Software Open Access
TreeDist: Distances Between Phylogenetic Trees
Martin R. Smith
An R package that 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>. Calculates the median of a set of trees under any distance metric.
Details and installation instructions are available at ms609.github.io/TreeDist.
| Name | Size | |
|---|---|---|
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ms609/TreeDist-0.0.0.9000.zip
md5:90f4ebd5bd20a79aea8c6e4bb41c5b46 |
997.0 kB | Download |
| All versions | This version | |
|---|---|---|
| Views | 173 | 129 |
| Downloads | 7 | 5 |
| Data volume | 5.4 MB | 5.0 MB |
| Unique views | 157 | 117 |
| Unique downloads | 7 | 5 |
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- Publication date:
- November 4, 2019
- DOI:
-
- Keyword(s):
- phylogenetics tree distance R R packages
- Related identifiers:
- Supplement to
- License (for files):
- GNU General Public License v3.0 only