Distances between each possible pairing of the 945 unrooted seven-leaf trees (equivalent to rooted 6-leaf trees). Following Kendall and Colijn (2016).
sevenTipDistances
Format
An object of class list of length 21.
Source
Scripts used to generate data objects are housed in the
data-raw
directory.
Details
Each list entry is named with the abbreviation of the corresponding tree distance method (see 'Methods tested' below).
Each item in the list contains a 945×945 matrix reporting the distance between each pair of seven-leaf trees. The first 630 trees are pectinate (tree shape 0), the final 315 are balanced (tree shape 1).
Methods tested
pid: Phylogenetic Information Distance (Smith 2020), normalized against the phylogenetic information content of the splits in the trees being compared.msid: Matching Split Information Distance (Smith 2020), normalized against the phylogenetic information content of the splits in the trees being compared.cid: Clustering Information Distance (Smith 2020), normalized against the entropy of the splits in the trees being compared.qd: Quartet divergence (Smith 2019), normalized against its maximum possible value for n-leaf trees.nye: Nye et al. tree distance (Nye et al. 2006), normalized against the total number of splits in the trees being compared.jnc2,jnc4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings prohibited ('no-conflict'), normalized against the total number of splits in the trees being compared.jco2,jco4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings permitted ('conflict-ok'), normalized against the total number of splits in the trees being compared.ms: Matching Split Distance (Bogdanowicz & Giaro 2012), unnormalized.mast: Size of Maximum Agreement Subtree (Valiente 2009), unnormalized.masti: Information content of Maximum Agreement Subtree, unnormalized.nni_l,nni_L,nni_t,nni_U,nni_u: Lower, best lower, tight upper, best upper, and upper bounds for nearest-neighbour interchange distance (Li et al. 1996), unnormalized. 'Best' lower bounds jump sharply when mismatched regions of a tree become large enough that a tight upper bound cannot be exactly calculated, so are discontinuous and cannot readily be compared between trees.spr: Approximate subtree prune and regraft SPR distance, unnormalized.tbr_l,tbr_u: Lower and upper bound for tree bisection and reconnection (TBR) distance, calculated using TBRDist; unnormalized.rf: Robinson-Foulds distance (Robinson & Foulds 1981), unnormalized.icrf: Robinson-Foulds distance, splits weighted by phylogenetic information content (Smith 2020), unnormalized.path: Path distance (Steel & Penny 1993), unnormalized.
References
Bogdanowicz D, Giaro K (2012). “Matching split distance for unrooted binary phylogenetic trees.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(1), 150--160. doi: 10.1109/TCBB.2011.48 .
Li M, Tromp J, Zhang L (1996). “Some notes on the nearest neighbour interchange distance.” In Goos G, Hartmanis J, Leeuwen J, Cai J, Wong CK (eds.), Computing and Combinatorics, volume 1090, 343--351. Springer, Berlin, Heidelberg. ISBN 978-3-540-61332-9 978-3-540-68461-9, doi: 10.1007/3-540-61332-3_168 .
Kendall M, Colijn C (2016). “Mapping phylogenetic trees to reveal distinct patterns of evolution.” Molecular Biology and Evolution, 33(10), 2735--2743. doi: 10.1093/molbev/msw124 .
Nye TMW, Liò P, Gilks WR (2006). “A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.” Bioinformatics, 22(1), 117--119. doi: 10.1093/bioinformatics/bti720 .
Robinson DF, Foulds LR (1981). “Comparison of phylogenetic trees.” Mathematical Biosciences, 53(1-2), 131--147. doi: 10.1016/0025-5564(81)90043-2 .
Smith MR (2019). “Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets.” Biology Letters, 15, 20180632. doi: 10.1098/rsbl.2018.0632 .
Smith MR (2020). “Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees.” Bioinformatics, online ahead of print. doi: 10.1093/bioinformatics/btaa614 .
Steel MA, Penny D (1993). “Distributions of tree comparison metrics---some new results.” Systematic Biology, 42(2), 126--141. doi: 10.1093/sysbio/42.2.126 .
Valiente G (2009). Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R, CRC Mathematical and Computing Biology Series. CRC Press, Boca Raton.
Examples
library('TreeTools', quietly = TRUE, warn.conflicts = FALSE) # Pectinate unrooted tree shape: plot(UnrootedTreeWithShape(0, 7))
