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# phangorn 

phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. 

To get an introduction into phylogenetic inference you want to look at: 
```
vignette("Trees", package="phangorn")
```


## Installation

You can install the the latest release `phangorn` of the package from
[CRAN](https://CRAN.R-project.org/package=phangorn), or the development version 
from [github](https://github.com/KlausVigo/phangorn) or
[r-universe](https://klausvigo.r-universe.dev/phangorn).
                                                                 
                                                                 
| Type        | Source          | Command                                                      |
|-------------|-----------------|--------------------------------------------------------------|
| Release     | CRAN            | `install.packages("phangorn")`                                             |
| Development | GitHub          | `remotes::install_github("KlausVigo/phangorn")`                            |
| Development | r-universe      | `install.packages('phangorn', repos = 'https://klausvigo.r-universe.dev')`    |

To install the development version you may need to install the Biostrings package from bioconductor first:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Biostrings")
```
To use all functionality you might install all you might need to install the 
`rgl` and `ggseqlogo` package.  
```
install.packages("rgl")
install.packages("ggseqlogo")
```
The development version usually depends on the latest `ape` development 
version and information to download can be found 
[here](https://emmanuelparadis.github.io/ape_installation.html). 

## Citation

If you use phangorn please cite:

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593 


License
-------
phangorn is licensed under the GPLv2.
