John Innes Centre, Norwich Research Park,
Colney Lane, Norwich, NR4 7UH, UK.

Telephone: +44(0) 1603 450597 (direct)
+44(0) 1603 450000 (switchboard)
Fax: +44(0)1603 450595

### New version!

A new version (March 2004) of newicktree is available. Changes from the December 2003 release are:

• Trees may be specified without branch lengths
• Node labels and branch labels are now fully supported
• Extra scaling parameter for the contemporary tips option.

### Overview

newicktree is a LaTeX package that allows the easy drawing of Newick (New Hampshire) format phylogenetic trees, by providing a high level interface to the PSTricks package.

On this page you will find links to the newicktree program file, its documentation, installation instructions and contact information. This section provides the briefest illustration of the operation of newicktree. For more information please consult the documentation.

The Newick format is the agreed standard format for the description of phylogenetic trees, and is generated (either on its own or as part of the NEXUS file format) by most, if not all, popular phylogenetic analysis packages. The format is intuitive and allows easy construction of simple trees by hand.

To draw a tree in a LaTeX document using newicktree, you would type the following:

\usepackage{..,newicktree,..}

...

\begin{newicktree}
\option1
..
\optionn
\drawtree{[Newick tree here]}
\end{newicktree}


The drawtree command is responsible for the actual drawing of the tree. The option commands provide the ability to use or ignore branch length information, display branch lengths and/or bootstrap values, scale the tree horizontally and vertically, change the text formatting, set the direction of growth of the tree, include a scalebar, and change the branch drawing style.

As well as supporting the full Newick format, newicktree provides the extra ability to label every branch individually with an arbitrary label, and to label the root node of a tree. For more detailed instructions please see the documentation.

### Installation Instructions

To use newicktree on your computer system you need the following:

A LaTeX installation including a dvi to ps converter.

The PSTricks package, including the subpackages pst-tree and pst-node. The file psttest.tex in the downloads section below will test your PSTricks installation. If you don't have PSTricks, you can get it from CTAN,via the PSTricks website,or perhaps by using the package management system that came with your LaTeX installation (for example MiKTeX's package management includes PSTricks). Consult the documentation for your LaTeX distribution or your computing department if you're unsure.

The whole of the newicktree package can be found in the file newicktree.sty, available from the downloads section below. To use newicktree, this file needs to be in a place on your filesystem where your LaTeX installation can find it. This is typically somewhere in your texmf tree, or in the current working directory. Again, consult the documentation for your LaTeX distribution or your computing department if you're unsure about what to do.

To check that you have installed newicktree correctly, please download and try to LaTeX the two test files in the download section. The first checks that your PSTricks installation is okay, and the second attempts to use newicktree to build a simple tree.

To use newicktree successfully, you need to read the documentation. This includes a full description of the tree drawing options, examples of what you might do with newicktree, a rough explanation of how newicktree works, a list of known issues, and troubleshooting advice.

File Last updated
newicktree.sty The newicktree package 1 March 2004
psttest.tex LaTeX file to test your PSTricks installation 15 Dec 2003
nttest.tex LaTeX file to test your newicktree installation 15 Dec 2003
ntdoc.ps
ntdoc.pdf
The newicktree documentation in PostScript or pdf formats (you only need one of these). 1 March 2004