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TreeDist  

Calculate and Map Distances Between Phylogenetic Trees
View on CRAN: Click here


Download and install TreeDist package within the R console
Install from CRAN:
install.packages("TreeDist")

Install from Github:
library("remotes")
install_github("cran/TreeDist")

Install by package version:
library("remotes")
install_version("TreeDist", "2.9.2")



Attach the package and use:
library("TreeDist")
Maintained by
Martin R. Smith
[Scholar Profile | Author Map]
First Published: 2020-06-30
Latest Update: 2023-10-25
Description:
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 calculating the median of sets of trees, and for computing the information content of trees and splits.
How to cite:
Martin R. Smith (2020). TreeDist: Calculate and Map Distances Between Phylogenetic Trees. R package version 2.9.2, https://cran.r-project.org/web/packages/TreeDist. Accessed 29 Apr. 2025.
Previous versions and publish date:
1.0.0 (2020-06-30 11:10), 1.1.1 (2020-07-10 17:40), 1.2.0 (2020-08-28 13:30), 1.2.1 (2020-09-17 15:10), 2.0.0 (2021-01-20 17:20), 2.0.2 (2021-01-27 14:20), 2.0.3 (2021-01-31 06:40), 2.1.0 (2021-07-12 09:50), 2.1.1 (2021-07-13 14:20), 2.2.0 (2021-09-13 17:30), 2.3.0 (2022-01-04 01:20), 2.4.0 (2022-03-23 08:50), 2.4.1 (2022-07-20 16:40), 2.5.0 (2022-10-07 15:50), 2.6.0 (2023-02-20 11:20), 2.6.1 (2023-05-01 16:30), 2.6.2 (2023-06-30 00:10), 2.6.3 (2023-08-25 12:50), 2.7.0 (2023-10-26 00:10), 2.8.0 (2024-07-26 10:30), 2.9.0 (2024-09-03 18:20), 2.9.1 (2024-09-07 11:20)
Other packages that cited TreeDist R package
View TreeDist citation profile
Other R packages that TreeDist depends, imports, suggests or enhances
Complete documentation for TreeDist
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