PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Libin, Pieter; Eynden, Ewout Vanden; Incardona, Francesca; Nowé, Ann; Bezenchek, Antonia; Sönnerborg, Anders; Vandamme, Anne‐Mieke; Theys, Kristof; Baele, Guy

doi:10.1093/bioinformatics/btx535

Cited by 20 publications

(22 citation statements)

References 10 publications

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“…VIRULIGN is particularly well suited to study the rapidly growing number of SARS-CoV-2 genomes made available [44], due to its efficient alignment algorithm that has linear computational complexity with respect to the number of sequences studied. Furthermore, VIRULIGN's flexible output formats (e.g., CSV file with headers corresponding to the genome annotation) facilitate its integration into analysis workflows, lowering the threshold for scientists to deliver advanced bioinformatics pipelines [45,46] and databases [47] 5). Table 2 shows the results for the SARS-CoV-2 RefSeq entry (NC_045512.2).…”

Section: Virulign: Codon-correct Multiple Sequence Alignmentsmentioning

confidence: 99%

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Hufsky¹,

Lamkiewicz²,

Almeida³

et al. 2020

Preprint

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SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding, and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are freely available online, either through web applications or public code repositories.

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Section: Virulign: Codon-correct Multiple Sequence Alignmentsmentioning

confidence: 99%

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Hufsky¹,

Lamkiewicz²,

Almeida³

et al. 2020

Preprint

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“…virus and patient data). iTol and PhyloGeoTool are particular examples that address this need by supporting interactive navigation of large phylogenies and exploration associated clinical and epidemiological data [79,80].…”

Section: Visualisation Toolsmentioning

confidence: 99%

Recent advances in computational phylodynamics

Baele

Dellicour

Suchard

et al. 2018

Current Opinion in Virology

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Time-stamped, trait-annotated phylogenetic trees built from virus genome data are increasingly used for outbreak investigation and monitoring ongoing epidemics. This routinely involves reconstructing the spatial and demographic processes from large data sets to help unveil the patterns and drivers of virus spread. Such phylodynamic inferences can however become quite time-consuming as the dimensions of the data increase, which has led to a myriad of approaches that aim to tackle this complexity. To elucidate the current state of the art in the field of phylodynamics, we discuss recent developments in Bayesian inference and accompanying software, highlight methods for improving computational efficiency and relevant visualisation tools. As an alternative to fully Bayesian approaches, we touch upon conditional software pipelines that compromise between statistical coherence and turnaround time , and we highlight the available software packages. Finally, we outline future directions that may facilitate the large-scale tracking of epidemics in near real time.

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“…SpreaD3 allows visualization of phylogeographic reconstructions from models implemented in the software package BEAST (25). PhyloGeoTool is a web application to navigate large phylogenies interactively and to explore associated clinical and epidemiological data (26). TreeLink displays phylogenetic trees alongside metadata in an interactive web application (27).…”

Section: Visualization and Interpretationmentioning

confidence: 99%

Real-Time Analysis and Visualization of Pathogen Sequence Data

Neher

Bedford

2018

J Clin Microbiol

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The rapid development of sequencing technologies has to led to an explosion of pathogen sequence data, which are increasingly collected as part of routine surveillance or clinical diagnostics. In public health, sequence data are used to reconstruct the evolution of pathogens, to anticipate future spread, and to target interventions. In clinical settings, whole-genome sequencing can identify pathogens at the strain level, can be used to predict phenotypes such as drug resistance and virulence, and can inform treatment by linking closely related cases. While sequencing has become cheaper, the analysis of sequence data has become an important bottleneck. Deriving interpretable and actionable results for a large variety of pathogens, each with its own complexity, from continuously updated data is a daunting task that requires flexible bioinformatic workflows and dissemination platforms. Here, we review recent developments in real-time analyses of pathogen sequence data, with a particular focus on the visualization and integration of sequence and phenotype data.

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PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context

Cited by 20 publications

References 10 publications

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Recent advances in computational phylodynamics

Real-Time Analysis and Visualization of Pathogen Sequence Data

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