README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->


```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```


# ips: interfaces to phylogenetic software

> NOTE: `ips` contains most functions that were formerly included in the `phyloch` package plus some more recent functions. Those `phyloch` functions related to tree plotting have been moved to the [`viper`](https://github.com/heibl/viper) package.

This is a bundle of functions that present **i**nterfaces to popular **p**hylogenetic **s**oftware for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states. In additions, there functions for reading, manipulating and writing phylogenetic data (multiple sequence alignments and phylogenetic trees).

## Introduction

There are several functions for reading and writing DNA sequences in FASTA, PHYLIP, and NEXUS format: `read.fas`, `read.phy`, `read.nex`, `write.fas`, `write.phy`, and `write.nex`.
Some functions are available for integrating BEAST with R. XML input files for BEAST can be generated with `rbeauti`. Two functions are designed to read TreeAnnotator output: `read.beast` will render an object of class `phylo` with additional node statistics appended as list elements. These additional node statistics will be lost be the subsequent use of `ladderize` or `rotate` (or similar functions that change the ordering of internal nodes).`read.beast.table` also parses the TreeAnnotator output, but returns a matrix of node statistics. 
This package itself does not implement techniques for phylogenetic analyses, but provides a series of wrappers for commonly used software packages. Sequence alignment can be done with the `mafft` and `prank`; cleaning of sequences with `gblocks` and `aliscore`. The function `raxml` and `mrbayes` are intended for phylogenetic tree search. Running `mrbayes` with argument `run = FALSE` can be used to create MrBayes-executable NEXUS files. Finally, wrappers are provided for `Multistate` in the `BayesTraits` package (see `multistateML` and `multistateMCMC`).
Several plotting functions (`HPDbars`, `clade.bars`, `box.clades`, `box.tips`, `tip.color`, `edge.color` have been moved to the `viper` package.

## Installation

`ips` is available via CRAN and can be installed:

```{r cran-installation, include=TRUE, echo=TRUE, eval=FALSE}
install.packages("ips")
```

Or you can install the development version via GitHub with:

```{r gh-installation, include=TRUE, echo=TRUE, eval=FALSE}
# install.packages("devtools")
devtools::install_github("heibl/ips")
```