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Using TRACER with LAMARC

LAMARC can produce output readable by the utility program TRACER, written by Andrew Rambaut and Alexei Drummond. We do not distribute TRACER. It can be found at:

http://evolve.zoo.ox.ac.uk/software.html?id=tracer

We thank the authors for producing this useful program. It is written in Java and runs on most systems as long as a Java runtime environment is available. TRACER is mainly intended for Bayesian runs. For each parameter being estimated, it can display summary statistics (mean, standard deviation, etc) and a graph of the change in that parameter as the run progresses. It can also show the correlation between pairs of parameters.

TRACER is very useful in diagnosing too-short Bayesian runs. If the trace graph shows a rising line, rather than a line which plateaus and varies around a particular value, the run is too short. Be aware, however, that while a bad-looking trace nearly guarantees a bad run, a good-looking trace cannot guarantee a good run. If there is a favorable region of parameter space which was never found, no examination of the regions which were found can reveal this.

A likelihood run of LAMARC cannot provide parameters to TRACER, as they are estimated only at the ends of chains (it is much too expensive to make additional estimates). The only use of TRACER in a likelihood run is to monitor the data-likelihood of the genealogies. Again, a rising line which does not plateau nearly proves a too-short run, whereas a nice plateau suggests but does not guarantee a good run.

LAMARC automatically writes a file suitable for TRACER for each chromosomal region it analyzes. The files are called "tracefile_regionname_replicate.txt". So the file containing information on the mtDNA region, first replicate, would be named "tracefile_mtDNA_1.txt". This file can be provided to TRACER as-is.

We welcome any input on how to make TRACER more useful with LAMARC, and visa versa.

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