runlim(1) [debian man page]
RUNLIM(1) General Commands Manual RUNLIM(1) NAME
runlim - a program to run benchmarks SYNOPSIS
runlim [ options ...] command [ arguments ...] DESCRIPTION
run is a tool that can be used to run and control benchmarks. It executes a given command with (optional) arguments, samples resource usage during the run, and kills the process (and its child processes) if a certain time and/or space limit is exhausted. Every 100 milliseconds, runlim takes a sample of the program's resource utilization, and logs status information to stderr every second. Optionally, the status can be logged to a file. Multi-threaded programs can be limited by setting a wall clock timeout. runlim follows the time accumulation scheme of GNU time for multi- threaded programs and programs that spawn multiple child-processes: time spent in each thread/child is summed up, unless you are only interested in walk clock time. OPTIONS
runlim accepts the following options: -h, --help Show summary of options. --version Show version of program. -o FILE, --output-file=FILE Overwrite or create FILE for output logging. -s NUM, --space-limit=NUM Set space limit to NUM megabytes. -t NUM, --time-limit=NUM Set time limit to NUM seconds. -r NUM, --real-time-limit=NUM Set real time limit to NUM seconds. -k, --kill Propagate signals. SEE ALSO
time(1), timelimit(1), timeout(1), time(7). AUTHOR
runlim was written by Armin Biere and Toni Jussila. This manual page was written by Thomas Krennwallner <tkren@kr.tuwien.ac.at>, for the Debian project (and may be used by others). February 11, 2011 RUNLIM(1)
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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)