Command line options:
input.infile.phy_ - The main input file, relaxed phylip format, containing sequence(s) .
infile.chainparamfile1_ - Select the first chain.param file to restart (name=chain1.param)
infile.chainparamfile2_ - Select the second chain.param file (name=chain1.param)
infile.chaintreefile1_ - Select the first chain.treelist file to restart (name=chain0.treelist)
infile.chaintreefile2_ - Select the second chain.treelist file (name=chain1.treelist)
infile.chaintracefile1_ - Select the first chain.trace file to restart (name=chain0.trace)
infile.chaintracefile2_ - Select the second chain.trace file (name=chain1.trace)
infile.chainmonfile1_ - Select the first chain.monitor file to restart (name=chain0.monitor)
infile.chainmonfile2_ - Select the second chain.monitor file (name=chain1.monitor)
User Configurable Parameters.
vparam.runtime_ - (Float) Maximum Hours to Run (up to 168 hours)
vparam.num_sites_ - (Integer) Number of sites in the data set no default; required.
vparam.datatype_ - (Excl)
vparam.acceptdiffval
vparam.giveupval_ - (Integer) Minimum number of cycles before giving up if "maxdiff" is still 1. default=10000
