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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 homologous recombination events that have disrupted the clonal inheritance.

Options:

Sets the number of iterations after burn-in (default is 50000)
Sets the number of burn-in iterations (default is 50000)
Sets the number of iterations between samples (default is 100)
Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)
Sets the initial value of theta to NUM (default is Watterson estimate)
Sets the initial value of delta to NUM (default is 0.001)
Sets the initial value of nu to NUM (default is 0.01)
Sets the initial value of R to NUM (default is initial theta/10)
Do update the value of theta
Do not update the value of delta
Do not update the value of nu
Do not update the value of R
Do not update the topology
Do not update the ages of the nodes
Remove all gaps
Remove all gaps at non-polymorphic positions
Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)
Use Newick file for initial tree
Sets the first parameter of the beta prior distribution of nu
Sets the second parameter of the beta prior distribution of nu
Use uniform priors for rho, theta and delta
Run in BURST mode
Run in UPGMA mode with a site-by-site bootstrap procedure
Run in UPGMA mode with a fragment-by-fragment bootstrap procedure
Sets the seed for the random number generator to NUM
Sets the rate of exponential growth (default is 0)
Ignores first block in the alignment
Clean-up the alignment before running ClonalFrame
Minimum distance between two reference sites (default is 50)
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).

1.2 February 2011