unknown(1) [debian man page]
UNKNOWN(1) General Commands Manual UNKNOWN(1) NAME
unknown - identify possible genotypes for unknowns SYNOPSIS
A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree. unknown [ -cl ] DESCRIPTION
unknown infers possible genotypes and mating combinations for parents with unknown genotypes for ilink(1), mlink(1) and linkmap(1). OPTIONS
-c Use conditional allele frequencies. -l Choose a good set of loop breakers automatically. RETURN VALUE
0 Successful completion ERRORS
10 File not found 255 Failure EXAMPLES
Normally, unknown(1) is run immediately prior to its sister programs, ilink(1), mlink(1) and linkmap(1), like this: unknown mlink FILES
unknown(1) reads the two files pedfile.dat and datafile.dat as its own input and produces various temporary files that are used as input to the next program. These temporary files are ipedfile.dat, upedfile.dat, speedfile.dat and newspeedfile.dat. NOTES
unknown(1) is part of the FASTLINK package, which is a re-implementation of the LINKAGE suite of computer tools that help investigate genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott. AUTHORS
Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al. This manual page was written by Elizabeth Barham <lizzy@soggytrousers.net> for the Debian GNU/Linux system (but may be used by others). WORD-WIDE-WEB http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html SEE ALSO
ilink(1), linkmap(1), lodscore(1), mlink(1). April 15, 2003 UNKNOWN(1)
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SDPA(1) General Commands Manual SDPA(1) NAME
SDPA - High-performance software package for SemiDefinite Programs SYNOPSIS
sdpa DataFile OutputFile [InitialPtFile] [-pt parameters] [-dimacs] [-numThreads numThreads] sdpa [options] files... sdpa --version DESCRIPTION
sdpa - "SDPA (SemiDefinite Programming Algorithm)" is one of the most efficient and stable software packages for solving SDPs based on the primal-dual interior-point method. SDP (SemiDefinite Program) is used for financial engineering, machine learning, control theory, sensor network problem, quantum chemistry, quantum information, combinatorial optimizaiton, polynomial optimization, and so on. Futher information on SDP and SDPA can be found at http://sdpa.sourceforge.net/ OPTIONS
---- option type 1 ---- sdpa DataFile OutputFile [InitialPtFile] [-pt parameters] [-dimacs] [-numThreads numThreads] parameters = 0 default, 1 fast (unstable), 2 slow (stable) example1-1: sdpa example1.dat example1.result example1-2: sdpa example1.dat-s example1.result example1-3: sdpa example1.dat example1.result example1.ini example1-4: sdpa example1.dat example1.result -pt 2 example1-5: sdpa example1.dat example1.result -dimacs example1-6: sdpa example1.dat example1.result -numThreads 4 ---- option type 2 ---- sdpa [option filename]+ -dd : data dense :: -ds : data sparse -id : init dense :: -is : init sparse -o : output :: -p : parameter -pt : parameters , 0 default, 1 fast (unstable) 2 slow (stable) example2-1: sdpa -o example1.result -dd example1.dat example2-2: sdpa -ds example1.dat-s -o example1.result -p param.sdpa example2-3: sdpa -ds example1.dat-s -o example1.result -pt 2 example2-4: sdpa -ds example1.dat-s -o example1.result -dimacs example2-5: sdpa -ds example1.dat-s -o example1.result -numThreads 4 ---- option type 3 ---- sdpa --version to print out version and exit. PARAMETER_FILE is decided by the following priority 1: The file assigned by '-p' option of 'option type 2'. For 'option type1', this is skipped. 2: ./param.sdpa For 'option type2', this is skipped. 3: /usr/share/sdpa/param.sdpa 4: Default parameter -dimacs printout dimacs information incurring additional computation cost -numThreads number of pthreads for internal computation AUTHOR
SDPA was written by SDPA Project <sdpa-developers@lists.sourceforge.net>. This manual page was written by Makoto Yamashita <Makoto.Yamashita@is.titech.ac.jp>. July 28, 2011 SDPA(1)