This command plots specified parameters in the .p file created by the program. The program prints two files during a MCMC analysis: a tree file and a parameter file. The parameter file has the extension ".p". This command, plot, makes an x-y graph of the parameter over the course of the chain. The command can be useful for visually diagnosing convergence for many of the parameters of the phylogenetic model. The parameter to be plotted is specified by the "parameter" option. Several parameters can be plotted at once by using the "match" option, which has a default value of "perfect". For example, if you were to set "parameter = pi" and "match = consistentwith", then all of the state frequency parameters would be plotted. You can also set "match=all", in which case all of the parameters are plotted.
Parameter Options Current Setting ------------------------------------------------------------ Filename <name> temp.p Burnin <number> 0 Parameter <name> lnL Match Perfect/Consistentwith/All Perfect ------------------------------------------------------------