ClonalFrame(1)
inference of bacterial microevolution using multilocus sequence data
Description
ClonalFrame
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)
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-M |
Do update the value of theta |
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-D |
Do not update the value of delta |
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-N |
Do not update the value of nu |
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-R |
Do not update the value of R |
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-T |
Do not update the topology |
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-A |
Do not update the ages of the nodes |
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-G |
Remove all gaps |
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-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
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-U |
Use uniform priors for rho, theta and delta |
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-B |
Run in BURST mode |
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-C |
Run in UPGMA mode with a site-by-site bootstrap procedure |
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-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)
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-I |
Ignores first block in the alignment |
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-L |
Clean-up the alignment before running ClonalFrame |
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-l |
Minimum distance between two reference sites (default is 50) |
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-v |
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).