MAP MANAGER, version 2.5
 Kenneth F. Manly, PhD
 Roswell Park Cancer Institute, Buffalo, NY 14263-0001 USA
 kmanly@mcbio.med.buffalo.edu

Files in this submission:
  MapMgr.readme: this file
  MapMgr25.rev: a description of revisions since version 2.4
  MapMgr25.sea.hqx: a self-extracting, binhexed archive which contains the
    Map Manager program and the users manual as a Microsoft Word 5.1 document.

Also available by ftp from mcbio.med.buffalo.edu:
  RIData.sea.hqx: mapping data from mouse recombinant inbred lines,
    collected by R.W. Elliott, Roswell Park Cancer Institute
    (over 2500 strain distribution patterns in 16 sets)
    (in the pub/ElliottRIData directory)
  manual.ps.Z:  the Map Manager manual as a compressed Postscript file
    
For those who have trouble with electronic distribution, the Map Manager program
  disk, including the Elliott data files, and a printed manual will be sent by
  mail upon request to the author at the address above.

Map Manager replaces the RI Manager program (rimgr167.hqx).  Map Manager will
  read RI Manager files, but RI Manager version 1 will not read Map Manager
  files.

SUMMARY

Map Manager is a program for a Macintosh personal computer which helps analyze
the results of genetic mapping experiments using intercrosses with codominant
markers, backcrosses or recombinant inbred (RI) strains in experimental plants
or animals.  It is a specialized database program which allows easy storage,
retrieval, and display of information from such mapping experiments, and it
also has tools for searching and for statistical analysis of the experimental
results.  These tools assist the user in determining linkage among loci and in
determining the order of loci.  It is not, however, designed for the analysis
of pedigree data.  This distribution of Map Manager is made  possible by a
subcontract from the NCHGR program grant for Mouse Genome Informatics to The
Jackson Laboratory (J. Nadeau, PI).

DESCRIPTION

Map Manager has recently been described in detail by Manly (1993).  It can
display the genotypes of backcross progeny or sets of recombinant inbred
strains as an ordered list of loci, automatically marking the location of
recombination events implied by the chosen order.  The user can easily reorder
loci in the list, and easily add or remove loci.  After each change, Map
Manager revises the location of implied recombination events and displays the
total number of implied recombination events.  Pairs of adjacent loci are
optionally tested for linkage using the statistics of the binomial distribution
as described by Silver (1985) or the Bayesian analysis of Neumann, (1990). 
Adjacent loci for which linkage is not significant are marked by placing a line
between the locus names, and this marking is also revised automatically after
every change in the list.

Map Manager can also display a genetic map derived from the data using the
order defined in the previously described window.  In this map the interlocus
distance is calculated as the maximum-likelihood estimate implied by the number
of recombination events between the loci.  Interlocus intervals which do not
meet the test for significant linkage; are shown as breaks in the map.

To complement the map, Map Manager can display a list of statistics pertaining
to the intervals between adjacent loci.  These include the number of crossovers
in each interval, the number of informative strains, the map distance and its
standard error, the 95% and 99% confidence intervals, and the LOD score.

Finally, Map Manager can display a list of the bibliographic references and
comments stored with each locus.

All forms of display can be printed or transferred to other Macintosh programs
for reports or publication.

Map Manager can perform three types of searches on the strain distribution
patterns (SDPs) in its database.  It can search for loci which are potentially
linked to a new locus.  By comparing SDPs, this search procedure evaluates the
statistical significance of the linkage; between the given locus and each locus
in the database, and it displays those which may be linked.  Second, it can
search for the one location with the fewest number of crossovers with adjacent
linked loci.  Finally, it can search for groups of three loci with more than
the expected number of double crossovers.  This last search is useful for
finding loci which may be mistyped in one or more strains.

Map Manager can also search for words or phrases among the locus names,
references, and comments in its databases.  This search can be performed on an
opened set of data, on an unopened file, or on all available Map Manager files.
This search is useful for finding data sets which include a given locus, for
finding information from a given author, or for finding loci characterized by a
given comment.

Manly, K.F. (1993). A Macintosh program for storage and analysis of
experimental genetic mapping data. Mammalian Genome 4, 303-313.

Neumann, P.E. (1990). Two-locus linkage analysis using recombinant inbred
strains and Bayes' theorem. Genetics 126, 277-284.

Silver, J. (1985). Confidence limits for estimates of gene linkage based on
analysis using recombinant inbred strains and backcrosses. J. Hered. 76,
436-440.