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.
Genetics Research FirstView Articles: published online 31 August 2011.

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:

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

Limits

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.

Impression

Get an impression of the software with the slide show:

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

Version information

JoinMap 4.1 is available for the following 32-bit MS-Windows ® platforms: XP, Vista and 7.
JoinMap 4.1 runs as 32-bit software under the 64-bit version of MS-Windows ® 7.
JoinMap 4.1 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

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 ® 4.1