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)
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HOCR(1) User Commands HOCR(1) NAME
hocr - Hebrew OCR utility DESCRIPTION
Usage: hocr [OPTION...] - Hebrew OCR utility Help Options: -?, --help Show help options --help-all Show all help options --help-file Show file options --help-image-proccesing Show image proccesing options --help-segmentation Show segmentation options --help-debug Show debug options File options -O, --images-out-path=PATH use PATH for output images -u, --data-out=FILE use FILE as output data file name -C, --save-copy save a compy of original image -b, --save-bw save proccesd bw image -B, --save-bw-exit save proccesd bw image and exit -l, --save-layout save layout image -L, --save-layout-exit save layout image and exit -f, --save-fonts save fonts -F, --save-fonts-exit save fonts images and exit Image proccesing options -T, --thresholding-type=NUM thresholding type, 0 normal, 1 none, 2 fine -t, --threshold=NUM use NUM as threshold value, 1..100 -a, --adaptive-threshold=NUM use NUM as adaptive threshold value, 1..100 -s, --scale=SCALE scale input image by SCALE 1..9, 0 auto -S, --no-auto-scale do not auto acale image -q, --rotate=DEG rotate image clockwise in deg. -Q, --no-auto-rotate do not auto rotate image Segmentation options -c, --colums setup=NUM colums setup: 1.. #colums, 0 auto, 255 free -x, --slicing=NUM use NUM as font slicing threshold, 1..250 -X, --slicing-width=NUM use NUM as font slicing width, 50..250 -w, --font-spacing=NUM font spacing: tight ..-1, 0, 1.. spaced Debug options -g, --draw-grid draw grid on output images -d, --debug print debuging information while running -D, --debug-extra print extra debuging information -y, --font-filter=NUM debug a font filter, use filter NUM -Y, --font-filter-list print a list of debug a font filters -j, --font-num-out print font numbers in output text Application Options: -i, --image-in=FILE use FILE as input image file name -o, --text-out=FILE use FILE as output text file name -h, --html-out output text in html format -N, --no-gtk do not use gtk for file input and output -z, --font=NUM use font NUM -n, --no-nikud do not recognize nikud -v, --version print version information and exit libhocr-0.10.5-i686-pc-linux-gnu-12022008 http://hocr.berlios.de Copyright (C) 2005-2008 Yaacov Zamir <kzamir@walla.co.il> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MER- CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. SEE ALSO gocr(1), ocrad(1), unpaper(1) hocr - Hebrew OCR utility February 2008 HOCR(1)