PhyD3 statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool PhyD3
info

Tool usage distribution map

This map represents all the scientific publications referring to PhyD3 per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Tree visualization chevron_right
Want to access the full stats & trends on this tool?

PhyD3 specifications

Information


Unique identifier OMICS_15753
Name PhyD3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format SVG, PNG, XML
Operating system Unix/Linux
Programming languages Javascript
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Michiel Van Bel

Information


Unique identifier OMICS_15753
Name PhyD3
Interface Web user interface
Restrictions to use None
Output format SVG, PNG, XML
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Michiel Van Bel

Publication for PhyD3

PhyD3 citations

 (5)
library_books

Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects

2018
Interdiscip Sci
PMCID: 5838210
PMID: 29383564
DOI: 10.1007/s12539-018-0282-7

[…] id sites, which can be configured dynamically to match user preferences. It also allows downloading a PDF or PNG file with the result. Another tab that includes a viewer is the “Tree View”. Using the PhyD3 JavaScript library (https://phyd3.bits.vib.be/), this view shows an unrooted phylogram/cladogram for each tree available in the record. It can be also configured and the result can be downloaded […]

library_books

Gene3D: Extensive prediction of globular domains in proteins

2017
Nucleic Acids Res
PMCID: 5753370
PMID: 29112716
DOI: 10.1093/nar/gkx1069

[…] is useful for a number of tasks, including identifying missed domain assignments, potential gene annotation artifacts and also genuine domain architecture changes. To do this we have made use of the PhyD3 JavaScript library (), which allows us to display domain architectures for a gene family along with duplication events and their associated confidence values. PhyD3 allows us to easily display t […]

library_books

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

2017
Nucleic Acids Res
PMCID: 5753339
PMID: 29069403
DOI: 10.1093/nar/gkx1002

[…] ersions relied on the externally developed software tool Archaeopteryx (previously ATV) () to display these phylogenetic trees. However, as Archaeopteryx is a Java applet-based solution, we developed PhyD3 (), an easily extensible JavaScript based alternative that can be used to add a variety of data charts to phylogenetic trees. PhyD3 can be used to visualize species trees as well as gene family […]

library_books

N protein from lambdoid phages transforms NusA into an antiterminator by modulating NusA RNA polymerase flap domain interactions

2015
Nucleic Acids Res
PMCID: 4499122
PMID: 25990722
DOI: 10.1093/nar/gkv479

[…] To test whether the combination of rpoB-G1045D (E. coli RNAP β-subunit) and nusA–V8A mutants induces synthetic defects in N-mediated in vivo antitermination, pHYD3011 plasmid expressing either WT or V8A NusA was transformed into the strains, RS1452 (having rpoB-G1045D and Plac-H-19B nutR-TR′-lacZYA reporter cassette) and RS1018 (having WT rpoB and Plac-H-1 […]

library_books

Redundancy of primary RNA binding functions of the bacterial transcription terminator Rho

2014
Nucleic Acids Res
PMCID: 4150792
PMID: 25081210
DOI: 10.1093/nar/gku690

[…] xpressed from pCL1920, and this process replaced the shelter plasmid expressing the rho.To study the effects of nusG mutants (Figure ), the strains RS1490, RS1458 and RS1430 were transformed with the pHYD3011 plasmids expressing mutant and WT NusG. In these strains, WT Rho was expressed from a low copy pCL1920 plasmid. The β-galactosidase activities were measured using a SpectraMax Plus microtiter […]


Want to access the full list of citations?
PhyD3 institution(s)
VIB-BITS Facility, Ghent, Belgium; Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

PhyD3 reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhyD3