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alakazam specifications

Information


Unique identifier OMICS_21399
Name alakazam
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Other
Computer skills Advanced
Stability No
Maintained No

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alakazam citations

 (5)
library_books

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence

2017
Sci Rep
PMCID: 5288646
PMID: 28148967
DOI: 10.1038/srep41531

[…] ameters were selected after visualisation of distance to nearest neighbour plots. Testing for significant differences in Ig diversity between the infection phases was conducted using testDiversity in Alakazam v.0.2.3 with 1000 bootstrap replicates. The selection pressure on Ig transcripts was estimated using observed and expected mutations and the Bayesian estimation of Antigen-driven SELectIoN (B […]

call_split

Investigating the effect of AS03 adjuvant on the plasma cell repertoire following pH1N1 influenza vaccination

2016
Sci Rep
PMCID: 5110968
PMID: 27849037
DOI: 10.1038/srep37229
call_split See protocol

[…] om PCR error, only clusters containing at least 50 sequences were used to create lineage trees. Subsampling down to 50 sequences was performed if there were more. Lineage trees were created using the alakazam software package. […]

library_books

Generation of Long Lived Bone Marrow Plasma Cells Secreting Antibodies Specific for the HIV 1 gp41 Membrane Proximal External Region in the Absence of Polyreactivity

2016
J Virol
PMCID: 5021391
PMID: 27466419
DOI: 10.1128/JVI.01089-16

[…] 3 for mouse 2 for detailed investigation. Downstream analyses were performed using tools from the Change-O suite (version 0.3.3-2016.04.22) and the associated R packages SHazaM (shazam_0.1.2.999) and alakazam (alakazam_0.2.3.999) (). Detailed information is available at http://immcantation.readthedocs.io. Sequences were assigned to the same clone when they shared the same IGHV gene, IGHJ gene, IGL […]

library_books

Repertoire comparison of the B cell receptor encoding loci in humans and rhesus macaques by next generation sequencing

2016
PMCID: 4973324
PMID: 27525066
DOI: 10.1038/cti.2016.42

[…] s. Furthermore, clustering was used to counteract potential dominance of expanded B-cell clones, and to eliminate sequence errors that arose during amplification and sequencing. We used the R-package alakazam in order to characterize clustered populations by calculating the Hill diversity indices, as well as Shannon's entropy and evenness metrics (). […]

call_split

B cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross reactive B cell activation

2016
Genome Med
PMCID: 4910312
PMID: 27312086
DOI: 10.1186/s13073-016-0322-z
call_split See protocol

[…] ng the prcomp function in the “stats” package []. Rarefaction analysis was conducted using the “iNEXT” package [] using a q value of 0.Lineage trees were constructed from sequence clusters using the “alakazam” package []. Lineages were only generated for clusters with at least 50 or 25 sequences depending on the analysis, and subsampling was performed if there were more than this number. The diver […]

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alakazam institution(s)
Yale University
alakazam funding source(s)
This work was supported by the National Institutes of Health [R01AI104739 to S.H.K.; T15LM07056 to N.T.G., T15LM07056 to J.A.V.H. from National Library of Medicine (NLM)] and by the United States-Israel Binational Science Foundation [2013395 to G.Y. and S.H.K.].

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