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Chromaseq specifications


Unique identifier OMICS_01017
Name Chromaseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Chromaseq citations


Multiple origins of downy mildews and mito nuclear discordance within the paraphyletic genus Phytophthora

PLoS One
PMCID: 5846723
PMID: 29529094
DOI: 10.1371/journal.pone.0192502

[…] leaned with Exo-SAP-IT (Thermo Fisher Scientific, Waltham MA, USA) according to manufacturer's instructions and Sanger sequencing performed by the UC Davis UCDNA Sequencing Facility (Davis, CA, USA). Chromaseq was used to call bases and assemble contigs [–]; sequences were uploaded to GenBank (). […]


Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male mediated gene flow to insular populations

PMCID: 5707830
PMID: 29214050
DOI: 10.1186/s40851-017-0084-5

[…] 0 °C were performed. Amplified DNA fragments were purified with isopropanol, and then formamide was added. Sequences were determined on an ABI 3730 DNA Analyzer, assembled and edited with phred/phrap/chromaseq [–], and aligned by using MUSCLE [] in MEGA7 [].Nine Y-linked microsatellite alleles (Y318.1, Y318.2, Y318.4, Y318.6, Y318.9, Y369.1, Y369.4, Y69217.1, and Y15020.1) were determined by using […]


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

[…] s 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 calls of ambiguity minimum secondary peak […]


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

[…] stems 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 MF370333‒MF370336).Sequences were incorporated int […]


An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)

Front Microbiol
PMCID: 5361657
PMID: 28382021
DOI: 10.3389/fmicb.2017.00350

[…] Biosystems, Foster City, CA, USA) using PCR primers (5 μM) at the University of Arizona Genomics Core.An assembly pipeline consisting of phred and phrap (Ewing and Green, ; Ewing et al., ) driven by Chromaseq (Maddison and Maddison, ) in Mesquite v.2.75 (Maddison and Maddison, ) was used to call bases and assemble bidirectional reads into contigs. Base calls were verified by manual inspection of […]


Clarifying the Cryptic Host Specificity of Blastocystis spp. Isolates from Alouatta palliata and A. pigra Howler Monkeys

PLoS One
PMCID: 5215913
PMID: 28056072
DOI: 10.1371/journal.pone.0169637
call_split See protocol

[…] ds were purified using the AxyPrep PCR Clean-up Kit (Axigen Biosciences, CA, USA) and sequenced on both strands by a commercial supplier. Chromatograms were evaluated with Mesquite software using the Chromaseq package [–], with phred and phrap algorithms for base calling, assigning quality values to each one and assembling contigs [–]. […]


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