SOLAR is a package of software to perform several kinds of statistical genetic analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. The name SOLAR stands for Sequential Oligogenic Linkage Analysis Routines.
SOLAR is Copyright © 1995-2004 Southwest Foundation for Biomedical Research. The authors are John Blangero, Kenneth Lange, Laura Almasy, Tom Dyer, Harald Göring, Jeff Williams and Charles Peterson. Parts of SOLAR consist of software developed by others; a complete list is provided in Appendix 3.
There is absolutely no warranty, expressed or implied, regarding SOLAR. Many features of SOLAR are considered experimental and may produce erroneous results under some circumstances, or even all circumstances. Usage of SOLAR presumes knowledge of Statistical Genetics concepts to prepare data files and interpret results correctly (see section 1.3 below for a note on the recommended references).
SOLAR runs on Sun Solaris 7 (SunOS 5.7) or later on both SPARC and x86 (PC) hardware, on linux systems equivalent to RedHat 7.1 or later on i386 compatible hardware only, on Digital Unix (OSF1) for the Alpha, and on Silicon Graphics Irix. At the time of initial release, however, SOLAR Version 2.0 is only available for Solaris/SPARC, Solaris/x86, and linux/i386. (The latest SOLAR version available for each system may vary; check our website at solar.sfbrgenetics.org for the latest officially supported releases.) Support is subject to change without notice.
SOLAR documentation is provided in two forms: online messages
using the SOLAR help
or usage commands,
and a full html formatted User Manual (which you are
now reading) which may be accessed from SOLAR with the doc command. The
help messages for each command form the
reference documentation which is also included in
Appendix 1 of the
html manual. There is also a README file
in the directory where you unpacked the SOLAR archive
which contains general notes about installing SOLAR, and a
README.news file which provides notes
about the current version (which are duplicated in Appendix 4 and the
change-notes command for official
releases).
Reference publications regarding SOLAR are listed in Appendix 2 and at the bottom of the main SOLAR web page. These publications concern the ideas and methodologies used in SOLAR while this manual is concerned only with the actual usage of SOLAR commands and options by a knowledgeable Statistical Genetics investigator.
The doc command
browses the full SOLAR documentation using the
Netscape browser, assuming it is installed on your
system and in your
PATH with the name
netscape.
solar> doc
By design, doc goes to the main index page, so that you can look up the
documentation for any command quickly. For a more
introductory and verbose (but less detailed) presentation,
click on the link at the top which says Go to full SOLAR Manual (Table of
Contents).
The doc command always starts a new
Netscape session (so as not to unload any page you
currently have open). If you already have a Netscape session
running, you will get a warning concerning the Netscape lock
file. Simply click on OK to procede to bring up the
SOLAR documentation. If you exit from this new
Netscape session, windows you brought up under previous
Netscape sessions will probably stay up.
If Netscape is not available on your system, you can find the location of the documentation files with the command:
solar> doc -whereis
/opt/appl/solar/2.0.7/doc
and then point your browser to that directory. If you are running SOLAR on a remote machine, you may need to copy the files back to your machine to browse them. Or, you may be able to access the SOLAR documentation over the Internet by starting at our website and then clicking on the SOLAR User's Guide link. On the website, the documentation starts at the Table of Contents, but from there you can click on the Go to Main Index link to browse the index to all commands.
SOLAR has a built-in help documentation feature. Giving the help command by itself will display the names of all the commands and a brief summary of what each one does.
solar> help
Giving the help command followed by the name of a particular SOLAR command will display the reference documentation for that command. For example, the command
solar> help polygenic
will display all the documentation about the
polygenic command.
There is also a short version of help for each command which is displayed with the usage command, for example:
solar> usage polygenic
will display a much shorter message which conveniently stays on your terminal window after you are done reading it.
Trademarks are mentioned above for reference only and are property of their respective holders.