Package: TreeSearch 1.8.0.9001

TreeSearch: Phylogenetic Analysis with Discrete Character Data

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.

Authors:Martin R. Smith [aut, cre, cph], Martin Brazeau [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TreeSearch/json (API)

# Install 'TreeSearch' in R:
install.packages('TreeSearch', repos = c('https://ms609.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ms609/treesearch/issues

Pkgdown/docs site:https://ms609.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-searchcpp

8.26 score 9 stars 45 scripts 902 downloads 3 mentions 115 exports 54 dependencies

Last updated from:4c88ce1ac9. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
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linux-devel-x86_64OK236
source / vignettesOK296
linux-release-arm64OK216
linux-release-x86_64OK230
macos-release-arm64OK146
macos-release-x86_64OK500
macos-oldrel-arm64OK153
macos-oldrel-x86_64OK383
windows-develOK205
windows-releaseOK209
windows-oldrelOK199
wasm-releaseOK165

Exports:.NonDuplicateRoot.UniqueExceptHitsAdditionTreeC_MorphyLengthCarter1CharacterLengthClusteringConcordanceClusterStringscNNIConcordanceTableConcordantInfoConcordantInformationConsistencycSPRDoNothingEasyTreesEasyTreesyEdgeListSearchEmptyPhyDatEvaluateExpectedLengthFitchFitchStepsGapHandlerGetMorphyLengthis.morphyPtrIWScoreIWTreeSearchJackknifeJackLabelsLengthAddedLog2Carter1LogCarter1MaximizeParsimonyMaximumLengthMinimumLengthMorphyBootstrapMorphyErrorCheckMorphyLengthMorphyTreeLengthMorphyWeightsMostContradictedFreqmpl_apply_tipdatampl_attach_rawdatampl_attach_symbolsmpl_delete_Morphympl_first_down_reconmpl_first_up_reconmpl_get_charac_weightmpl_get_gaphandlmpl_get_num_characmpl_get_num_internal_nodesmpl_get_numtaxampl_get_symbolsmpl_init_Morphympl_new_Morphympl_second_down_reconmpl_second_up_reconmpl_set_charac_weightmpl_set_gaphandlmpl_set_num_internal_nodesmpl_set_parsim_tmpl_translate_errormpl_update_lower_rootmpl_update_tipMultiRatchetMutualClusteringConcordanceNNINNISwapPhyDat2MorphyPhylogeneticConcordancePlotCharacterPolEscapaPrepareDataIWPrepareDataProfilePresContQAColQALegendQColQuartetConcordanceQuartetResolutionRandomMorphyTreeRandomTreeScoreRatchetRatchetConsensusRearrangeEdgesResampleRootedNNIRootedNNISwapRootedSPRRootedSPRSwapRootedTBRRootedTBRSwapSetMorphyWeightsSharedPhylogeneticConcordanceSingleCharMorphySPRSPRMovesSPRSwapSPRWarningStepInformationStopUnlessBifurcatingSuboptimalitySuccessiveApproximationsSuccessiveWeightsTaxonInfluenceTBRTBRMovesTBRSwapTBRWarningTreeLengthTreeSearchUnloadMorphyWhenFirstHitWithOneExtraStep

Dependencies:abindapebase64encbitbit64bslibcachemcliclustercodetoolscolorspacecommonmarkdigestfastmapfastmatchfontawesomefsfutureglobalsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclelistenvmagrittrmatrixStatsmemoisemimenlmeotelparallellyPlotToolspromisesprotoclustR6rappdirsrbibutilsRcppRdpackrlangRoguesassshinyshinyjssourcetoolsstringiTreeDistTreeToolswithrxtable

Getting started: Simple tree searches
Getting started | Command line tree search | Evaluating clade support | Exploring taxon stability | Implied weighting | Constraining a search | Where next? | References
Rendered fromtree-search.Rmdusingknitr::rmarkdown

Last update: 2026-01-16
Started: 2021-05-14

Tree search with custom optimality criteria
Using custom optimality criteria | Maximizing tree balance | Maximizing tree distance | Searching using implied weights | What next? | References
Rendered fromcustom.Rmdusingknitr::rmarkdown

Last update: 2025-07-10
Started: 2021-04-14

Getting started: Exploring tree space
Loading trees into the GUI | Exploring the consensus | The structure of tree space | Tree space analysis in R | Generate distances | Identify clustering structure | Mapping tree space | Using tree clustering to understand tree space structure | Where next? | References
Rendered fromtree-space.Rmdusingknitr::rmarkdown

