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unknown(1) [debian man page]

UNKNOWN(1)						      General Commands Manual							UNKNOWN(1)

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 <> for the Debian GNU/Linux system (but may be used by others). WORD-WIDE-WEB SEE ALSO
ilink(1), linkmap(1), lodscore(1), mlink(1). April 15, 2003 UNKNOWN(1)

Check Out this Related Man Page

ILINK(1)						      General Commands Manual							  ILINK(1)

ilink - GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions SYNOPSIS
ilink [options] ipedfile.dat pedfile.dat DESCRIPTION
This manual page documents briefly the ilink command. In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux distribution requires each program to have a manpage. Any enhancement would be greatly apreciated. ilink is part of the fastlink software package. ILINK uses the GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions. If you use the default scripts produced by lcp, your initial guess for theta is .1 in every dimension. GEMINI evaluates each theta by its likelihood, seeking to find theta vectors that have a higher pedigree likelihood. The GEMINI procedure has multiple iterations. Each iteration corresponds to one line of output. Each iteration includes multiple likelihood function evaluations. Each iteration has two phases. In Phase I GEMINI seeks to improve the current best theta. In Phase II, GEMINI esti- mates the gradient of the likelihood with respect to the current best theta vector. In the first iteration, Phase I only evaluates the likelihood at the initial candidate theta. When ILINK prints out a line such as: maxcensor can be reduced to -32767, it has completed the first likelihood function evaluation. On long runs, this fact can be used to estimate running time. A reasonable rough estimate for the number of function evaluations is 10*(number of dimensions of theta vector). The number of dimensions of the theta vector is one fewer than the number of loci in most cases. If male- theta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). Esti- mating other parameters (with fitmodel set to true) can also increase the number of dimensions. To learn more about ilink it might be useful to read the file /usr/share/doc/fastlink/README.ILINK if you have a Debian GNU/Linux system. OPTIONS
There might be options but I did not found any information about them. Please foreward any information about them to <> SEE ALSO
linkmap(1), lodscore(1), mlink(1), unknown(1). Word-Wide-Web: AUTHOR
: Alejandro Schaeffer <> and others This manual page was written by Andreas Tille <>, for the Debian GNU/Linux system (but may be used by others). April 15, 2003 ILINK(1)
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