Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific website and not easily reusable or extensible. To address these limitations, we developed heat-tree, a collection of software packages in JavaScript, R, and Python for interactive visualization, manipulation, and editing of phylogenetic trees and their associated metadata. Heat-tree allows for the creation of customizable, web-compatible tree visualizations that can be easily embedded in R Markdown, Jupyter Notebooks, and Quarto documents, as well as directly in HTML/JavaScript applications and websites. The package supports radial and rectangular tree layouts, automated translation of metadata values into visual encodings on the tree, interactive tree editing, and export capabilities for publication-quality figures. All visualization parameters are definable programmatically or interactively using the comprehensive graphical user interface included with each visualization. Heat-tree was designed to be a user-friendly software package for interactive tree viewing, manipulation, editing, and self-contained, embeddable visualization across software environments.

Digital object identifiers (DOIs) are a class of persistent identifier (PID) assigned to an object to ensure that it can always be uniquely identified and, ideally, accessed reliably. Each DOI is a un...

Science has become obsessed with publishing numbers. With this new satirical proposal, have we reached peak metric?

Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens an...

Upon introduction, clonal pathogen populations are expected to go through a genetic bottleneck followed by gradual clonal divergence. Two distinct and purely clonal lineages of the sudden oak death pa...

Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. Although established workflows exist for analysis of single metabarcodes, these are...

The oomycete Phytophthora infestans is a damaging crop pathogen. Here, the authors show that a group of P. infestans secreted enzymes play roles in penetration and colonization of host plants by oxidi...

An open access journal publishing multi-, inter- and transdisciplinary research that addresses global challenges in agriculture and the environment. The editors welcome research from a wide range of f...

Species population sizes fluctuate over time, and these temporal dynamics play a key role in governing the maintenance of biodiversity. Although modeling approaches have been developed to characterize...

Species population sizes fluctuate over time, and these temporal dynamics play a key role in governing the maintenance of biodiversity. Although modeling approaches have been developed to characterize...

We are thrilled to announce that Google Translate has recently added “Deanspeak” to its suite of language-detection tools. In addition to offering ...

Bluesky posts about science garner more likes and reposts than similar ones on X.

Out-of-pocket ACA premium payments will likely increase about 75% on average next year due to Congressional actions.

We conduct a randomized controlled trial to understand how early-2025 AI tools affect the productivity of experienced open-source developers working on their own repositories. Surprisingly, we find th...

Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

The source of the trouble is “paper mills,” businesses or individuals that charge fees to publish fake studies in legitimate journals.

One of the agency’s largest and most storied research facilities will be closed along with most forest research stations

Fungi typically occur in environments where numerous and diverse other microbes occur as well, often resulting in fierce competition for nutrients and habitat. To support fungal fitness in these envir...

Some studies containing instructions in white text or small font — visible only to machines — will be withdrawn from preprint servers.

Research-funding cuts and immigration changes threaten some of America’s economic advantages.

The replication of DNA in Escherichia coli*

Oregon has no reports so far of people contracting the virus. But it's still wise to cover up and prevent bites, health officials say.

Estas diferencias se asociaron a mutaciones y secuencias únicas detectadas mediante análisis genómico y ensayos en microfluidos.Respuesta diferencial en olivo y arándanoLas inoculaciones en ...

An exciting opportunity for an Independent Fellowship in Plant-Associated Microbial Interactions has arisen at the John Innes Centre. To read the full job description for this role…

“There is a lot of pressure to essentially leave the country or not pursue research,” one Ph.D. student says

Experts worry that if vaccination rates do not improve, deadly outbreaks will become the new normal.

The OSU Plant Clinic offers expert analysis, guidance for disease control, and hands-on learning support as part of Oregon State’s larger Extension and research mission.

“There is a lot of pressure to essentially leave the country or not pursue research,” one Ph.D. student says