Heat-tree: Cross-Platform Software for Interactive and Embeddable Phylogenetic Tree Visualization and Editing | PhytoFrontiers™

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.

doi.org

Understanding DOIs for preprints: how openRxiv assigns and manages persistent identifiers - openRxiv

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...

openrxiv.org

Introducing the j-metric: a true measure of what matters in academia

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

nature.com

PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification

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...

biorxiv.org

Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology®

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...

apsjournals.apsnet.org

Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology®

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...

apsjournals.apsnet.org

Oomycetes manipulate plant innate immunity through galacturonide oxidases - Nature Communications

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...

doi.org

CABI Agriculture and Bioscience - Special Issues: Invasive Pathogens| CABI Digital Library

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...

cabidigitallibrary.org

Genomic demography predicts community dynamics in a temperate montane forest

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...

science.org

Genomic demography predicts community dynamics in a temperate montane forest

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...

science.org

Faculty, Rejoice: Gmail Can Now Translate “Deanspeak”

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

mcsweeneys.net

Research posts on Bluesky are more original — and get better engagement

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

nature.com

Liz Weston: Married couple faces likely 300% increase in their medical insurance premiums

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

oregonlive.com

Measuring the Impact of Early-2025 AI on Experienced Open-Source Developer Productivity

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...

metr.org

A diverse and distinct microbiome inside living trees - Nature

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...

nature.com

Scientific Journals Can’t Keep Up With Flood of Fake Papers

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

wsj.com

Dryad | Data -- Deep-learning-based annotation of 230 superasterid genomes reveals a harmonized dataset of 91,366 NLRs

doi.org

USDA reorganization will cut agricultural and forest research

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

science.org

AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins

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...

biorxiv.org