beast

Bayesian phylogenetic inference for evolutionary analysis of molecular sequences

brewmacoslinux

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Bayesian Evolutionary Analysis Sampling Trees

beastbeaglelogcombinertreeannotator

Run BEAST analysis with an XML configuration file$ beast -seed 12345 myanalysis.xml

Combine multiple BEAST log files and remove burn-in$ logcombiner -burnin 1000 run1.log run2.log combined.log

Generate maximum clade credibility tree from posterior samples$ treeannotator -burnin 1000 -heights mean output.trees output.tree