Last update: 2025-07-10
Started: 2022-08-15

Tree search with Profile parsimony
Getting started | Scoring a tree, and conducting a tree search | View the results | Where next? | References
Rendered fromprofile.Rmdusingknitr::rmarkdown

Last update: 2025-07-10
Started: 2018-02-21

Getting started: Installing R and TreeSearch
Installation | Simple installation | For advanced users | What next?
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2025-02-07
Started: 2018-02-21

Profile parsimony
Scope of this document | A philosophy of parsimony | Application of Occam's Razor | An information theoretic basis | Implementation | Where next | References
Rendered fromprofile-scores.Rmdusingknitr::rmarkdown

Last update: 2023-07-17
Started: 2018-02-21

Readme and manuals

Help Manual

Help pageTopics
Addition treeAdditionTree
All SPR treesAllSPR
Number of trees with _m_ stepsCarter1 Log2Carter1 LogCarter1
Character lengthCharacterLength FastCharacterLength
Cluster similar stringsClusterStrings
Plot concordance tableConcordanceTable
Evaluate the concordance of information between a tree and a datasetConcordantInfo ConcordantInformation Evaluate
100 simulated data matricescongreveLamsdellMatrices
Consistency and retention "indices"Consistency
'cSPR()' expects a tree rooted on a single tip.cSPR
Expected lengthExpectedLength
Read how a Morphy Object handles the inapplicable tokenGapHandler
Thirty datasets with inapplicable datainapplicable.citations inapplicable.datasets inapplicable.phyData inapplicable.trees
Is an object a valid Morphy object?is.morphyPtr
Calculate the parsimony score of a tree given a datasetFitch IWScore TreeLength TreeLength.list TreeLength.multiPhylo TreeLength.numeric TreeLength.phylo
Jackknife resamplingJackknife
Label nodes with jackknife support valuesJackLabels
Contribution of character to leaf instabilityLengthAdded PolEscapa
Find most parsimonious treesEasyTrees EasyTreesy MaximizeParsimony Resample
Minimum and Maximum lengths possible for a characterMaximumLength MaximumLength.character MaximumLength.numeric MinimumLength MinimumLength.character MinimumLength.numeric MinimumLength.phyDat MinimumSteps
Parsimony RatchetMorphyBootstrap MultiRatchet Ratchet RatchetConsensus
Set and get the character weightings associated with a Morphy object.MorphyWeights SetMorphyWeights
Frequency of most common contradictory splitMostContradictedFreq
Nearest neighbour interchange (NNI)cNNI NNI NNISwap RootedNNI RootedNNISwap
Initialize a Morphy object from a 'phyDat' objectPhyDat2Morphy
Plot the distribution of a character on a treePlotCharacter PlotCharacter.list PlotCharacter.multiPhylo PlotCharacter.phylo
Prepare data for Profile ParsimonyPrepareDataIW PrepareDataProfile
Group present or contradicted scorePresCont
Empirically counted profiles for small treesprofiles
Generate colour to depict the amount and quality of observationsQACol QALegend QCol
Relationship between four taxaQuartetResolution
Random postorder treeRandomMorphyTree
Parsimony score of random postorder treeRandomTreeScore
Rearrange edges of a phylogenetic treeRearrangeEdges
Tree topology for matrix simulationreferenceTree
Morphy object from single characterSingleCharMorphy
Concordance factorsClusteringConcordance MutualClusteringConcordance PhylogeneticConcordance QuartetConcordance SharedPhylogeneticConcordance SiteConcordance
Subtree pruning and rearrangement (SPR)RootedSPR RootedSPRSwap SPR SPRMoves SPRMoves.matrix SPRMoves.phylo SPRSwap
Information content of a character known to contain _e_ stepsStepInformation
Details the attributes of a morphy objectsummary.morphyPtr
Rank taxa by their influence on phylogenetic resultsTaxonInfluence
Tree bisection and reconnection (TBR)RootedTBR RootedTBRSwap TBR TBRMoves TBRMoves.matrix TBRMoves.phylo TBRSwap
Destroy a Morphy objectUnloadMorphy
When was a tree topology first hit?WhenFirstHit
Number of trees with one extra stepWithOneExtraStep