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clonalframe(1) [debian man page]

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 homolo-
       gous 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 <tille@debian.org>, for the Debian project (but may be used by others).

February 2011								1.2							    ClonalFrame(1)

Check Out this Related Man Page

SSHMENU(1)						      General Commands Manual							SSHMENU(1)

NAME

       sshmenu - GNOME applet for connecting to hosts using SSH.

DESCRIPTION

       The  SSHMenu  applet  puts  all your most frequently used SSH connections on a handy menu in your GNOME panel (see below for non-GNOME ver-
       sions.  Click on a host name to open a new gnome-terminal window with an ssh connection to the selected host.  Set up SSH options (such	as
       port forwarding etc) and select a gnome terminal profile (for colour schemes, font sizes etc) using the preferences dialog.

       Add the applet to a GNOME panel in the normal way: right click on the panel, select 'Add to Panel' and then select the SSH Menu Applet from
       the list.

       Configure the applet using the 'Preferences' option on the applet menu.

STANDALONE VERSIONS

       The SSHMenu application uses the GTK GUI toolkit but is not dependent on the GNOME desktop environment.	Two  alternative  wrapper  scripts
       are provided:

       sshmenu-gnome  -  provides  all	the functionality of the SSHMenu applet but in a standalone application window that could (for example) be
       swallowed into the panel of an alternative desktop environment.

       sshmenu - provides similar functionality to sshmenu-gnome, but without any GNOME dependencies.  Notably, xterm is used  instead	of  gnome-
       terminal.

       The Hacker's Guide ( http://sshmenu.sourceforge.net/dev/hackers_guide.html ) describes a number of ways in which the SSHMenu can be further
       customised.

OPTIONS

       The applet is not invoked from the command-line however the standalone versions recognise the following options	and  can  be  extended	to
       recognise more:

       -c FILE, --config-file FILE
	      read and write config information to FILE instead of the default $HOME/.sshmenu

       -d NUM, --debug NUM
	      set debug level to NUM (default: 0)

       -s NUM, --socket-window-id NUM
	      use  the	XEmbed	protocol  to embed the SSHMenu user interface in the window identified by NUM instead of creating a new, top-level
	      window,

       -V, --version
	      output version information and exit

AUTHOR

       sshmenu-applet was written by Grant McLean <grant@mclean.net.nz>

								   July 4, 2006 							SSHMENU(1)
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