Seq Workshop/2009

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Course overview

Recent updates to the course

Free software that will allow you to simultaneously assemble reads and view chromatograms:

Note: All of these require a moderate level of comfort working in a Unix or Linux environment

  • The Staden Package: [1]
  • Phred/Phrap/Consed: [2]
  • Hawkeye/AMOS: [3]
  • MacGDE: [4]
    • Back in the day, Jonathan wrote a guide to using GDE: [5]
  • Vector NTI: as of December, 2008, Vector NTI is no longer free
  • Mesquite: is free, but the module that allows you to do this (Chromaseq) is not yet avaialable to the public

Not free, but cheaper than Sequencher, and offer a free trial

CodonCode Aligner [6]

  • runs on Mac OSX and Windows, this is a replacement for the free TraceViewer that these guys used to offer]
  • SUPER easy to use

DNABaser [7]

  • runs natively on Windows or on a Mac if you install virtual Windows
  • easy to use, but Geneious is easier
  • they also offer some free file format converters which can come in handy when using the free packages and a chromatogram viewer to look at several chromatograms in a folder quickly

Geneious [8]

  • runs on Mac OSX and Windows
  • SUPER easy to use

Free sequence analysis packages

  • Mega [9]
  • Sewer [10]
  • See also the Wikipedia page on this [11]