PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Bioinformatics
Lukasz KreftMichiel Van Bel

Abstract

Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/ . klaas.vandepoele@ugent.vib.be or michiel.vanbel@ugent.vib.be. Supplementary data ar...Continue Reading

References

Oct 29, 2009·BMC Bioinformatics·Mira V Han, Christian M Zmasek

❮ Previous
Next ❯

Citations

Nov 8, 2017·Nucleic Acids Research·Tony E LewisJonathan Lees
Oct 27, 2017·Nucleic Acids Research·Michiel Van BelKlaas Vandepoele
May 23, 2019·Nucleic Acids Research·Balakrishnan SubramanianWei-Hua Chen
Sep 29, 2019·Database : the Journal of Biological Databases and Curation·Lingfeng MaoLongjiang Fan
May 8, 2020·International Journal of Systematic and Evolutionary Microbiology·Michio SuzukiKen Maeda
Nov 17, 2019·The FEBS Journal·Antonio J M RibeiroJanet M Thornton
May 3, 2018·Nucleic Acids Research·Sebastian Proost, Marek Mutwil
Aug 21, 2019·Frontiers in Public Health·Kristof TheysGuy Baele
Dec 11, 2019·Database : the Journal of Biological Databases and Curation·Muniba FaizaYonghua Wang
Jun 11, 2020·Archives of Microbiology·Hilal Ay
Apr 17, 2019·Plant Methods·Ramin Rahni, Kenneth D Birnbaum
Feb 26, 2019·Database : the Journal of Biological Databases and Curation·Tian LiYuan-Yi Peng
May 18, 2019·Nature Communications·Jan P Meier-Kolthoff, Markus Göker
Nov 14, 2018·Bioinformatics·Alex Warwick VesztrocyHenning Redestig
Nov 4, 2020·International Journal of Systematic and Evolutionary Microbiology·Jiajie ZhangZong-Jun Du
Nov 26, 2020·Nucleic Acids Research·Guignon ValentinRouard Mathieu
Feb 26, 2021·International Journal of Systematic and Evolutionary Microbiology·Huda MahmoudSusan Eapen
Apr 29, 2021·International Journal of Systematic and Evolutionary Microbiology·Huda MahmoudLiny Jose
May 14, 2021·Systematic Biology·William J BakerFélix Forest
Jul 2, 2021·Nucleic Acids Research·François BucchiniKlaas Vandepoele
Aug 20, 2021·Journal of Invertebrate Pathology·Shaohui WuDavid I Shapiro-Ilan
Sep 21, 2021·International Journal of Systematic and Evolutionary Microbiology·Wan-Ni LuWen-Jun Li

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.