Evidence map›Paper›PMID 40640711›Full record

ArticleBMC bioinformatics2025

PhyloScape: interactive and scalable visualization platform for phylogenetic trees.

Jiajia Wang, Bo Zhang, Linglu Zheng, Yan Chen, Chunyang Zhang, Guojiao Lin, Zhen Meng, Xuezhi Wang, Yuanchun Zhou

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Jiajia Wang *Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Bo Zhang *Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Linglu Zheng *Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Yan ChenComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Chunyang ZhangComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Guojiao LinComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Zhen MengComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China. zhenm99@cnic.cn.
Xuezhi WangComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.
Yuanchun ZhouComputer Network Information Center, Chinese Academy of Sciences, Beijing, 100083, China.

Funding

Informatization Plan of Chinese Academy of Sciences CAS-WX2023ZX01-11the Strategic Priority Research Program of the Chinese Academy of Sciences XDB31030000the Strategic Priority Research Program of the Chinese Academy of Sciences XDB38030300
6 · The paper itself

Abstract

backgroundWith the accumulation of phylogenomic data and the growing demand for bioinformatics analyses, it has become increasingly important and complex to construct evolutionary relationships for different research purposes. Therefore, the ability to support multiple scenarios has become an essential need for phylogenetic visualization.

resultsIn this study, we present PhyloScape, a web-based application for interactive visualization of phylogenetic trees that can be used stand-alone or as a toolkit deployed on the users' website. The platform supports customizable multiple visualization features and is equipped with a flexible metadata annotation system, providing researchers with publishable, interactive views of trees. PhyloScape extensions include views of amino acid identity, geometry, and protein structure, which are applicable to various areas such as microbial taxonomy, pathogen phylogeny, and plant conservation. Trees published on the website can be efficiently shared and integrated into the users' own system via a unique address.

conclusionsAs a scalable platform, PhyloScape provides a variety of online plug-ins that users can easily combine for specific scenarios. PhyloScape is freely available at http://darwintree.cn/PhyloScape .

Indexed as

Computational BiologyPhylogenySoftwareComputer GraphicsInternetUser-Computer InterfaceEvolutionJavaScript libraryPhylogenetic tree visualizationPlug-inWeb application

Identifiers

PMID40640711
PMCPMC12243251

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.