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ClonalFrame - Online in the Cloud

Run ClonalFrame in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command ClonalFrame that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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