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- BEAST Software - Bayesian Evolutionary Analysis Sampling Trees | BEAST . . .
BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run BEAST-Users mailing list Users are strongly advised to join the BEAST mailing-list This will be used to announce new versions and advise users about bugs and problems
- First Tutorial | BEAST Documentation
BEAST can also import FASTA files (as long as the sequences have been aligned) or BEAST XML files (in which case the data will imported but the models and settings will not) Once loaded, the alignment will be displayed in the main window in a table: If you want to look at the actual alignment, double click on the row in the table
- Frequently Asked Questions | BEAST Documentation
We have renamed the release that would have been called BEAST v1 10 5 as BEAST X v10 5 0 This is to distinguish it from the independent project called BEAST 2 – see: https: www beast2 org These projects have been running in parallel for many years which has restricted this BEAST project to using the v1 major release version and only
- Estimating rates and dates from time-stamped sequences | BEAST . . .
To inform BEAUti BEAST about the sampling dates of the sequences, go to the Tips menu and select the “Use tip dates” option By default all the taxa are assumed to have a date of zero (i e the sequences are assumed to be sampled at the same time; BEAST considers the present or most recent sampling time as time 0)
- Phylogeographic diffusion in discrete space | BEAST Documentation
The first step will be to convert an alignment file in fasta format into a BEAST XML input file This is done using the program BEAUti (this stands for Bayesian Evolutionary Analysis Utility) This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis
- Downloading and installing BEAST on UNIX Linux
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)
- BEAGLE | BEAST Documentation
Using BEAGLE with BEAST 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
- LogCombiner | BEAST Documentation
BEAST will often write numbers in scientific notation to maintain precision Some software programs may have problems with this, so this option will convert these to decimal numbers Renumber output states If selected, this will renumber the output states to a sequential series Resample states at lower frequency
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