JoinMap ^® 4

Software for the calculation of genetic linkage maps in experimental populations of diploid species

JoinMap provides high quality tools that allow detailed study of the experimental data and the generation of publication-ready map charts. The intuitive MS-Windows ® user interface of JoinMap invites to a better exploration of the data. For instance, you can perform several diagnostical tests, both before and after the actual map calculation, and you can remove potentially erroneous loci and individuals from the map calculations by a simple mouse-click.

New features

With this edition JoinMap is taking another big step in linkage analysis software! Many new features were added, some improving the user interface, others supplying more powerful methods, for instance:

data management: copy and paste your marker data from MS-Excel into JoinMap; easily check for coding errors;
new population types: advanced intermated families and advanced backcross families, of any given generation;
more criteria to study the linkage group formation: linkage LOD, independende test P-value, recombination frequency;
use existing maps (of multiple groups) or existing groupings to create the linkage groups of a new population;
this is very handy when employing markers with known map positions in new populations, and also when expanding your map with an additional set of markers;
use the so-called strongest cross link information to verify assignments of markers to groups;
very fast computation of high density maps with the new mapping algorithm according to Jansen, et al, 2001. TAG 102: 1113-1122 based on Monte Carlo Maximum Likelihood: the algorithm needs only couple of minutes for a 100 markers linkage group!!;
(the new mapping algorithm and the regression mapping algorithm of JoinMap 3.0 are available side by side)
(for the outbreeder full-sib family (CP) the new mapping algorithm is limited to pseudo-testcross analyses, i.e. a map for each of the two parental meioses separately)
get an idea of plausible map positions of markers;
graphical genotyping;
bar and XY charts;
print preview.

Features

an intuitive MS-Windows user interface, which adds a lot of practical functionality
all analyses are based upon just a single input file in plain text format with a flexible layout
also imports MAPMAKER raw data format (data types: f2 intercross, f2 backcross, ri self)
experimental population types: BC1, F2, RIL, F1-derived and F2-derived DH, outbreeder full-sib family
powerful determination of linkage groups
automatic determination of linkage phases for outbreeder full-sib family
several diagnostics, before and after the actual map calculation:
- test segregation distortion
- check similarity of loci
- check similarity of individuals
- calculate genotype probabilities conditional on map and flanking genotypes to discover double recombinations
- test heterogeneity of recombination estimates between different populations
combine ('join') data derived from several sources into an integrated map
map charts, with many adjustable features and exportable to MS-Word ® and MS-PowerPoint ®
copying of results to clipboard for additional use in MS-Excel ®
print or export results, e.g. export maps for use in MapQTL ®
no limits to the amount of loci, linkage groups, etcetera, apart from the physical memory (RAM) of the computer
manual in Acrobat ® Reader PDF file format
easy-to-use InstallShield ® installer

Impression

Get an impression of the software with the slide show:

JoinMap ® 4 slide show (size: ~0.9 MB).

Version information

JoinMap 4 is available for the following 32-bit MS-Windows ® platforms: XP, Vista and 7.
JoinMap 4 is not available for any 64-bit MS-Windows ® platforms.
JoinMap 4 is not supported under the MS-Windows ® 95, 98, ME, NT and 2000 platforms.
Previous versions are no longer available.

The original version of JoinMap was published in 1993 in The Plant Journal by Piet Stam [1]. Version 2.0 of JoinMap was presented at the Plant Genome III Conference, January 1995, San Diego, California, USA [2].

References

Stam, 1993. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. The Plant Journal 3: 739-744
Stam, 1995. JoinMap 2.0 deals with all types of plant mapping populations. Plant Genome III Abstracts, World Wide Web site: www.intl-pag.org.

Support

If needed, support will be given to help you get the software running and solve problems not described in the manual. This support is limited to advice by e-mail to <support(at)kyazma.nl>. A list of frequently asked questions is presented at this web site.

JoinMap is a registered trademark

JoinMap ® 4