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:
TreeDist_2.9.1.tar.gz
TreeDist_2.9.1.zip(r-4.5)TreeDist_2.9.1.zip(r-4.4)TreeDist_2.9.1.zip(r-4.3)
TreeDist_2.9.1.tgz(r-4.4-x86_64)TreeDist_2.9.1.tgz(r-4.4-arm64)TreeDist_2.9.1.tgz(r-4.3-x86_64)TreeDist_2.9.1.tgz(r-4.3-arm64)
TreeDist_2.9.1.tar.gz(r-4.5-noble)TreeDist_2.9.1.tar.gz(r-4.4-noble)
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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')) |
Bug tracker:https://github.com/ms609/treedist/issues
phylogeneticstree-distancephylogenetic-treestree-distancestrees
Last updated 2 days agofrom:07d53a68aa. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 04 2024 |
R-4.5-win-x86_64 | OK | Nov 04 2024 |
R-4.5-linux-x86_64 | OK | Nov 04 2024 |
R-4.4-win-x86_64 | OK | Nov 04 2024 |
R-4.4-mac-x86_64 | OK | Nov 04 2024 |
R-4.4-mac-aarch64 | OK | Nov 04 2024 |
R-4.3-win-x86_64 | OK | Nov 04 2024 |
R-4.3-mac-x86_64 | OK | Nov 04 2024 |
R-4.3-mac-aarch64 | OK | Nov 04 2024 |
Exports:.TreeDistanceAllSplitPairingsCalculateTreeDistanceClusteringEntropyClusteringInfoClusteringInfoDistClusteringInfoDistanceCompareAllConsensusInfoDifferentPhylogeneticInfoDistanceFromMedianDistFromMedEntropyExpectedVariationGeneralizedRFGetParallelInfoRobinsonFouldsInfoRobinsonFouldsSplitsIslandsJaccardRobinsonFouldsJaccardSplitSimilarityKCDiameterKCVectorKendallColijnKMeansPPLAPJVLnTreesConsistentWithTwoSplitsLog2TreesConsistentWithTwoSplitsMappingQualityMapTreesMASTInfoMASTSizeMatchingSplitDistanceMatchingSplitDistanceSplitsMatchingSplitInfoMatchingSplitInfoDistanceMatchingSplitInfoSplitsMeanCentDistMeanCentroidDistMeanCentroidDistanceMeanMSTEdgeMeanNNMeilaMutualInformationMeilaVariationOfInformationMSTSegmentsMutualClusteringInfoMutualClusteringInformationMutualClusteringInfoSplitsNNIDiameterNNIDistNormalizeInfoNyeSimilarityNyeSplitSimilarityPathDistPathVectorPhylogeneticInfoDistancePlot3ProjectProjectionQualityReduceTreesReportMatchingRobinsonFouldsRobinsonFouldsInfoRobinsonFouldsMatchingRobinsonFouldsSplitsSetParallelSharedPhylogeneticInfoSharedPhylogeneticInfoSplitsSpectralClusteringSpectralEigensSplitDifferentInformationSplitEntropySplitsCompatibleSplitSharedInformationSplitVectorSplitwiseInfoSPRDistStartParallelStopParallelStrainColSumOfRangesSumOfVariancesSumOfVarsTreeDistanceTreeDistPlotTreesConsistentWithTwoSplitsVisualizeMatching
Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRCurlRdpackrlangsassshinyshinyjssourcetoolsTreeToolswithrxtable
Analysing landscapes of phylogenetic trees
Rendered fromlandscapes.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2023-04-18
Started: 2022-08-24
Calculate tree similarity with 'TreeDist'
Rendered fromUsing-TreeDist.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-08-22
Started: 2019-08-30
Comparing sets of trees from different analyses
Rendered fromcompare-treesets.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2022-04-28
Started: 2022-04-28
Comparing splits using information theory
Rendered frominformation.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2022-09-19
Started: 2019-10-19
Contextualizing tree distances
Rendered fromusing-distances.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-08-22
Started: 2019-10-19
Extending the Robinson-Foulds metric
Rendered fromRobinson-Foulds.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-06-28
Started: 2019-08-30
