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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

 (18)
call_split

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
PMCID: 5658410
PMID: 29074854
DOI: 10.1038/s41598-017-14095-4
call_split See protocol

[…] 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., drms were analyzed in the protease and rt […]

library_books

A22 Increase in the numbers of HIV 1 non B subtypes and potential recombinant forms circulating among Slovenian MSM in recent years

2017
PMCID: 5565932
PMID: 28845249
DOI: 10.1093/ve/vew036.021

[…] were obtained for 252 msm patients who were included in the present study. sequences were analyzed using the following automatic subtyping tools: rega 2.0, rega 3.0, comet hiv-1 1.0, jphmm, and scueal. sequences that gave divergent subtyping results were considered to be potential recombinant forms. temporal trend of the proportion of non-b and potential recombinant sequences (both combined […]

library_books

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

2017
PMCID: 5221827
PMID: 28068413
DOI: 10.1371/journal.ppat.1006000

[…] 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 […]

library_books

HIV Drug Resistance Among Children Initiating First Line Antiretroviral Treatment in Uganda

2016
PMCID: 4931746
PMID: 26723018
DOI: 10.1089/aid.2015.0215

[…] biological laboratories sa, france) for data storage. drug resistance mutations (drms) were scored according to the 2010 international aids society–usa list. subtypes were determined using the scueal hiv-1 subtyping tool and additional analysis with the rega algorithm version 2.0 once required., group comparisons for categorical data were performed using the chi-square or fisher's exact […]

library_books

Proceedings of The 8th Romanian National HIV/AIDS Congress and The 3rd Central European HIV Forum

2016
PMCID: 4928154
PMID: 27356504
DOI: 10.1186/s12879-016-1480-8

[…] were obtained for 252 msm patients which were included in the present study. sequences were analyzed using the following automatic subtyping tools: rega 2.0, rega 3.0, comet hiv-1 1.0, jphmm and scueal. sequences that gave divergent subtyping results were considered to be potential recombinant forms. temporal trend of the proportion of non-b and potential recombinant sequences (both combined […]

library_books

Characterization of HIV Transmission in South East Austria

2016
PMCID: 4788428
PMID: 26967154
DOI: 10.1371/journal.pone.0151478

[…] using partial hiv-1 pol sequences including the regions encoding reverse transcriptase and protease. all sequences were subtyped using the subtype classification using evolutionary algorithms (scueal) program []., all sequences were made publicly available. the genbank accession numbers for the pol sequences included in this analysis are ku574281—ku574539. the study was conducted according […]


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

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