Post date: Oct 08, 2020 8:54:53 PM
Run 9 -
Log Combiner
Use log combiner to combine chain results together. Log combiner is a program you downloaded along with the other Beast programs. It is simple but may take some minutes. You need to combine the .tree and .log files separately. The files must come from the same xml file (maybe it will throw an error with non-finished chains?)
Load into Tracer
Load the .log file and look at the ESS values: ESS stands for Effective Sample Size. It is a value calculated for a parameter, that estimates how many independent draws from the posterior distribution that the Markov Chain is equivalent to. If the ESS is low, the estimate of the parameter from the posterior distribution will be poor. It is like the sample size of experimental mesurements, N. If N is low, std deviation will be high. It is the same with ESS, you did a high N to get a small std deviation.
If the ESS is bad, ways to increase it are: more chains, longer chains, more sampling of the chains.
More about the ESS: https://beast.community/ess_tutorial
Tree annotator
This is to make the tree.
FigTree
This is to visualize the tree.