One good reason to use Phred for base callingis higher accuracy: in one study, Phred made "40-50%fewer errors" "than the ABI software" ( Ewinget al.1998a, Genome Research 8:175-85 ). PHD files - text files which contain base call and quality information, which can later be used during contig editing by Consed and similar programs.Quality files in FASTA (or XPAB) format.Sequence files in FASTA (or XBAP) format.SCF files with Phred's base calls and quality values.Phred can produce a variety of different output files: Applied Biosystems (ABI) chromatogram files.The SCF format is a "universal" format for trace sequence files that is supported by many different programs and manufacturers. SCF ("Standard Chromatogram Format") files.Phred can read input files in thefollowing formats: Phred is a base-calling program for DNA sequence traces.Phred reads DNA sequence chromatogram files and analyzes the peaks to call bases, assigning quality scores ("Phred scores") to each base call. For scientists who would like to use Phred on Windows or Mac OS X from a user-friendly graphical interface, CodonCode Corporation offers CodonCodeAligner. For information about Phrap,Cross_match, and Consed, please visit Since Phred was developed for easy integration into automated data processing pipelines, Phred does not provide a graphical user interface. This page gives a brief description of Phred. Phred iswidely used by the largest academic and commercial DNA sequencinglaboratories. Phil Green and Brent Ewing, and is distributed by CodonCode Corporation under license from the University of Washington. Phred is a base calling program for DNA sequence traces Phred executables for Windows, Mac OS X, Linux, and Unix are available fromCodonCode Corporation as part of the PHRED - PHRAP package. If this guitar holds up like I think it will, it'll be mine for a very, very long time.Phred - Quality Base Calling Phred - Quality Base Calling The price seems to fit all things considered, but I'm interested in hearing what others think about the guitar based on the link. Though pricey, they're still priced a couple thousand less than other notable Langeudoc models like Forshage or Crow Hill (which are amazing in their own right, and probably a very, very safe bet!). I was wondering if anyone here has ever played their R2 models before, knows someone who has, or, even better, if anyone has experience owning one. Obviously, I'd much rather play the guitar prior to buying, but that's not an option here. However, at $5500-$6500-ish, these things aren't cheap. Aside from being made in the US, the R2 looks to answer all of these critiques about the Dockstar and Reprise models: the hardware and wiring is great, comes with quality pickups, and optional Schaller M6 locking tuners (+$20 upgrade). One thing I've heard consistently about Phred guitars is that the lower-tier models are actually pretty darn good for what you pay, but sometimes they would really benefit from an upgrade here or there. The R2 is their premium line modeled after the famed Languedoc of Phish fame. Right now I'm thinking about buying an R2 Koa. Hey folks, there really aren't any threads dedicated to Phred Instruments, aside from the occasional one about a specific model, but I'm hoping we could use a more general one to talk about our experiences and share any feedback.
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