Package: TreeDist 2.9.1

Martin R. Smith

TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Authors:Martin R. Smith [aut, cre, cph, prg], Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]

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TreeDist.pdf |TreeDist.html✨
TreeDist/json (API)
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Peer review:

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

On CRAN:

phylogeneticstree-distancephylogenetic-treestree-distancestrees

87 exports 28 stars 3.72 score 48 dependencies 5 dependents 4 mentions 76 scripts 896 downloads

Last updated 2 days agofrom:47353a7a6a. Checks:OK: 9. Indexed: no.

Exports:.TreeDistanceAllSplitPairingsCalculateTreeDistanceClusteringEntropyClusteringInfoClusteringInfoDistClusteringInfoDistanceCompareAllConsensusInfoDifferentPhylogeneticInfoDistanceFromMedianDistFromMedEntropyExpectedVariationGeneralizedRFGetParallelInfoRobinsonFouldsInfoRobinsonFouldsSplitsIslandsJaccardRobinsonFouldsJaccardSplitSimilarityKCDiameterKCVectorKendallColijnKMeansPPLAPJVLnTreesConsistentWithTwoSplitsLog2TreesConsistentWithTwoSplitsMappingQualityMapTreesMASTInfoMASTSizeMatchingSplitDistanceMatchingSplitDistanceSplitsMatchingSplitInfoMatchingSplitInfoDistanceMatchingSplitInfoSplitsMeanCentDistMeanCentroidDistMeanCentroidDistanceMeanMSTEdgeMeanNNMeilaMutualInformationMeilaVariationOfInformationMSTSegmentsMutualClusteringInfoMutualClusteringInformationMutualClusteringInfoSplitsNNIDiameterNNIDistNormalizeInfoNyeSimilarityNyeSplitSimilarityPathDistPathVectorPhylogeneticInfoDistancePlot3ProjectProjectionQualityReduceTreesReportMatchingRobinsonFouldsRobinsonFouldsInfoRobinsonFouldsMatchingRobinsonFouldsSplitsSetParallelSharedPhylogeneticInfoSharedPhylogeneticInfoSplitsSpectralClusteringSpectralEigensSplitDifferentInformationSplitEntropySplitsCompatibleSplitSharedInformationSplitVectorSplitwiseInfoSPRDistStartParallelStopParallelStrainColSumOfRangesSumOfVariancesSumOfVarsTreeDistanceTreeDistPlotTreesConsistentWithTwoSplitsVisualizeMatching

Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRCurlRdpackrlangsassshinyshinyjssourcetoolsTreeToolswithrxtable