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Phrap specifications


Unique identifier OMICS_01429
Name Phrap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence and quality files
Input format FASTA
Output data Standard error, contig sequences, contig qualities
Output format FASTA
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 0.990319
Stability Stable
C compiler
Maintained Yes




No version available



  • person_outline Philip Green

Publication for Phrap

Phrap citations


Zinc Deficiency‐Like Syndrome in Fleckvieh Calves: Clinical and Pathological Findings and Differentiation from Bovine Hereditary Zinc Deficiency

PMCID: 5866964
PMID: 29424482
DOI: 10.1111/jvim.15040
call_split See protocol

[…] ing reactions were done for both strands with BigDye Terminator v1.1 Cycle Sequencing Kit. Electrophoresis of purified sequencing reactions was performed on the ABI 3130xl Genetic Analyzer. The Phred/Phrap/Polyphred software suite, , was used for base calling, sequence alignment, and polymorphism detection. Sequences were viewed with Consed. To avoid false results because of DNA desamination, amp […]


Global mtDNA genetic structure and hypothesized invasion history of a major pest of citrus, Diaphorina citri (Hemiptera: Liviidae)

Ecol Evol
PMCID: 5756889
PMID: 29321868
DOI: 10.1002/ece3.3680

[…] with primers from the original PCR reactions on an ABI 3730 automatic sequencer (Applied Biosystems, Foster City, CA, USA), using BigDye technology. The chromatographs were interpreted with Phred and Phrap (Green, ; Green & Ewing, ) using the Chromaseq module (Maddison & Maddison, ) implemented in the Mesquite (Maddison & Maddison, ). Quality threshold was set high, for base trimming to 49 and for […]


Structure analysis of capsid protein of Porcine circovirus type 2 from pigs with systemic disease

PMCID: 5914143
PMID: 29128395
DOI: 10.1016/j.bjm.2017.08.007
call_split See protocol

[…] fication Kit (Applied Biosystems, Foster City, CA, USA). The nucleotide sequences were determined using an ABI3130xl Genetic Analyzer.The obtained sequences were analyzed and assembled with the Phred/Phrap/Consed softwares., For the phylogenetic analysis, 46 PCV2 complete genome sequences, including other representative sequences of PCV2a, PCV2b, PCV2c and PCV2d available in GenBank database (htt […]


Novel arsenic transforming bacteria and the diversity of their arsenic related genes and enzymes arising from arsenic polluted freshwater sediment

Sci Rep
PMCID: 5593903
PMID: 28894204
DOI: 10.1038/s41598-017-11548-8

[…] s, USA). The vector sequences were removed using the web-based tool VecScreen ( and sequences were assembled into contigs using the software package Phred/Phrap/Consed ( Chimeras were identified using Bellerophon ( sequences were aligned in MEGA 6.0 using […]


Differentiating Botulinum Neurotoxin Producing Clostridia with a Simple, Multiplex PCR Assay

Appl Environ Microbiol
PMCID: 5583490
PMID: 28733282
DOI: 10.1128/AEM.00806-17

[…] plied Biosystems, Foster City, CA, USA). Products were sequenced on an ABI3130 genetic analyzer (Applied Biosystems, Foster City, CA, USA). Sanger reads were called with PHRED (, ) and assembled with PHRAP ( via CodonCode Aligner (CodonCode Corporation, Centerville, MA, USA). The amplicon sequence was identified with BLAST (). The amplicon sequence was also aligned to reference seque […]


Reinstatement of Eschatoporiini Blaisdell, 1906, a unique tribe of blind cavernicolous Tenebrionidae from California, with a new species from Napa County (Coleoptera, Tenebrionidae, Lagriinae)

PMCID: 5672585
PMID: 29118594
DOI: 10.3897/zookeys.688.13575

[…] hnology Core Facility using a 3730 XL Applied Biosystems automatic sequencer. Assembly of multiple chromatograms of each gene fragment and initial base calls were made with Phred v. 0.020425.c () and Phrap v. 0.990319 () as orchestrated by Mesquite’s Chromaseq v. 1.12 package (, ) with subsequent modifications by Chromaseq and manual inspection. Final sequences are available on GenBank (accessions […]


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Phrap institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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