Post date: Jul 17, 2020 9:12:55 PM
Filtering scripts can be found here: /uufs/chpc.utah.edu/common/home/gompert-group1/data/aspen/gbs_pando_plus/Variants_mem_bcftools
BEAST
BEAST is not a black-box into which you can put your data and expect an
easily interpretable answer. It requires careful inspection of the output
to check that it has performed correctly and usually will need tweaking,
adjustment and a number of runs to get a valid answer. Sorry.
Convert sequences from NEXUS to XML format:
java -cp lib/launcher.jar beast.app.beauti.BeautiLauncher
Run BEAST:
java -jar lib/launcher.jar input.xml (input.xml is converted file)
They reccomend to install the BEAGLE library. (BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.)
BEAST is an extremely complex program and as such will inevitably have
bugs. Please email us to discuss any problems:
<r.bouckaert@auckland.ac.nz>
<alexei@cs.auckland.ac.nz>
<a.rambaut@ed.ac.uk>
<msuchard@ucla.edu>
The BEAST users' mailing-list
<https://groups.google.com/forum/#!forum/beast-users>
The website for beast is here:
<http://beast2.org/>