Seq Workshop/2009

Course overview

Recent updates to the course

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

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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

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

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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]