Molecular phylogenetics: principles and practice

Z Yang, B Rannala - Nature reviews genetics, 2012 - nature.com
Phylogenies are important for addressing various biological questions such as relationships
among species or genes, the origin and spread of viral infection and the demographic …

TAPAS: an open-source software package for translational neuromodeling and computational psychiatry

S Frässle, EA Aponte, S Bollmann… - Frontiers in …, 2021 - frontiersin.org
Psychiatry faces fundamental challenges with regard to mechanistically guided differential
diagnosis, as well as prediction of clinical trajectories and treatment response of individual …

[HTML][HTML] First Sagittarius A* event horizon telescope results. III. Imaging of the galactic center supermassive black hole

K Akiyama, A Alberdi, W Alef, JC Algaba… - The Astrophysical …, 2022 - iopscience.iop.org
First Sagittarius A* Event Horizon Telescope Results. III. Imaging of the Galactic Center
Supermassive Black Hole - IOPscience Skip to content IOP Science home Accessibility Help …

First Sagittarius A* event horizon telescope results. IV. Variability, morphology, and black hole mass

K Akiyama, A Alberdi, W Alef, JC Algaba… - The Astrophysical …, 2022 - iopscience.iop.org
In this paper we quantify the temporal variability and image morphology of the horizon-scale
emission from Sgr A*, as observed by the EHT in 2017 April at a wavelength of 1.3 mm. We …

dynesty: a dynamic nested sampling package for estimating Bayesian posteriors and evidences

JS Speagle - Monthly Notices of the Royal Astronomical Society, 2020 - academic.oup.com
We present dynesty, a public, open-source, python package to estimate Bayesian posteriors
and evidences (marginal likelihoods) using the dynamic nested sampling methods …

[PDF][PDF] Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

MA Suchard, P Lemey, G Baele, DL Ayres… - Virus …, 2018 - academic.oup.com
Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package
has become a primary tool for Bayesian phylogenetic and phylodynamic inference from …

The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the substitution rate

JH Tay, AF Porter, W Wirth… - Molecular Biology and …, 2022 - academic.oup.com
The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly
generated genome data. These data have revealed the emergence of lineages with …

Model selection may not be a mandatory step for phylogeny reconstruction

S Abadi, D Azouri, T Pupko, I Mayrose - Nature communications, 2019 - nature.com
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …

Species tree inference with BPP using genomic sequences and the multispecies coalescent

T Flouri, X Jiao, B Rannala… - Molecular biology and …, 2018 - academic.oup.com
The multispecies coalescent provides a natural framework for accommodating ancestral
genetic polymorphism and coalescent processes that can cause different genomic regions …

Ten millennia of hepatitis B virus evolution

A Kocher, L Papac, R Barquera, FM Key, MA Spyrou… - Science, 2021 - science.org
Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health
problem, but its past diversity and dispersal routes are largely unknown. We generated HBV …