SCUEAL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SCUEAL
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Tool usage distribution map

This map represents all the scientific publications referring to SCUEAL per scientific context
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Associated diseases

This word cloud represents SCUEAL usage per disease context
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Popular tool citations

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Protocols

SCUEAL specifications

Information


Unique identifier OMICS_06321
Name SCUEAL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Versioning


No version available

Documentation


Information


Unique identifier OMICS_06321
Name SCUEAL
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

Documentation


Publication for SCUEAL

SCUEAL citations

 (26)
call_split

HIV 1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

2018
PLoS One
PMCID: 5919638
PMID: 29698470
DOI: 10.1371/journal.pone.0196670
call_split See protocol

[…] rug-resistance mutations (SDRMs) on the WHO list to unify TDR reporting between programs and countries [].The HIV-1 subtype was determined by using Rega version 3.0, Comet version 2.2, jpHMM-HIV, and SCUEAL [–].Fisher’s exact test was used for categorical data and t-statistics for continuous data using OpenEpi version 3.01; associations with p < 0.05 were considered significant []. […]

library_books

A high HIV 1 strain variability in London, UK, revealed by full genome analysis: Results from the ICONIC project

2018
PLoS One
PMCID: 5794160
PMID: 29389981
DOI: 10.1371/journal.pone.0192081

[…] ference lies on the prevalence of CRFs, which was 6.2% in that report in contrast to the 18.1% (3-fold higher) presented here. We demonstrate here how using the pol sequence alone, in this case using SCUEAL as Dolling and colleagues did, underestimated the proportion of CRFs–other subtyping tools, such as COMET, will face other limitations depending on the exact subtyping algorithm. This highlight […]

library_books

Gag P2/NC and pol genetic diversity, polymorphism, and drug resistance mutations in HIV 1 CRF02_AG and non CRF02_AG infected patients in Yaoundé, Cameroon

2017
Sci Rep
PMCID: 5658410
PMID: 29074854
DOI: 10.1038/s41598-017-14095-4

[…] methods using the MEGA.v.5 software. The reliability of the branching orders was determined using 70% bootstrap robustness for subtype assignation,. Recombination among HIV-1 subtypes was assessed by SCUEAL, COMET, SimPlot, Splitstree, and Rega subtyping tool v.3. The results obtained using each of the five genotyping tools were similar and concordant. […]

call_split

Social and Genetic Networks of HIV 1 Transmission in New York City

2017
PLoS Pathog
PMCID: 5221827
PMID: 28068413
DOI: 10.1371/journal.ppat.1006000
call_split See protocol

[…] stage at diagnosis was assigned using BED testing, which is capable of providing a reasonable picture of HIV population-level incidence in the United States [, ]. HIV-1 subtyping was performed using SCUEAL []. For the purpose of this analysis, HIV-1 sequences were classified into B or non-B subtypes. Multivariate and univariate logistic regression analysis was used to model the probability of an […]

library_books

From antiretroviral therapy access to provision of third line regimens: evidence of HIV Drug resistance mutations to first and second line regimens among Ugandan adults

2016
BMC Res Notes
PMCID: 5180399
PMID: 28010730
DOI: 10.1186/s13104-016-2309-7

[…] ABI 3500 machine (Applied Biosystems). Sequences were base-called using Sequencher v5.2.4 and sequence alignments performed using BioEdit v7.2.5 [] and SeaView v4.0 []. HIV-1 subtyping was done using SCUEAL and REGA online software [], and Recombinant Identification Program (RIP). Drug resistance mutations (DRMs) were interpreted using the Stanford HIVdb Program. Assigned DRMs were interpreted usi […]

call_split

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

2016
Sci Rep
PMCID: 5027562
PMID: 27642070
DOI: 10.1038/srep32251
call_split See protocol

[…] vrdb.org). Sequences cover protease and 900 bases of reverse transcriptase. After age, sex, risk group and ethnicity were attached, the data were anonymised and delinked. Subtypes were assigned using SCUEAL and REGA. The three most common subtypes were B (48.6%), C (24.4%), and A1 (4.0%). Ethical approval was given by the London Multicentre Research Ethics Committee (MREC/01/2/10; 5 April 2001).As […]


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SCUEAL institution(s)
Department of Medicine, University of California San Diego, La Jolla, CA, USA

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