEscapa.R R/TreeSearch_utilities.R R/Sectorial.R R/data_manipulation.R R/TaxonInfluence.R R/SPR.R R/Jackknife.R R/data.R R/ClusterStrings.R R/mpl_visualise.R R/TBR.R R/RandomTreeScore.R R/NNI.R R/IWScore.R R/Ratchet.R R/tree_length.R R/length_range.R R/tree_rearrangement.R R/mpl_morphy_objects.R R/ReleaseQuestions.R R/QuartetResolution.R R/PlotCharacter.R R/Bootstrap.R R/zzz.R R/mpl_morphyex.R R/WhenFirstHit.R R/pp_info_extra_step.r R/MaximizeParsimony.R R/ci-ri.R R/ImposeConstraint.R R/CustomSearch.R R/SuccessiveApproximations.R
src/TreeSearch-init.c
src/statedata.c
src/morphy_score.cpp
src/RMorphy.c
src/mpl.h
src/RcppExports.cpp
src/fitch.h
src/RMorphyUtils.c
src/RMorphyUtils.h
src/fitch.c
src/statedata.h
src/RMorphy.h
src/morphydefs.h
src/morphy.c
src/wagner.h
src/wagner.c
src/build_postorder.h
src/mpl.c
src/morphy.h
src/mplerror.h
src/rearrange.cpp
inst/preamble.tex
inst/REFERENCES.bib
inst/CITATION
inst/WORDLIST
inst/apa-old-doi-prefix.csl
inst/doc/profile-scores.html
inst/doc/profile.Rmd inst/doc/profile-scores.Rmd
inst/doc/custom.html
inst/doc/custom.R inst/doc/tree-space.R
inst/doc/tree-search.html
inst/doc/profile-scores.R
inst/doc/profile.html
inst/doc/tree-search.Rmd inst/doc/custom.Rmd inst/doc/profile.R inst/doc/tree-search.R
inst/doc/getting-started.html
inst/doc/tree-space.html
inst/doc/tree-space.Rmd inst/doc/getting-started.Rmd
inst/datasets/Capa2011.nex
inst/datasets/Longrich2010.nex
inst/datasets/Agnarsson2004.nex
inst/datasets/Sano2011.nex
inst/datasets/Rougier2012.nex
inst/datasets/Zanol2014.nex
inst/datasets/Griswold1999.nex
inst/datasets/Dikow2009.nex
inst/datasets/Wills2012.nex
inst/datasets/Wetterer2000.nex
inst/datasets/Asher2005.nex
inst/datasets/Sansom2010.nex
inst/datasets/OLeary1999.nex
inst/datasets/Eklund2004.nex
inst/datasets/Shultz2007.nex
inst/datasets/DeAssis2011.nex
inst/datasets/Vinther2008.nex
inst/datasets/Sun2018.nex
inst/datasets/Wortley2006.nex
inst/datasets/Aria2015.nex
inst/datasets/Loconte1991.nex
inst/datasets/Geisler2001.nex
inst/datasets/OMeara2014.nex
inst/datasets/Wilson2003.nex
inst/datasets/Aguado2009.nex
inst/datasets/Schulze2007.nex
inst/datasets/Zhu2013.nex
inst/datasets/Conrad2008.nex
inst/datasets/Rousset2004.nex
inst/datasets/Giles2015.nex
inst/datasets/Liljeblad2008.nex
inst/tests/benchmark_timing.R inst/Parsimony/app.R
inst/Parsimony/www/app.css
inst/Parsimony/www/images/Glade.jpg
build/vignette.rds
build/partial.rdb
tests/testthat.R tests/spelling.R tests/testthat/test-TaxonInfluence.R tests/testthat/test-zzz-tree-rearrange.R tests/testthat/test-iw-scoring.R tests/testthat/test-pp-random-tree.R tests/testthat/test-MaximizeParsimony.R tests/testthat/test-length_range.R tests/testthat/test-RMorphy.R tests/testthat/test-RandomTreeScore.R tests/testthat/test-tree_length.R tests/testthat/test-ClusterStrings.R tests/testthat/test-AdditionTree.R tests/testthat/test-pp-fitch.R tests/testthat/test-rearrange.cpp.R tests/testthat/test-PolEscapa.R tests/testthat/test-TreeSearch_utilities.R tests/testthat/test-mpl_morphy_objects.R tests/testthat/test-CustomSearch.R tests/testthat/test-PlotCharacter.R tests/testthat/test-Jackknife.R tests/testthat/test-data_manipulation.R tests/testthat/test-NNI.R tests/testthat/test-Concordance.R tests/testthat/test-WhenFirstHit.R tests/testthat/test-pp-info_extra_step.R tests/testthat/test-QuartetResolution.R
tests/testthat/_snaps/PlotCharacter/plotchar-110iiqqii100.svg
tests/testthat/_snaps/PlotCharacter/plotchar-out-of-sequence.svg
tests/testthat/_snaps/PlotCharacter/plotchar-210ii100ii21.svg
tests/testthat/_snaps/PlotCharacter/plotchar-23ii1iiii032.svg
