Package: TreeDist 2.9.1

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]

TreeDist_2.9.1.tar.gz
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TreeDist.pdf |TreeDist.html
TreeDist/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

phylogeneticstree-distancephylogenetic-treestree-distancestrees

10.13 score 29 stars 5 packages 91 scripts 795 downloads 4 mentions 87 exports 48 dependencies

Last updated 2 days agofrom:07d53a68aa. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-win-x86_64OKNov 04 2024
R-4.5-linux-x86_64OKNov 04 2024
R-4.4-win-x86_64OKNov 04 2024
R-4.4-mac-x86_64OKNov 04 2024
R-4.4-mac-aarch64OKNov 04 2024
R-4.3-win-x86_64OKNov 04 2024
R-4.3-mac-x86_64OKNov 04 2024
R-4.3-mac-aarch64OKNov 04 2024

Exports:.TreeDistanceAllSplitPairingsCalculateTreeDistanceClusteringEntropyClusteringInfoClusteringInfoDistClusteringInfoDistanceCompareAllConsensusInfoDifferentPhylogeneticInfoDistanceFromMedianDistFromMedEntropyExpectedVariationGeneralizedRFGetParallelInfoRobinsonFouldsInfoRobinsonFouldsSplitsIslandsJaccardRobinsonFouldsJaccardSplitSimilarityKCDiameterKCVectorKendallColijnKMeansPPLAPJVLnTreesConsistentWithTwoSplitsLog2TreesConsistentWithTwoSplitsMappingQualityMapTreesMASTInfoMASTSizeMatchingSplitDistanceMatchingSplitDistanceSplitsMatchingSplitInfoMatchingSplitInfoDistanceMatchingSplitInfoSplitsMeanCentDistMeanCentroidDistMeanCentroidDistanceMeanMSTEdgeMeanNNMeilaMutualInformationMeilaVariationOfInformationMSTSegmentsMutualClusteringInfoMutualClusteringInformationMutualClusteringInfoSplitsNNIDiameterNNIDistNormalizeInfoNyeSimilarityNyeSplitSimilarityPathDistPathVectorPhylogeneticInfoDistancePlot3ProjectProjectionQualityReduceTreesReportMatchingRobinsonFouldsRobinsonFouldsInfoRobinsonFouldsMatchingRobinsonFouldsSplitsSetParallelSharedPhylogeneticInfoSharedPhylogeneticInfoSplitsSpectralClusteringSpectralEigensSplitDifferentInformationSplitEntropySplitsCompatibleSplitSharedInformationSplitVectorSplitwiseInfoSPRDistStartParallelStopParallelStrainColSumOfRangesSumOfVariancesSumOfVarsTreeDistanceTreeDistPlotTreesConsistentWithTwoSplitsVisualizeMatching

Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRCurlRdpackrlangsassshinyshinyjssourcetoolsTreeToolswithrxtable

Analysing landscapes of phylogenetic trees

Rendered fromlandscapes.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2023-04-18
Started: 2022-08-24

Calculate tree similarity with 'TreeDist'

Rendered fromUsing-TreeDist.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-08-22
Started: 2019-08-30

Comparing sets of trees from different analyses

Rendered fromcompare-treesets.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2022-04-28
Started: 2022-04-28

Comparing splits using information theory

Rendered frominformation.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2022-09-19
Started: 2019-10-19

Contextualizing tree distances

Rendered fromusing-distances.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-08-22
Started: 2019-10-19

Extending the Robinson-Foulds metric

Rendered fromRobinson-Foulds.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-06-28
Started: 2019-08-30

Generalized Robinson-Foulds distances

Rendered fromGeneralized-RF.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-04-23
Started: 2019-09-01

Tree space analysis

Rendered fromtreespace.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-06-28
Started: 2020-09-28

Trees with different leaves

Rendered fromdifferent-leaves.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2023-02-17
Started: 2023-02-17

Readme and manuals

Help Manual

Help pageTopics
Variation of information for all split pairingsAllSplitPairings
Cluster size statisticscluster-statistics DistanceFromMedian DistFromMed MeanCentDist MeanCentroidDist MeanCentroidDistance MeanMSTEdge MeanNN SumOfRanges SumOfVariances SumOfVars
Distances between each pair of treesCompareAll
Entropy in bitsEntropy
Find islands from distance matrixIslands
Jaccard–Robinson–Foulds metricJaccardRobinsonFoulds JaccardSplitSimilarity
Kendall–Colijn distanceKCDiameter KCVector KendallColijn PathVector SplitVector
k-means++ clusteringKMeansPP
Solve linear assignment problem using LAPJVLAPJV
Faithfulness of mapped distancesMappingQuality ProjectionQuality
Graphical user interface for mapping distances and analysing tree spaceMapTrees Project
Maximum Agreement Subtree sizeMASTInfo MASTSize
Matching Split DistanceMatchingSplitDistance MatchingSplitDistanceSplits
Median of a set of treesmedian.multiPhylo
Use variation of clustering information to compare pairs of splitsMeilaMutualInformation MeilaVariationOfInformation
Add minimum spanning tree to plot, colouring by stressMSTSegments StrainCol
Approximate Nearest Neighbour Interchange distanceNNIDiameter NNIDist
Nye _et al_. (2006) tree comparisonNyeSimilarity NyeSplitSimilarity
Path distancePathDist
Pseudo-3D plottingPlot3
Collapse areas of agreement between two treesReduceTrees
Robinson–Foulds distances, with adjustments for phylogenetic information contentInfoRobinsonFoulds InfoRobinsonFouldsSplits Robinson-Foulds RobinsonFoulds RobinsonFouldsInfo RobinsonFouldsMatching RobinsonFouldsSplits
Eigenvalues for spectral clusteringSpectralClustering SpectralEigens
Entropy of two splitsSplitEntropy
Are splits compatible?SplitsCompatible
Shared information content of two splitsLnTreesConsistentWithTwoSplits Log2TreesConsistentWithTwoSplits SplitDifferentInformation SplitSharedInformation TreesConsistentWithTwoSplits
Approximate the Subtree Prune and Regraft (SPR) distance.SPRDist SPRDist.list SPRDist.multiPhylo SPRDist.phylo
Calculate distances in parallelGetParallel SetParallel StartParallel StopParallel
Information-based generalized Robinson–Foulds distancesClusteringInfoDist ClusteringInfoDistance DifferentPhylogeneticInfo ExpectedVariation MatchingSplitInfo MatchingSplitInfoDistance MatchingSplitInfoSplits MutualClusteringInfo MutualClusteringInformation MutualClusteringInfoSplits PhylogeneticInfoDistance SharedPhylogeneticInfo SharedPhylogeneticInfoSplits TreeDistance
Information content of splits within a treeClusteringEntropy ClusteringEntropy.list ClusteringEntropy.multiPhylo ClusteringEntropy.phylo ClusteringEntropy.Splits ClusteringInfo ClusteringInfo.list ClusteringInfo.multiPhylo ClusteringInfo.phylo ClusteringInfo.Splits ConsensusInfo SplitwiseInfo TreeInfo
Visualize a matchingVisualizeMatching