Cloanalyst statistics

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Cloanalyst specifications

Information


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 in publications

 (5)
PMCID: 5856820
PMID: 29549260
DOI: 10.1038/s41467-018-03565-6

[…] 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, ., the complexes analyzed in this study were superposed by least squares fitting in coot or pymol. all graphical representations with protein crystal structures, including stereo images, […]

PMCID: 5776812
PMID: 29255041
DOI: 10.1073/pnas.1715471115

[…] select for resistance mutations not previously fixed. vaccines designed to elicit polyclonal responses targeting more than one conserved epitope might avoid such an outcome., 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., we obtained monoclonal […]

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

[…] or ≥2 antibodies with the same vh and jh rearrangement, and hcdr3 length, paired with the same light chain were counted as a single unique antibody. antibody immunogenetics were inferred by cloanalyst software program , abs, antibodies; env, envelope, we isolated 415 total antibodies from 16 adult rhesus macaques vaccinated with ch505 tf alone or sequential envelope regimens […]

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

[…] 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 []., pcr-amplifed sequences were transiently expressed as previously described []. briefly, linear expression cassettes were constructed by placing the pcr-amplified vh and vl chain genes […]

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

[…] 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 […]


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