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jsPhyloSVG specifications

Information


Unique identifier OMICS_04258
Name jsPhyloSVG
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.55
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Samuel A. Smits <>

Publication for jsPhyloSVG

jsPhyloSVG in pipeline

2016
PMCID: 5104318
PMID: 27832061
DOI: 10.1371/journal.pcbi.1005128

[…] libraries, such as d3.js and biojs [,], are useful sources of visualization methods to display all or selected subsets of large, complex, and heterogeneous biological data sets []. for example, jsphylosvg [] draws phylogenetic trees and cytoscape.js [] draws networks. often an artistically talented student can be recruited to help with this, but consider hiring a professional consultant […]


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jsPhyloSVG in publications

 (6)
PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0

[…] estimation of the mean genome length and for the estimation of relative abundance and size for each taxon. the phylogenetic tree were generated by an open-source javascript library called jsphylosvg. the phylogenetic trees were based on the reference sequences and the kogelberg biosphere reserve virome sequences, and computed with 100 bootstraps. further analysis of the sequences […]

PMCID: 5224473
PMID: 27899609
DOI: 10.1093/nar/gkw1027

[…] 2.1.0) (), bwa (version 0.7.9) (), faqcs (version 1.33) (), fasttree (version 2.1) (), gottcha (version 1.0b) (), idba_ud (version 1.1.1) (), spades (version 3.5.0) (), jbrowse (version 1.11.6) (), jsphylosvg (version 1.55) (), kraken (version 0.10.4-beta) (), kronatools (version 2.4) (), metaphlan(version 1.7.7) (), mummer3 (version 3.23) (), phage_finder (version 2.1) (), phame (biorxiv […]

PMCID: 5104318
PMID: 27832061
DOI: 10.1371/journal.pcbi.1005128

[…] libraries, such as d3.js and biojs [,], are useful sources of visualization methods to display all or selected subsets of large, complex, and heterogeneous biological data sets []. for example, jsphylosvg [] draws phylogenetic trees and cytoscape.js [] draws networks. often an artistically talented student can be recruited to help with this, but consider hiring a professional consultant […]

PMCID: 4682392
PMID: 26678286
DOI: 10.1186/1471-2164-16-S12-S8

[…] omega version 1.2.0 []. the phylogenetic inference was done in by phyml 3.0 [] (model gtr + g + i) with user defined bootstrap iterations. the circular phylogenetic tree topology is generated by jsphylosvg library []., we implemented bootscan [] and simplot [] methods in evidence to detect possible recombination events and graphically present the results. briefly, multiple sequence […]

PMCID: 3852387
PMID: 24142924
DOI: 10.1534/g3.113.008185

[…] backend, blast service using the ruby-based sequenceserver (a. priyam, b. j. woodcroft, y. wurm, unpublished data) in conjunction with ncbi blast+ (; ), graphical gene tree rendering using the jsphylosvg javascript library (), jalview 2 () applet as the alignment viewer, and gbrowse 2 () as the genome annotation viewer., for inference of the species phylogeny, we performed maximum […]


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jsPhyloSVG institution(s)
Department of Biological Sciences, San José State University, San José, CA, USA

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