Molecular Biology & EvolutionDaniel Huson introduces displacement-optimized tanglegrams (DO-tanglegrams), a new approach that applies equally to trees and rooted phylogenetic networks, performing better than cophylo on trees and then NN-tanglegram on networks.
McArthur et al. present piqtree, an easy to use, open-source Python package that provides Python script-based control of IQ-TREEโs phylogenetic inference engine.
@sishuowang & Meade introduce phyloHessian to enable the use of complex mixture substitution models in molecular dating. Empirical analysis of ancient symbiont lineages leads to a revised understanding of their host association origins.
Robbins, Liu & Kelly present RECUR, a method for identifying recurrent amino acid substitutions from multiple sequence alignments that is fast, easy to use, and scalable to thousands of sequences.
Deng et al. present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes.
Martรญ-Gรณmez et al. developed gpmap-tools, integrating models for inference, phenotypic imputation, and error estimation from multiplex assays of variant effect data or natural sequences in the presence of genetic interactions.
GenomeBiolEvolAnchieri et al. benchmark the inference of selection with aDNA-like time series datasets, showing that ApproxWF can accurately estimate selection with datasets of โผ100 individuals when selection is strong.
Ramos-Gonzรกlez et al. present PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships.
Malik et al. present the web-based Structome-AlignViewer, for evaluating structure-aware alignments through spatial mapping of alignment columns to protein structures, and quantitative confidence scoring.
Shankar et al. present the updated MicrobeTrace 2.0 as a next-generation, interoperable tool for genomic epidemiology and data-driven public health response.
