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

2017 ◽  
Vol 33 (18) ◽  
pp. 2946-2947 ◽  
Author(s):  
Łukasz Kreft ◽  
Alexander Botzki ◽  
Frederik Coppens ◽  
Klaas Vandepoele ◽  
Michiel Van Bel
Keyword(s):  
Phylogenetic Tree ◽  
Functional Genomics ◽  
Data Visualization ◽  
Tree Viewer

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

2017 ◽  
Author(s):  
Łukasz Kreft ◽  
Alexander Botzki ◽  
Frederik Coppens ◽  
Klaas Vandepoele ◽  
Michiel Van Bel
Keyword(s):  
Phylogenetic Tree ◽  
Functional Genomics ◽  
Open Source ◽  
Web Sites ◽  
Phylogenetic Trees ◽  
Biological Data ◽  
Web Technologies ◽  
Link Type ◽  
Current Implementation ◽  
Tree Viewer

AbstractMotivation:Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise 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.Results: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 visualisation 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.Availability: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/.Contact:[email protected]

scholarly journals ggtreeExtra: Compact visualization of richly annotated phylogenetic data

2021 ◽  
Author(s):  
Guangchuang Yu ◽  
shuangbin xu ◽  
Zehan Dai ◽  
Pingfan Guo ◽  
Xiaocong Fu ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Data Visualization ◽  
Heterogeneous Data ◽  
Data Types ◽  
Specific Data ◽  
Domain Specific ◽  
Phylogenetic Data ◽  
Evolutionary Context ◽  
Tree Data

Abstract We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioocnductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It extends the applications of phylogenetic tree in different disciplines by making more domain specific data to be available to visualize and interpret on the evolutionary context.

scholarly journals ggtreeExtra: Compact visualization of richly annotated phylogenetic data

2021 ◽  
Author(s):  
Shuangbin Xu ◽  
Zehan Dai ◽  
Pingfan Guo ◽  
Xiaocong Fu ◽  
Shanshan Liu ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Data Visualization ◽  
Heterogeneous Data ◽  
Data Types ◽  
Specific Data ◽  
Domain Specific ◽  
Phylogenetic Data ◽  
Evolutionary Context ◽  
Tree Data

Abstract We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioconductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It extends the applications of phylogenetic tree in different disciplines by making more domain specific data to be available to visualize and interpret on the evolutionary context.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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