Generalized Robinson-Foulds distances
Rendered fromGeneralized-RF.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-04-23
Started: 2019-09-01
Tree space analysis
Rendered fromtreespace.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-06-28
Started: 2020-09-28
Trees with different leaves
Rendered fromdifferent-leaves.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2023-02-17
Started: 2023-02-17
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Variation of information for all split pairings | AllSplitPairings |
Cluster size statistics | cluster-statistics DistanceFromMedian DistFromMed MeanCentDist MeanCentroidDist MeanCentroidDistance MeanMSTEdge MeanNN SumOfRanges SumOfVariances SumOfVars |
Distances between each pair of trees | CompareAll |
Entropy in bits | Entropy |
Find islands from distance matrix | Islands |
Jaccard–Robinson–Foulds metric | JaccardRobinsonFoulds JaccardSplitSimilarity |
Kendall–Colijn distance | KCDiameter KCVector KendallColijn PathVector SplitVector |
k-means++ clustering | KMeansPP |
Solve linear assignment problem using LAPJV | LAPJV |
Faithfulness of mapped distances | MappingQuality ProjectionQuality |
Graphical user interface for mapping distances and analysing tree space | MapTrees Project |
Maximum Agreement Subtree size | MASTInfo MASTSize |
Matching Split Distance | MatchingSplitDistance MatchingSplitDistanceSplits |
Median of a set of trees | median.multiPhylo |
Use variation of clustering information to compare pairs of splits | MeilaMutualInformation MeilaVariationOfInformation |
Add minimum spanning tree to plot, colouring by stress | MSTSegments StrainCol |
Approximate Nearest Neighbour Interchange distance | NNIDiameter NNIDist |
Nye _et al_. (2006) tree comparison | NyeSimilarity NyeSplitSimilarity |
Path distance | PathDist |
Pseudo-3D plotting | Plot3 |
Collapse areas of agreement between two trees | ReduceTrees |
Robinson–Foulds distances, with adjustments for phylogenetic information content | InfoRobinsonFoulds InfoRobinsonFouldsSplits Robinson-Foulds RobinsonFoulds RobinsonFouldsInfo RobinsonFouldsMatching RobinsonFouldsSplits |
Eigenvalues for spectral clustering | SpectralClustering SpectralEigens |
Entropy of two splits | SplitEntropy |
Are splits compatible? | SplitsCompatible |
Shared information content of two splits | LnTreesConsistentWithTwoSplits Log2TreesConsistentWithTwoSplits SplitDifferentInformation SplitSharedInformation TreesConsistentWithTwoSplits |
Approximate the Subtree Prune and Regraft (SPR) distance. | SPRDist SPRDist.list SPRDist.multiPhylo SPRDist.phylo |
Calculate distances in parallel | GetParallel SetParallel StartParallel StopParallel |
Information-based generalized Robinson–Foulds distances | ClusteringInfoDist ClusteringInfoDistance DifferentPhylogeneticInfo ExpectedVariation MatchingSplitInfo MatchingSplitInfoDistance MatchingSplitInfoSplits MutualClusteringInfo MutualClusteringInformation MutualClusteringInfoSplits PhylogeneticInfoDistance SharedPhylogeneticInfo SharedPhylogeneticInfoSplits TreeDistance |
Information content of splits within a tree | ClusteringEntropy ClusteringEntropy.list ClusteringEntropy.multiPhylo ClusteringEntropy.phylo ClusteringEntropy.Splits ClusteringInfo ClusteringInfo.list ClusteringInfo.multiPhylo ClusteringInfo.phylo ClusteringInfo.Splits ConsensusInfo SplitwiseInfo TreeInfo |
Visualize a matching | VisualizeMatching |