Web based genome comparison tool

• JDotter
  • A java based tool designed to compare whole genome
  • Runs comparison operations locally
  • Need a java install thing
• M-GCAT
  • in C and Python
  • Runs locally from command line??? => could generate on server. Too much work for server?
• Dotplot MEDEA
  • This is what I want!
  • At its minimum, the MEDEA Dot Plot only needs JSON formatted data for the sequences and JSON formatted data for alignments.
  • Need to calculate alignments
    • http://www.fantascienza.net/leonardo/so/dotplot/dotplot.html
    • >>> import Bio.Align.Applications >>> dir(Bio.Align.Applications)
    • from Bio.Emboss.Applications import NeedleCommandline
• Multi MEDIA
  • Multigenome comparison tool

For Computation

• TBA
  • documentation and publication
• MUGSY
  • publication
  • Most recently released... claims to be comparable but faster than other alignment tools.
  • Output = Multiple Alignment Format (MAF)