SCUEAL protocols

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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

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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 in pipelines

 (2)
2017
PMCID: 5658410
PMID: 29074854
DOI: 10.1038/s41598-017-14095-4

[…] 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 […]

2015
PMCID: 4340098
PMID: 25889106
DOI: 10.1186/s12985-015-0244-1

[…] classification using evolutionary algorithms (scueal) was used to test for both intra and inter subtype recombinants in the partial hiv-1 pol and in sequences (http://www.datamonkey.org/dataupload_scueal.php) []., the 2010 hiv-1 group m reference sequence dataset (n = 39), from the lanl database (http://www.hiv.lanl.gov/), was used to subtype our sequences, using phylogenetic inference. […]


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SCUEAL in publications

 (17)
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 […]

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 […]

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 […]

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 […]

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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