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CodonCode corporation phred
Phred, supplied by CodonCode corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/codoncode+phred/phred/pmc00151486-167-9-10
Average 90 stars, based on 1 article reviews
phred - by Bioz Stars, 2026-09
90/100 stars

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Software:

Article Title: Factors Influencing the Sensitivity and Specificity of Conventional Sequencing in Human Immunodeficiency Virus Type 1 Tropism Testing
Article Snippet: .. Base calling is an error-prone process, the accuracy of which is estimated by base-calling software such as Phred (CodonCode Corp.), which estimates the relative likelihood of a base-calling error ( 22 – 24 ). ..

Article Title: Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks
Article Snippet: A total of 13 nuclear loci (4CL, EBS, FT3, GI, M002, M007D1, PCH, Sb16, Sb29, Sb62, se1364, se1390, and xy1420) were sequenced using an ABI 3130xl Genetic Analyzer (Applied Biosystems, Foster City, CA) following the methods in Li et al. ( ). .. Sequence data were base‐called using PHRED with CodonCode Aligner software (CodonCode Corporation) and checked using MEGA version 5.0 (Kumar et al. ). ..

Article Title: Factors Influencing the Sensitivity and Specificity of Conventional Sequencing in Human Immunodeficiency Virus Type 1 Tropism Testing
Article Snippet: .. Base calling is an error-prone process, the accuracy of which is estimated by base-calling software such as Phred (CodonCode Corp.), which estimates the relative likelihood of a basecalling error (22–24). ..

Sequencing:

Article Title: Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks
Article Snippet: A total of 13 nuclear loci (4CL, EBS, FT3, GI, M002, M007D1, PCH, Sb16, Sb29, Sb62, se1364, se1390, and xy1420) were sequenced using an ABI 3130xl Genetic Analyzer (Applied Biosystems, Foster City, CA) following the methods in Li et al. ( ). .. Sequence data were base‐called using PHRED with CodonCode Aligner software (CodonCode Corporation) and checked using MEGA version 5.0 (Kumar et al. ). ..

Article Title: Identification of stress-responsive genes in Ammopiptanthus mongolicus using ESTs generated from cold- and drought-stressed seedlings
Article Snippet: White clones grown on screening LB medium (Amp/IPTG/X-Gal) were recovered by random colony selection and inserts were sequenced from the 5′ end using T7 primer and an ABI 3730 capillary sequencer in Shanghai United Gene Institute of China. .. Standard sequence processing tools, Phred [ ], Phrap and Cross_match [ , ], were used with Codoncode InterPhace ( http://www.codoncode.com ). ..

Article Title: Isolation and characterization of microsatellite markers in the Serra Spanish mackerel, Scomberomorus brasiliensis.
Article Snippet: Thirteen nuclear-encoded microsatellites from a genomic DNA library of Serra Spanish mackerel, Scomberomorus brasiliensis, were isolated and characterized.. The microsatellites include 10 perfect repeats (eight tetranucleotide and two dinucleotide) and three imperfect repeats (two tetranucleotide and one dinucleotide).. An additional five microsatellites, isolated originally from two congeneric species (S. cavalla and S. niphonius), were characterized in S. brasiliensis.

Article Title: Soybean polymorphisms and methods of genotyping
Article Snippet: Automated sequencers are available from, for example, Applied Biosystems, Foster City, Calif. (ABI PRISM® SYSTEMS); Pharmacia Biotech, Inc., Piscataway, N.J. (Pharmacia ALF), LI-COR, Inc., Lincoln, Nebr. (LI-COR 4,000) and Millipore, Bedford, Mass. (Millipore BaseStation). .. Sequence base calling from trace files and quality scores are assigned by PHRED which is available from CodonCode Corporation, Dedham, Mass. and is described by Brent Ewing, et al. “Base-calling of automated sequencer traces using phred”, 1998, Genome Research, Vol. ..

Plasmid Preparation:

Article Title: Isolation and characterization of microsatellite markers in the Serra Spanish mackerel, Scomberomorus brasiliensis.
Article Snippet: Thirteen nuclear-encoded microsatellites from a genomic DNA library of Serra Spanish mackerel, Scomberomorus brasiliensis, were isolated and characterized.. The microsatellites include 10 perfect repeats (eight tetranucleotide and two dinucleotide) and three imperfect repeats (two tetranucleotide and one dinucleotide).. An additional five microsatellites, isolated originally from two congeneric species (S. cavalla and S. niphonius), were characterized in S. brasiliensis.



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