Software Downloads and Information
[download site for the sequence alignment and phylogenetic tree program Bonsai]

Other Software Downloads:

Java Runtime Environment (JRE): this is necessary to run any of my programs, which are all written in Java. Download the most recent version from Sun: (click the "Download Now" button). If you use MacOSX you already have a JRE, and if you use Windows or Linux you might already have a JRE. If you encounter problems lauching my software, try installing the newest JRE from the link above.

GFF Parser: a simple program that lets you quickly parse data from GFF 2.0 files (which are flat-text genome data files). Updated 12/18/02.

Etho: a highly configurable keyboard-driven event timer. Useful for recording and analyzing events in a laboratory setting.

Karkinos: a way-cool cancer growth simulator that is useful for teaching.

Strain Collection Searching: software that lets you search tab-delimited data sets, currently specifically tailored for the Thomas lab worm strain, allele, and oligo data sets. It wouldn't be hard to configure it to view any tab-delimited text data format. It makes easy things like finding all strains with dpy-5 and an unc them. Also, sort by any field and other bells and whistles.


- Introduction to Bonsai: philosophy, utility, features.

- Full set of Bonsai documentation, including specific program guide and essays on understanding trees and alignments. Needs updating.

To initiate a Bonsai download, click the link below. The Bonsai executables for Windows, MacOSX, and Linux are all included in the same download. The archives should unpack into a single folder named "bonsai", and inside you will find RTF files describing how to complete the installation and run Bonsai.

- Bonsai download (zip archive) - new build 2/7/2007.

Java Runtime Environment (JRE): this is necessary to run any of my programs, which are all written in Java. Use the link near the top of this page to download the latest version free. Mac users will have to get the JRE via the Apple web site, but there should be links from the above site to the appropriate Apple site.

James H. Thomas, Department of Genome Sciences, University of Washington, 2/8/2007