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JoinMap ® 5

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

JoinMap is an MS-Windows ® program for the calculation of genetic linkage maps in experimental populations of diploid species. The software can deal with the common types of experimental population, including the full-sib family (F1) of a cross between two individuals of an outbreeding species. It provides high quality tools that allow detailed study of the experimental data. The intuitive user interface invites to a better exploration of the data. It is easy to perform various diagnostical tests, both before and after the actual map calculation. Subsequently, any locus or individual with possibly erroneous observations can be excluded from the calculations by a simple mouse-click, after which a new and improved map may be calculated.

This present version number 5 builds on its predecessor, v4.1. While preserving the user interface and workflow with the program on the whole, v5 has many enhancements over v4.1, several of which are quite significant. Most are intended as improvements for working with very large sets of genetic markers. In brief, the major technical improvements are: (a) the change towards 64-bit software, (b) the use of an embedded database system for storing all data, and (c) the parallelization of some calculations. The change to 64-bit allows access to more system memory, which is useful for very large datasets. Using an embedded database system greatly improves the responsiveness of the user interface with large datasets; due to the embedded property, the database system requires no special installation and usage instructions, everything is taken care of by the program. Finally, parallelization increases the computational speed on systems with a multi-core processor, of which all available computational cores can be utilized. In addition to these technical improvements, several aspects of the various algorithms and the user interface are enhanced. The important advances are described in the next section.

Enhancements introduced with v5

New feature 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:



The facts that JoinMap v5 is 64-bit software and uses a database system make it suitable for working with thousands of loci. The software does not have a built-in fixed limit regarding the maximum number of loci, with the exception of the Dataset tabsheet which can accomodate a maximum of one million loci (although that amount was not tested). The software was tested to work fine with a dataset of 50,000 loci. Please note, however, that the production of a reliable high resolution linkage map does require a population of sufficient size containing the necessary segregation information.

With this version of JoinMap, the speed of the hard disk drive will now become a limiting factor in dealing with large datasets. For instance, a dataset of 50,000 loci in an F2 population will produce a table of ~1.2 billion records of pairwise data that must be stored, resulting in a database file of over 30 GB in size, which will require some time to write.


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 5 is 64-bit software for the 64-bit MS-Windows 10 platform. 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.