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Test Data
(See Additional Info. page for more details about the test data.)
Segminator II
Segminator II has been developed by John Archer, David Robertson and Andrew Rambaut as part of a project funded by the BBSRC (project grant: BB/H012419/1). It is a tool for the analysis of viral short read data generated on the 454 Life Sciences and Illumina sequencing platforms and is specifically designed to allow for the identification of variation within temporally sampled data.


Figure 1: Main display area of Segminator II

Following the mapping and pairwise alignment of reads, data that is immediately accessible in tabulated format includes:
  • per site coverage,
  • per site base frequencies,
  • consensus sequence,
  • per site mean quality of non-consensus nucleotides,
  • entropy,
  • codon frequencies,

    and through the interface (Fig. 1) further features allow for:

  • a quick phylogenetic scan of clusters within the data using the TreeDar feature,
  • the management of multiple datasets within a single project,
  • easy visual comparison of any two datasets within a given project
  • detailed phylogenetic analysis of reads spanning a selected region of the template with the ability to track individual codon states around the tree.
This site contains a description of the software, the parameters used within the software as well as the program itself in the format of a downloadable zip file containing the jar file and all necessary external libraries.

A further example usage of the software is available here as a poster which is the bases of our current submitted publication.