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.

🔗 https://doi.org/10.1093/molbev/msag036

#evobio #molbio #compbio

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.

🔗 https://doi.org/10.1093/molbev/msag028

#evobio #molbio #compbio

Martí-Gómez 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.

🔗 https://doi.org/10.1093/molbev/msag023

#evobio #molbio #compbio

Anchieri et al. benchmark the inference of selection with aDNA-like time series datasets, showing that ApproxWF can accurately estimate selection with datasets of ∼100 individuals when selection is strong.

🔗 https://doi.org/10.1093/gbe/evaf234

#genome #evolution #compbio

Ramos-González et al. present PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships.

🔗 https://doi.org/10.1093/molbev/msag011

#evobio #molbio #compbio

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.

🔗 https://doi.org/10.1093/gbe/evag004

#genome #evolution #compbio

Shankar et al. present the updated MicrobeTrace 2.0 as a next-generation, interoperable tool for genomic epidemiology and data-driven public health response.

🔗 https://doi.org/10.1093/molbev/msaf334

#evobio #molbio #compbio

In 1952, Alan Turing proposed that simple chemical reactions + diffusion could create spots, stripes, and spirals in nature. 70 years later, we're still finding his equations everywhere—from zebrafish stripes to cardiac arrhythmias. Math predicting biology at its finest.

#CompBio #MathBiology #Biophysics

In a new Review, Peede et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods.

🔗 https://doi.org/10.1093/gbe/evaf229

#genome #evolution #compbio

Thawornwattana, Rannala & Yang use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors.

🔗 https://doi.org/10.1093/molbev/msaf327

#evobio #molbio #compbio

Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.

🔗 https://doi.org/10.1093/molbev/msaf313

#evobio #molbio #compbio

#compchem #compbio Good read: Fast Parametrization of Martini3 Models for Fragments and Small Molecules https://pubs.acs.org/doi/10.1021/acs.jctc.5c01178

‪#compchem #compbio Last preprint of the year: "Fast, systematic and robust relative binding free energies for simple and complex transformations : dual-LAO".

https://arxiv.org/abs/2512.17624
Great work by N. Ansari.
(qubit-pharma). Another nice collab with J. Hénin.

‪💫 We just released the weights of the #FeNNixBio1 foundation machine learning model for drug design! 💫

Weights: https://github.com/FeNNol-tools/FeNNol-PMC
FeNNol code: https://github.com/FeNNol-tools/FeNNol
The models are distributed under the open source ASL license (non-commercial academic research). #compchem #compbio

To address uncertainty in model choice for reconstructing population history, Xu et al. introduce a new Bayesian model averaging (BMA) framework.

🔗 https://doi.org/10.1093/molbev/msaf297

#evobio #molbio #compbio

Mirchandani et al. introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST).

🔗 https://doi.org/10.1093/molbev/msaf282

#evobio #molbio #compbio

Szymanski et al. developed quicksand, an open-source Nextflow pipeline designed for rapid and accurate taxonomic classification of mammalian mitochondrial DNA in sedimentary ancient DNA samples.

🔗 https://doi.org/10.1093/molbev/msaf305

#evobio #molbio #compbio #aDNA

Can't wait to read this thriller by Carsten Kutzner that dropped: "Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster" /hj

In seriousness, this sounds like a really cool, and difficult, problem! Looking forward to seeing how they approached it.
#fediscience #compbio

Huang et al. present SAI, a Python package for computing introgression statistics, and demonstrate its application in two datasets.

🔗 https://doi.org/10.1093/molbev/msaf295

#evobio #molbio #compbio

Rahman, Smith & Szpiech present selscan v2.1, a dynamic programming algorithm to improve runtime and memory usage in the calculation of extended haplotype homozygosity.

🔗 https://doi.org/10.1093/molbev/msaf275

#evobio #molbio #compbio