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
oggz-diff(1) General Commands Manual oggz-diff(1)NAME
oggz-diff -- Hexdump the packets of two Ogg files and output differences
SYNOPSIS
oggz-diff [options] [OGGZDUMP_OPTIONS] [DIFF_OPTIONS] file1.ogg file2.ogg
options: [--verbose ] [-v | --version ] [-h | --help ]
OGGZDUMP_OPTIONS: [-b | --binary ] [-x | --hexadecimal ] [-c content-type | --content-type content-type ] [-s serialno | --serialno
serialno ] [-O | --hide-offset ] [-S | --hide-serialno ] [-G | --hide-granulepos ] [-P | --hide-packetno ]
DIFF_OPTIONS: [-q | --brief ] [-C NUM | --context[=NUM] ] [-u | -U NUM | --unified[=NUM] ] [-e | --ed ] [--normal ] [--rcs ] [-y
| --side-by-side ] [-l | --paginate ]
Description
oggz-diff is a sh script which uses oggz-dump to generate hexadecimal packet dumps of each input file, then outputs the difference between
these dumps using diff.
Options
oggz-diff forwards a subset of options accepted by oggz-dump and diff. See oggz-dump(1) and diff(1) for more detail.
oggz-dump format options
-b, --binary
Generate a binary dump of each packet
-x, --hexadeciaml
Generate a hexadecimal dump of each packet
oggz-dump filtering options
-c content-type, --content-type content-type
Dump only the logical bitstreams for a specific content-type. Run oggz-known-codecs(1) for a full list of codecs known by the
installed version of oggz.
-s serialno, --serialno serialno
Dump only the logical bitstream with specified serialno.
-O, --hide-offset
Hide the byte offset field of the preamble for each packet dumped. This is particularly useful when comparing Ogg bitstreams that
differ only in page structure.
-S, --hide-serialno
Hide the serialno field of the preamble for each packet dumped. This is particularly useful when comparing Ogg bitstreams that
differ only in serialno assignment.
-G, --hide-granulepos
Hide the granulepos field of the preamble for each packet dumped.
-P, --hide-packetno
Hide the packetno field of the preamble for each packet dumped.
diff options
The -w (--ignore-all-space) option to diff is always implied.
-q, --brief
Output only whether files differ.
-C NUM, --context[=NUM]
Output NUM lines of copied context.
-u, -U NUM, --unified[=NUM]
Output NUM (default 3) lines of unified context.
-e, --ed Output an ed script.
--normal Output a normal diff.
--rcs Output an RCS format diff.
-y, --side-by-side
Output in two columns.
-l, --paginate
Pass the output through pr to paginate it.
Miscellaneous options
--verbose Display verbose messages.
-v, --version
Display version information and exit.
-h, --help
Display usage information and exit.
AUTHOR
Conrad Parker
COPYRIGHT
Copyright (C) 2003 CSIRO Australia
SEE ALSO oggz-dump(1), diff(1), patch(1)oggz-diff(1)