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:
-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 <[email protected]>, for the Debian project (but may be used by others).