ClonalFrame(1)						      General Commands Manual						    ClonalFrame(1)

NAME

       ClonalFrame - inference of bacterial microevolution using multilocus sequence data

SYNOPSIS

       ClonalFrame [OPTIONS] inputfile outputfile

DESCRIPTION

       ClonalFrame  identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homolo-
       gous recombination events that have disrupted the clonal inheritance.

       Options:

       -x NUM Sets the number of iterations after burn-in (default is 50000)

       -y NUM Sets the number of burn-in iterations (default is 50000)

       -z NUM Sets the number of iterations between samples (default is 100)

       -e NUM Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)

       -m NUM Sets the initial value of theta to NUM (default is Watterson estimate)

       -d NUM Sets the initial value of delta to NUM (default is 0.001)

       -n NUM Sets the initial value of nu to NUM (default is 0.01)

       -r NUM Sets the initial value of R to NUM (default is initial theta/10)

       -M     Do update the value of theta

       -D     Do not update the value of delta

       -N     Do not update the value of nu

       -R     Do not update the value of R

       -T     Do not update the topology

       -A     Do not update the ages of the nodes

       -G     Remove all gaps

       -H     Remove all gaps at non-polymorphic positions

       -t NUM Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)

       -w FILE
	      Use Newick file for initial tree

       -a NUM Sets the first parameter of the beta prior distribution of nu

       -b NUM Sets the second parameter of the beta prior distribution of nu

       -U     Use uniform priors for rho, theta and delta

       -B     Run in BURST mode

       -C     Run in UPGMA mode with a site-by-site bootstrap procedure

       -c     Run in UPGMA mode with a fragment-by-fragment bootstrap procedure

       -S NUM Sets the seed for the random number generator to NUM

       -E NUM Sets the rate of exponential growth (default is 0)

       -I     Ignores first block in the alignment

       -L     Clean-up the alignment before running ClonalFrame

       -l     Minimum distance between two reference sites (default is 50)

       -v     Verbose mode

AUTHOR

       ClonalFrame was written by Xavier Didelot.

       This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (but may be used by others).

February 2011								1.2							    ClonalFrame(1)