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#### R Package
The stable version of <code>phyclust</code> is available on
<a href="http://cran.r-project.org/web/packages/phyclust/index.html"
target="_blank">CRAN</a> or
<a href="http://cran.r-project.org/mirrors.html"
target="_blank">mirror sites</a>
from <a href="http://www.r-project.org"
target="_blnak">R-project</a>, or
in the following:
- Developing code (github):
<a href="https://github.com/snoweye/phyclust"
target="_blank">phyclust</a>
---
#### Installation
- An R is necessary.
- The <code>phyclust</code> requires the other R package,
<a href="http://cran.r-project.org/web/packages/ape/index.html"
target="_blank">
<code>ape</code></a>,
for phylogenetic tree illustrations and for calculations.
The <code>ape</code> is available from its
<a href="http://ape.mpl.ird.fr/" target="_blank">original home</a> or
<a href="http://cran.r-project.org/" target="_blank">CRAN</a>.
<br>
<b>Note</b>: the <code>ape</code> requires other packages such as
<code>gee</code>, <code>nlme</code> and <code>lattice</code>
that are also available from CRAN.
- Some easy ways to install <code>phyclust</code>,
* Use the R command to install from the download file,
```
SHELL> R CMD INSTALL phyclust_0.1-1.tar.gz
```
* Use the install function inside of R from the CRAN.
```
R> install.packages("phyclust")
```
* Use "<code>Install package(s) from local zip files...</code>"
from the R menu in a window environment.
---
#### C Library
- Stable version:
* Source code:
<a href="./download/phyclust-c_0.1-5.tar.gz">phyclust-c_0.1-5.tar.gz</a>
The core of <code>phyclust</code> is implemented in C and
in a modular way, including flexible data structures and function pointers
which allow easy extension to other data types, evolutionary
models and optimization algorithms.
The <code>C</code> core accesses <code>R</code> functions,
for optimizations and random number generation, using the
<code>R API</code>, but it can also be
compiled as a standalone library for linking to other applications.
The testing codes for some main functions are also provided, and
it is possible to develop command line interface or standalone software
based on <code>phyclust-c</code> without using R.
---
#### PHP Web Interface
- Source code:
<a href="./download/phyclust-php_0.1-1.tar.gz">phyclust-php_0.1-1.tar.gz</a>
There is a accessible version web interface
which is an example for using <code>phyclust</code>
and can be extended to a web service.
An executable R and the
<code>phyclust</code> R package are required for this interface,
and the interface is only tested on the Linux environment.
---
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