Seq Workshop/2009

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:


 * Phred/Phrap/Consed:


 * Hawkeye/AMOS:


 * MacGDE:
 * Back in the day, Jonathan wrote a guide to using GDE:


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

= Free sequence analysis packages =
 * Mega
 * Sewer
 * See also the Wikipedia page on this