https://github.com/ms609/tbrdist
An R package to calculate tree rearrangement distances
https://github.com/ms609/tbrdist
algorithms bioinformatics distance-calculation phylogenetic-trees phylogenetics r
Last synced: about 2 months ago
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An R package to calculate tree rearrangement distances
- Host: GitHub
- URL: https://github.com/ms609/tbrdist
- Owner: ms609
- License: gpl-3.0
- Created: 2019-11-19T13:29:57.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2026-04-17T13:03:12.000Z (3 months ago)
- Last Synced: 2026-04-17T14:32:57.730Z (3 months ago)
- Topics: algorithms, bioinformatics, distance-calculation, phylogenetic-trees, phylogenetics, r
- Language: C
- Homepage: https://ms609.github.io/TBRDist
- Size: 957 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Codemeta: codemeta.json
- Zenodo: .zenodo.json
- Agents: AGENTS.md
Awesome Lists containing this project
README
# TBRDist
[](https://github.com/ms609/TBRDist/actions/workflows/R-CMD-check.yml)
[](https://codecov.io/gh/ms609/TBRDist)
[](https://cran.r-project.org/package=TBRDist)
[](https://ms609.github.io/usage#tbrdist)
[](https://doi.org/10.5281/zenodo.3548332)
[](https://www.repostatus.org/#inactive)
'TBRDist' is an R package that calculates rearrangement distances between
phylogenetic trees using C++ algorithms
by [Chris Whidden](https://web.cs.dal.ca/~whidden/):
- **Unrooted trees** (`TBRDist()`, `USPRDist()`, `ReplugDist()`): TBR, SPR,
and Replug distances based on the algorithms of
[Whidden and Matsen (2017)](https://arxiv.org/abs/1511.07529).
The C++ implementation has diverged from the upstream
[uspr](https://github.com/cwhidden/uspr) library with optimizations
including integer-encoded tree identity (replacing Newick string
round-tripping), precomputed SPR lookup tables for small trees, and
reduced heap allocation in the A\* search and branch-and-bound routines,
yielding roughly 2.5× faster computation.
- **Rooted trees** (`RSPRDist()`): Rooted SPR distances via
[rspr](https://github.com/cwhidden/rspr), implementing the exact
fixed-parameter algorithm (with cluster decomposition) of Whidden, Beiko,
and Zeh (2013). Supports exact distances, a linear-time 3-approximation, and
maximum agreement forest output.
The uSPR distance is a natural distance metric with respect to phylogenetic
tree search, as common tree search and sampling software mainly use SPR
operations (or NNI operations, a subset of SPR operations). The uSPR distance
is also a lower bound on the number of lateral gene transfer events required to
explain the difference between a reference/species tree and a gene tree.
Note that the uSPR distance is NP-hard to compute (as are the TBR and replug
distances) and the running time of most of the algorithms used in this software
scales exponentially with the distance computed.
The unrooted functions are aimed at trees with up to 50 leaves and uSPR
distances up to 14. The rooted `RSPRDist()` can handle much larger trees
(200+ leaves, distances > 50).
# Installation
Install and load the library from CRAN as follows:
```
install.packages('TBRDist')
library('TBRDist')
```
You can install the development version thus:
```r
if(!require(devtools)) install.packages("devtools")
devtools::install_github('ms609/TBRDist')
```
Advanced users wishing to access the source code should note that the project
contains [submodules](https://github.blog/2016-02-01-working-with-submodules/).
To download the contents of these subdirectories, clone the project using
`git clone --recursive https://github.com/ms609/TBRDist`,
or if you've already cloned the project, run
`git submodule update --init --recursive`.
# Citation
If you use unrooted distances (`TBRDist`, `USPRDist`, `ReplugDist`) in your
research, please cite:
> Whidden C, Matsen FA IV (2019). Calculating the Unrooted
> Subtree-Prune-and-Regraft Distance. _IEEE/ACM Transactions on Computational
> Biology and Bioinformatics_ 16(3):898–911.
> doi:[10.1109/TCBB.2018.2802911](https://doi.org/10.1109/TCBB.2018.2802911)
If you use rooted SPR distances (`RSPRDist`), please cite:
> Whidden C, Beiko RG, Zeh N (2013). Fixed-Parameter Algorithms for Maximum
> Agreement Forests. _SIAM Journal on Computing_ 42(4):1431–1466.
> doi:[10.1137/110845045](https://doi.org/10.1137/110845045)
A citation to the R package itself would also be appreciated:
> Smith MR (2019). TBRDist: Rearrangement Distances Between Phylogenetic Trees.
> doi:[10.5281/zenodo.3548333](https://doi.org/10.5281/zenodo.3548333)
# Notes
Some text in this README file originates from the ['uspr' readme](https://github.com/cwhidden/uspr/blob/master/README.md).
Please note that the 'TBRDist' project is released with a
[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.