tests/testthat/_snaps/PlotCharacter/plotchar-10101iiiii01.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-11ii1qqii111.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-320iiqq3ii21.svg
tests/testthat/_snaps/PlotCharacter/plotchar-110iiqiii100.svg
tests/testthat/_snaps/PlotCharacter/plotchar-10iiii11iii1.svg
tests/testthat/_snaps/PlotCharacter/plotchar-01iiiiii0101.svg
tests/testthat/_snaps/PlotCharacter/plotchar-21ii3qqii032.svg
tests/testthat/_snaps/PlotCharacter/plotchar-1234d45baacgttt.svg
tests/testthat/_snaps/PlotCharacter/plotchar-iiii1111iiii.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-11iiiiiii100.svg
tests/testthat/_snaps/PlotCharacter/plotchar-23ii1qqii032.svg
tests/testthat/_snaps/PlotCharacter/plotchar-1iii1111iii1.svg
tests/testthat/_snaps/PlotCharacter/plotchar-1iiii1iiii1i.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-23qq1qqqq032.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-11iiqqqqii11.svg
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tests/testthat/_snaps/PlotCharacter/plotchar-i1i1i1ii1i1i.svg
tests/testthat/_snaps/PlotCharacter/plotchar-iiii1010iiii.svg
tests/testthat/_snaps/PlotCharacter/plotchar-1100iiii1100.svg
tests/testthat/_snaps/Jackknife/plot-jackknife.svg
vignettes/gui_cluster_cons.png
vignettes/gui_start.png
vignettes/profile.Rmd vignettes/profile-scores.Rmd
vignettes/gui_sun_space.png
vignettes/gui_trees_loaded.png
vignettes/gui_rogue.png
vignettes/tree-search.Rmd vignettes/custom.Rmd
vignettes/gui_space.png
vignettes/tree-space.Rmd vignettes/getting-started.Rmd
vignettes/gui_char.png
vignettes/gui_consensus.png
data/congreveLamsdellMatrices.RData
data/inapplicable.datasets.rda
data/referenceTree.RData
data/inapplicable.phyData.rda
data/profiles.rda
data/inapplicable.citations.R
data/inapplicable.trees.rda
man/mpl_first_up_recon.Rd man/mpl_update_lower_root.Rd man/PlotCharacter.Rd man/TreeLength.Rd man/is.morphyPtr.Rd man/SPR.Rd man/TBR.Rd man/MinimumLength.Rd man/AllSPR.Rd man/mpl_new_Morphy.Rd man/referenceTree.Rd man/dot-GapHandler.Rd man/mpl_second_down_recon.Rd man/SingleCharMorphy.Rd man/mpl_update_tip.Rd man/RandomMorphyTree.Rd man/MorphyWeights.Rd man/dot-CombineResults.Rd man/cSPR.Rd man/WhenFirstHit.Rd man/LengthAdded.Rd man/profiles.Rd man/SiteConcordance.Rd man/mpl_attach_rawdata.Rd man/mpl_get_numtaxa.Rd man/mpl_translate_error.Rd man/mpl_delete_rawdata.Rd man/ClusterStrings.Rd man/MorphyTreeLength.Rd man/congreveLamsdellMatrices.Rd man/NNI.Rd man/Ratchet.Rd man/Jackknife.Rd man/RandomTreeScore.Rd man/CharacterLength.Rd man/SuccessiveApproximations.Rd man/ConcordantInformation.Rd man/mpl_first_down_recon.Rd man/mpl_attach_symbols.Rd man/UnloadMorphy.Rd man/Suboptimality.Rd man/MaximizeParsimony.Rd man/mpl_get_num_internal_nodes.Rd man/mpl_second_up_recon.Rd man/WithOneExtraStep.Rd man/mpl_get_charac_weight.Rd man/mpl_get_num_charac.Rd man/DoubleNNI.Rd man/TaxonInfluence.Rd man/GapHandler.Rd man/dot-UniqueExceptHits.Rd man/StepInformation.Rd man/JackLabels.Rd man/mpl_delete_Morphy.Rd man/mpl_set_charac_weight.Rd man/mpl_init_Morphy.Rd man/StopUnlessBifurcating.Rd man/PhyDat2Morphy.Rd man/AdditionTree.Rd man/mpl_set_num_internal_nodes.Rd man/dot-NonDuplicateRoot.Rd man/Consistency.Rd man/RearrangeEdges.Rd man/mpl_apply_tipdata.Rd man/inapplicable.datasets.Rd man/PrepareDataProfile.Rd man/summary.morphyPtr.Rd man/TreeSearch.Rd man/TBRWarning.Rd man/MorphyErrorCheck.Rd man/mpl_get_symbols.Rd man/Carter1.Rd man/mpl_set_parsim_t.Rd man/QuartetResolution.Rd man/mpl_get_gaphandl.Rd
man/figures/Flow.svg
TreeSearch documentation built on Aug. 26, 2023, 9:06 a.m.

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