JoinMap is a desktop application for constructing genetic linkage maps from segregation data generated in experimental populations. It helps geneticists and breeders transform genotype data into ordered linkage groups and high‑quality maps suitable for downstream analyses such as QTL mapping and genome anchoring.
Key capabilities:
- Supports common diploid population types (F2, backcross, recombinant inbred lines, doubled haploids) and outcrossing (CP) populations.
- Handles co-dominant and dominant marker types (e.g., SNPs, SSRs, AFLPs) with missing-data tolerance.
- Assigns markers to linkage groups using pairwise recombination estimates and LOD thresholds.
- Orders markers with regression and maximum-likelihood algorithms; calculates map distances with Haldane or Kosambi functions.
- Quality control tools for segregation distortion checks, duplicate markers/individuals, genotyping-error detection, and data filtering.
- Map refinement via rippling, marker re-assignment, and consensus/integrated mapping across datasets.
- Visualization of pairwise linkage matrices and linkage-group maps; export to common formats for tools such as MapChart and QTL analysis software.
- Comprehensive reports summarizing map length, marker density, linkage group composition, and diagnostics.
Typical uses include building high-density linkage maps for crop or model species, preparing inputs for QTL studies, and supporting breeding and quantitative genetics research. JoinMap is widely used in academic and applied settings for reliable, reproducible map construction on Windows desktops.
JoinMap is developed by Plant Research International BV (PRI) and is used by 3 users of Software Informer. The most popular versions of this product among our users are: 3.0, 4.0 and 4.1. The names of program executable files are JoinMap.exe, JoinMap3.exe, JoinMap4.1.exe, JoinMap4.exe and JoinMap5.exe.
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