Technical Details
Citation & Credit


Chromaseq: a package for processing chromatograms and sequence data in Mesquite

Lead developers
David R. Maddison, Oregon State University
Wayne P. Maddison, University of British Columbia

Code contributors
Danny Mandel
Jeremy Parson


The Chromaseq package integrates the processing of chromatograms within Mesquite. With Chromaseq installed, and the programs Phred and Phrap, you can:

  1. Organize a directory of chromatograms into subdirectories corresponding to genes and samples
  2. Assemble them into contigs (with the help of Phred and Phrap)
  3. Import the contig sequences into Mesquite, and have Chromaseq automatically trim them, adjust base calls as appropriate, etc.
  4. View the chromatograms for each sequence by touching a special tool on that sequence in Mesquite's matrix editor
  5. Edit the base calls in a chromatogram viewer

In addition, there are a few other tools in Chromaseq that aid with GenBank submission, chromatogram organization, and data visualization.

Chromaseq version 1.3 requires Mesquite 3.3 or later, as well as Phred and Phrap.

The following sections provide introductory information about Chromaseq:

More information is available by clicking on the links at the left.