Bioinformatics toolkit
Screenshot of Mallard - a 16S rRNA chimera detection tool.

Mallard

A program for screening 16S rRNA clone libraries, and similar multiple sequence alignments for chimeras and other anomalies.

To download Mallard click on the button below. Alternatively visit this site's download page.

Download Mallard

Please make sure you have the Java Runtime Environment installed on your computer.

Citation

KE Ashelford et al. (2006) "New Screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras." Applied and Environmental Microbiology, 72(9): 5734-5741.

Summary

The program is based on the Pintail algorithm which works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene. It is released under the terms of the GNU General Public Licence and is freely available from this site.

A quick guide to using Mallard

  1. From the File menu, select Open Sequence File and load a suitable input file.
  2. Select Run to generate a DE plot of the supplied data.
  3. Select Identify Outliers to identify outlier DE values and generate a list of likely anomalous sequences.

For a more complete explanation of how to use the program, click here.

Program requirements

Mallard is written in Java, and will therefore run on any operating system capable of supporting this runtime environment. Java is available on Microsoft Windows, Apple Mac OS X, and other Unix platforms including Linux. Please refer to this page for further details.  Note: Mallard requires Java version 1.4.x or later.

  • Click here to download Mallard.
  • Click here to download the Java Runtime Environment.

Help and tutorial

For a more complete explanation of how to use the program, click here.

For worked example, click here.

Author and Contact details

This software was designed and written by Dr Kevin Ashelford. Any comments, suggestions or bug reports - please contact me at ashelford@cardiff.ac.uk.

This work has been supported by the Biotechnology and Biological Sciences Research Council (BBSRC).