Provided by: clonalframe_1.2-10build1_amd64
ClonalFrame - inference of bacterial microevolution using multilocus sequence data
ClonalFrame [OPTIONS] inputfile outputfile
ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous 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
ClonalFrame was written by Xavier Didelot. This manual page was written by Andreas Tille <firstname.lastname@example.org>, for the Debian project (but may be used by others).