Some notes on pattern compression and speeding up BEAST analysis
Pattern compression for fun and profit by Andrew Rambaut & Philippe Lemey To calculate the likelihood of a tree given a sequence alignment, the log likelihood of each site (column in the alignment) is evaluated independently and then summed across all sites in the alignment. The likelihood of any...
BEAST X (v10.5.0-beta3) released
We are pleased to announce the release of BEAST X (v10.5.0-beta3)
A less-than-brief, non-comprehensive, introduction to BEAST development BEAST is scientific software for statistical analyses. This means there are many things you will eventually need to know. And this cannot be stressed enough, you don’t need to know all this right now! The purpose of this document is to provide...
Ebola Virus Local Clock Analysis
In 2014 there was an outbreak of Ebola virus disease in the Democratic Republic of Congo. When the first genome sequences were published (Maganga et al. 2014) it was noticed that the amount of divergence from the earliest EBOV genomes from the 1970s was considerably less than for the West...
Measuring BEAST performance
When running BEAST it reports the time taken to calculate a certain number of states (e.g., minutes/million states). It is obviously tempting to compare this time between runs as a measure of performance. However, unless you are testing the performance of the same XML file on different hardware or for...
BEAST v1.10.4 released
We are pleased to announce the release of BEAST v1.10.4 BEAST v1.10.4 fixes a bug when trying to specify a burnin on the command line version of LogCombiner. It also introduces two new command line options specific to BEAGLE v3.1 (-beagle_threading_off and -beagle_thread_count). Download BEAST v1.10.4...
BEAST v1.10.3 released
We are pleased to announce the release of BEAST v1.10.3 BEAST v1.10.3 fixes an important bug where performance was degraded when using BEAGLE 3 on CPUs (compared with using BEAGLE 2 or using GPUs). Download BEAST v1.10.3 binaries for Mac, Windows and UNIX/Linux
BEAST v1.10.0 released
We are pleased to announce the release of BEAST v1.10 BEAST v1.10.0 is a major new version with many new features which focus on flexibility of model specification, integration of different data sources, and increasing the speed and efficiency of sampling. The new version coincides with the...
BEAST v1.8.4 released
BEAST v1.8.4 has been released: 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...
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