Provided by: clonalframe_1.2-10build1_amd64

**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 homologous recombination events that have disrupted the clonal inheritance. Options:-xNUM Sets the number of iterations after burn-in (default is 50000)-yNUM Sets the number of burn-in iterations (default is 50000)-zNUM Sets the number of iterations between samples (default is 100)-eNUM Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)-mNUM Sets the initial value of theta to NUM (default is Watterson estimate)-dNUM Sets the initial value of delta to NUM (default is 0.001)-nNUM Sets the initial value of nu to NUM (default is 0.01)-rNUM Sets the initial value of R to NUM (default is initial theta/10)-MDo update the value of theta-DDo not update the value of delta-NDo not update the value of nu-RDo not update the value of R-TDo not update the topology-ADo not update the ages of the nodes-GRemove all gaps-HRemove all gaps at non-polymorphic positions-tNUM Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)-wFILE Use Newick file for initial tree-aNUM Sets the first parameter of the beta prior distribution of nu-bNUM Sets the second parameter of the beta prior distribution of nu-UUse uniform priors for rho, theta and delta-BRun in BURST mode-CRun in UPGMA mode with a site-by-site bootstrap procedure-cRun in UPGMA mode with a fragment-by-fragment bootstrap procedure-SNUM Sets the seed for the random number generator to NUM-ENUM Sets the rate of exponential growth (default is 0)-IIgnores first block in the alignment-LClean-up the alignment before running ClonalFrame-lMinimum distance between two reference sites (default is 50)-vVerbose mode

**AUTHOR**

ClonalFramewas 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).