Package: TreeSearch 1.5.1

Martin R. Smith

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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NEWS

Peer review:

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

On CRAN:

bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-search

109 exports 5 stars 2.12 score 63 dependencies 3 mentions 51 scripts 519 downloads

Last updated 3 days agofrom:3bd6fab8e1. Checks:OK: 7 NOTE: 2. Indexed: no.

Exports:.NonDuplicateRoot.UniqueExceptHitsAdditionTreeC_MorphyLengthCarter1CharacterLengthClusteringConcordanceClusterStringscNNIConcordantInfoConcordantInformationConsistencycSPRDoNothingEasyTreesEasyTreesyEdgeListSearchEmptyPhyDatEvaluateFitchFitchStepsGapHandlerGetMorphyLengthis.morphyPtrIWScoreIWTreeSearchJackknifeJackLabelsLengthAddedLog2Carter1LogCarter1MaximizeParsimonyMaximumLengthMinimumLengthMorphyBootstrapMorphyErrorCheckMorphyLengthMorphyTreeLengthMorphyWeightsmpl_apply_tipdatampl_attach_rawdatampl_attach_symbolsmpl_delete_Morphympl_delete_rawdatampl_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_tipMultiRatchetMutualClusteringConcordanceNNINNISwapPhyDat2MorphyPhylogeneticConcordancePlotCharacterPolEscapaPrepareDataIWPrepareDataProfileQuartetConcordanceQuartetResolutionRandomMorphyTreeRandomTreeScoreRatchetRatchetConsensusRearrangeEdgesResampleRootedNNIRootedNNISwapRootedSPRRootedSPRSwapRootedTBRRootedTBRSwapSetMorphyWeightsSharedPhylogeneticConcordanceSingleCharMorphySPRSPRMovesSPRSwapSPRWarningStepInformationStopUnlessBifurcatingSuboptimalitySuccessiveApproximationsSuccessiveWeightsTaxonInfluenceTBRTBRMovesTBRSwapTBRWarningTreeLengthTreeSearchUnloadMorphyWhenFirstHitWithOneExtraStep

Dependencies:apebase64encbitbit64bitopsbslibcachemcliclustercodetoolscolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsfutureglobalsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclelistenvmagrittrmatrixStatsmemoisemimenlmeparallellyPlotToolspromisesprotoclustR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRCurlRdpackRfastrlangRoguesassshinyshinyjssourcetoolsTreeDistTreeToolswithrxtable