Cloanalyst statistics

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Cloanalyst specifications

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Unique identifier OMICS_20614
Name Cloanalyst
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Cloanalyst citations

 (5)
library_books

HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope

2018
Nat Commun
PMCID: 5856820
PMID: 29549260
DOI: 10.1038/s41467-018-03565-6

[…] ancestor given the number of mutations observed in the antibody of interest. Reconstruction of the DH270 clonal genealogy and corresponding clonal lineage tree was generated with the software package Cloanalyst, . […]

library_books

Conserved epitope on influenza virus hemagglutinin head defined by a vaccine induced antibody

2017
Proc Natl Acad Sci U S A
PMCID: 5776812
PMID: 29255041
DOI: 10.1073/pnas.1715471115

[…] We used the program Cloanalyst (, ) to annotate isolated paired heavy-light VDJ/VJ sequences, to infer intermediates and the UCA, and to reconstruct the phylogenetic tree of the clonal lineage. […]

library_books

Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations

2017
Nat Commun
PMCID: 5701043
PMID: 29170366
DOI: 10.1038/s41467-017-01336-3

[…] es were isolated via single-cell PCR, . The gene sequences were then computationally analyzed and immunogenetics (gene family and segment IDs, mutation frequency, CDR3 length) determined using rhesus Cloanalyst program–. Antibody sequences were studied using the 2015 Cloanalyst rhesus gene library. Antibody clonal lineages were inferred as sequences that had the same IGHV VDJ rearrangement and CDR […]

library_books

Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV 1 vaccine trial

2017
PLoS Pathog
PMCID: 5342261
PMID: 28235027
DOI: 10.1371/journal.ppat.1006182

[…] nced with a BigDye Sequencing kit (Applied Biosystems) on an ABI 3700 sequencer. VH and VL chain gene rearrangements, clonal relatedness, UCA and intermediate ancestor (IA) inferences were made using Cloanalyst []. […]

library_books

Assigning and visualizing germline genes in antibody repertoires

2015
PMCID: 4528417
PMID: 26194754
DOI: 10.1098/rstb.2014.0240

[…] /cmccoy/ighutil), a simple Smith–Waterman alignment-based program previously used in an evolutionary analysis of immunoglobulin repertoires [], vdj (http://github.com/laserson/vdj), as used in [] and Cloanalyst (v. 2015/1), a model-based approach using algorithms described in []. With the exception of vdj and vdjalign, which used a larger reference dataset, all programs employed the same F + ORF r […]


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