https://github.com/ropensci/phylogram
Dendrograms for Evolutionary Analysis
https://github.com/ropensci/phylogram
peer-reviewed r r-package rstats
Last synced: 5 months ago
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Dendrograms for Evolutionary Analysis
- Host: GitHub
- URL: https://github.com/ropensci/phylogram
- Owner: ropensci
- Created: 2017-01-17T02:07:39.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-12-09T21:21:54.000Z (almost 6 years ago)
- Last Synced: 2025-05-03T06:45:07.915Z (5 months ago)
- Topics: peer-reviewed, r, r-package, rstats
- Language: R
- Homepage: https://docs.ropensci.org/phylogram
- Size: 939 KB
- Stars: 11
- Watchers: 7
- Forks: 3
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- Codemeta: codemeta.json
Awesome Lists containing this project
README
# phylogram
[](https://doi.org/10.21105/joss.00790)
[](https://cran.r-project.org/package=phylogram)
[](https://cran.r-project.org/package=phylogram)
[](https://github.com/ropensci/onboarding/issues/212)
[](https://travis-ci.org/ropensci/phylogram)
[](https://codecov.io/github/ropensci/phylogram)
[](http://www.repostatus.org/#active)
[](http://www.gnu.org/licenses/gpl-3.0)
[](https://doi.org/10.5281/zenodo.1293634)
[](http://orcid.org/0000-0002-7332-7931)
--------------------------------------------------------------------------------
The **phylogram** R package is a tool for for developing
phylogenetic trees as deeply-nested lists known as "dendrogram" objects.
It provides functions for conversion between "dendrogram" and
"phylo" class objects, as well as several tools for command-line tree
manipulation and import/export via Newick parenthetic text.
This improves accessibility to the comprehensive range of object-specific
analytical and tree-visualization functions found across a wide array of
bioinformatic R packages.
### Installation
To download **phylogram** from CRAN and load the package, run
```R
install.packages("phylogram")
library("phylogram")
```
To download the latest development version from GitHub, run:
```R
devtools::install_github("ropensci/phylogram", build_vignettes = TRUE)
library("phylogram")
```
### Example: reading and writing trees
Consider the simple example of a tree with three members named
"A", "B" and "C", where "B" and "C" are more closely related
to eachother than they are to "A".
An unweighted Newick string for this tree would be "(A,(B,C));".
This text can be imported as a
dendrogram object using the `read.dendrogram` function
as follows:
```R
library("phylogram")
newick <- "(A,(B,C));"
x <- read.dendrogram(text = newick)
plot(x)
```
The following command writes the object back to the console in
Newick format without edge weights:
```R
write.dendrogram(x, edges = FALSE)
```
The syntax is similar when reading and writing text files,
except that the `text` argument is replaced by `file` and a
valid file path is passed to the function.
To convert the dendrogram to a "phylo" object, run
```R
y <- as.phylo(x)
```
These and more examples are available in the package vignette.
To view the vignette, run `vignette("phylogram-vignette")` or access it
directly from [CRAN](https://CRAN.R-project.org/package=phylogram).
### Help
An overview of the package with links to the function documentation can be found by running
```R
?phylogram
```
If you experience a problem using this package please
either raise it as an issue on [GitHub](http://github.com/ropensci/phylogram/issues)
or post it on the **phylogram** [google group](https://groups.google.com/group/phylogram).
### Acknowledgements
This software was developed at
[Victoria University of Wellington](http://www.victoria.ac.nz/)
with funding from a Rutherford Foundation Postdoctoral Research Fellowship
award from the Royal Society of New Zealand.
[](https://ropensci.org)