Résultats de recherche
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without ...
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs. The current version of BEAGLE will only work with BEAST v1.6 or later.
First Tutorial. An introductory tutorial to getting started with BEAST. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST.
BEAST can be downloaded from the following link: BEAST X v10.5.0-beta5 - UNIX/Linux version 46.2MB; This will download a compressed tar archive (a ‘.tgz’ file).
Tracer. Tracer is a graphical tool for visualization and diagnostics of MCMC output. Tracer (now at version 1.7.2) is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory ...
Phylogeographic diffusion in discrete space. This chapter provides a step-by-step tutorial on reconstructing the spatial dispersal and cross-species dynamics of rabies virus (RABV) in North American bat populations based on a set of 372 nucleoprotein gene sequences (nucleotide positions: 594–1353). The data set comprises a total of 17 bat ...
17 juin 2016 · Download BEAST v1.8.4 binaries for Mac, Windows and UNIX/Linux. Version 1.8.4 released 17th June 2016. New Features: New structured list of citations printed to screen before running. Option ('-citation_file') to write citation list to file. Option in BEAUti Priors panel to set parameters to 'Fixed Value'.
Installing BEAST. BEAST has been developed in Java, which allows the same code to run on any platform that has the Java software installed. We have also created packages for each of the common operating systems to provide a user-interface that is ‘native’ and familiar.
Features. Cross-platform graphical tree display. Three different tree styles: rectangular, polar and radial. Display of node heights, branch lengths, support values and other annotations. Node height range bars if available. Collapse of clades into triangles. Colouring of branches and tip labels. Colouring by annotation (for example, support ...
Installing BEAST. Unzip the downloaded compressed ZIP archive (currently BEAST.v10.5.0-beta5.zip). The unzipped files contain executable binaries for BEAST, BEAUti, LogCombiner, TreeAnnotator and TreeStat. Double-clicking on those files will automatically start the corresponding program. BEAGLE acceleration library
