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).