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Expected in April: stable early release of JoinMap ® version 5

JoinMap ® 4.1

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 introduced with version 4.1

The only, but very important, enhancement of version 4.1 of JoinMap is the ability to use the multipoint maximum likelihood mapping algorithm on populations of type CP, i.e. the outbreeding species full-sib family. The new method has a very high speed at computing dense maps for CP populations. For instance, a linkage group of about 250 good quality SNP markers (a mix of <hkxhk>, <lmxll> and <nnxnp> segregation types) is estimated in about 8 minutes (on a regular PC). The method is described in a paper that was accepted for publication:

Van Ooijen, J.W. (2011). Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species.
Genetics Research, accepted: June 2011, published: (2011) 93, 5, 343-349.

Projects of JoinMap version 4 can be opened and will automatically be converted into projects of version 4.1.

New features introduced with version 4

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:



This edition is not suitable for handling thousands of (SNP) markers. The capacity of the Dataset node and of the Groupings tabsheets depend largely on the amount of free RAM memory. Because the software is 32-bit, it can only address upto 4 GB of memory. Because this memory also is used by the MS-Windows operating system itself, in practice the maximum available is 2 to 3 GB. Also when running JoinMap from 64-bit MS-Windows, the maximum remains the same, any surplus of 64-bit memory cannot be used. The Dataset node and the Groupings tabsheets were tested to handle a set of 3000 markers for a 100 individuals. The high density mapping algorithm is able to deal succesfully with linkage groups of 300 good quality markers. By removing the redundancy in huge datasets JoinMap may be possible to deal with these data. Feel free to try it out in the evaluation version.


Get an impression of the software with the slide show:
JoinMap 4  slide show   JoinMap ® 4 slide show (size: ~0.9 MB).

Version information

JoinMap 4.1 is available as 32-bit software for the 32- and 64-bit MS-Windows platforms Vista, 7, 8, 8.1 and 10. Other MS-Windows platforms are not supported. 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].


  1. Stam, 1993. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. The Plant Journal 3: 739-744.
  2. Stam, 1995. JoinMap 2.0 deals with all types of plant mapping populations. Plant Genome III Abstracts.


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)>. A list of frequently asked questions is presented at this web site.