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https://github.com/ms609/quartet

R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
https://github.com/ms609/quartet

bioinformatics comparison cran phylogenetic-trees phylogenetics quartet quartet-distance research-tool tree

Last synced: 19 days ago
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R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)

Host: GitHub
URL: https://github.com/ms609/quartet
Owner: ms609
Created: 2017-01-30T13:34:42.000Z (about 8 years ago)
Default Branch: master
Last Pushed: 2024-09-03T08:31:29.000Z (5 months ago)
Last Synced: 2024-09-15T17:14:23.474Z (5 months ago)
Topics: bioinformatics, comparison, cran, phylogenetic-trees, phylogenetics, quartet, quartet-distance, research-tool, tree
Language: C++
Homepage: https://ms609.github.io/Quartet/
Size: 13.9 MB
Stars: 9
Watchers: 4
Forks: 5
Open Issues: 8
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- Code of conduct: CODE_OF_CONDUCT.md
- Codemeta: codemeta.json

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# Quartet

'[Quartet](https://ms609.github.io/Quartet/)' is an R package that calculates 

the quartet distance between two trees (Estabrook _et al._ 1985),

a measure of their similarity based on the number of shared four-taxon subtrees.

The quartet distance outperforms a number of widely used tree distances 

(e.g. the Robinson–Foulds, path, and rearrangement distances) against a number

theoretical and practical measures (Steel & Penny 1993; Smith 2020),

and is particularly valuable in the construction of tree spaces (Smith 2021).

'Quartet' uses the 'tqDist' algorithm (Brodal _et al._ 2004; Sand _et al._ 2014).

Unlike many other implementations, it distinguishes between quartets that are

contradicted by one tree,

and quartets that are simply absent due to a lack of resolution (i.e.

the presence of polytomies; see Smith 2019).

'Quartet' makes this distinction in both the quartet metric (function

`QuartetStatus()`) and the partition metric (i.e. Robinson-Foulds distance;

function `SplitStatus()`).

## Using the package

Install and load the library from CRAN as follows:

```

install.packages('Quartet')

library('Quartet')

```

For the latest features, install the development version:

```r

if(!require("curl")) install.packages("curl")

if(!require("remotes")) install.packages("remotes")

remotes::install_github("ms609/Quartet")

```

You will need [Rtools](https://cran.r-project.org/bin/windows/Rtools/) installed 

in order to build the development version from source.

View the [function reference](https://ms609.github.io/Quartet/reference/)

and [basic usage instructions](https://ms609.github.io/Quartet/articles/Using-Quartet.html).

## Known limitations

Quartet supports trees with up to 477 leaves.  Larger trees contain more 

quartets than can be represented by R's signed 32-bit integers.

The underlying 'tqDist' library may handle trees with up to 568 leaves,

and 64-bit integer representations could increase this number further.  

Making either of these improvements within the R package 

would require substantial additional work, but could be implemented -- do

[file an issue](https://github.com/ms609/Quartet/issues/new/) if this would be

useful to you.

## References

- Brodal G.S., Fagerberg R., Pedersen C.N.S. 2004. Computing the quartet 

  distance between evolutionary trees in time O(_n_ log _n_). 

  Algorithmica 38:377–395.

- Estabrook G.F., McMorris F.R., Meacham C.A. 1985. Comparison of undirected 

  phylogenetic trees based on subtrees of four evolutionary units. 

  Syst. Zool. 34:193–200.

- Sand A., Holt M.K., Johansen J., Brodal G.S., Mailund T., Pedersen C.N.S. 2014.

  tqDist: a library for computing the quartet and triplet distances between 

  binary or general trees. 

  Bioinformatics 30:2079–2080. https://doi.org/10.1093/bioinformatics/btu157

- Smith, M.R. 2019. Bayesian and parsimony approaches reconstruct 

  informative trees from simulated morphological datasets. Biol. Lett.

  15:20180632. https://doi.org/10.1098/rsbl.2018.0632

- Smith, M.R. 2020. Information theoretic generalized Robinson–Foulds metrics 

  for comparing phylogenetic trees. Bioinformatics, 36:5007–5013.

  https://dx.doi.org/10.1093/bioinformatics/btaa614

- Smith, M.R. 2022. Robust analysis of phylogenetic tree space. 

  Systematic Biology, syab100.

  https://dx.doi.org/10.1093/sysbio/syab100

- Steel, M. and Penny, D. 1993. Distributions of tree comparison metrics:

  some new results. Syst. Biol. 42: 126-141.

  https://doi.org/10.1093/sysbio/42.2.126

Please note that the 'Quartet' project is released with a

[Contributor Code of Conduct](https://ms609.github.io/Quartet/CODE_OF_CONDUCT.html).

By contributing to this project, you agree to abide by its terms.