FsLinkageMap 2.1

A Windows software for constructing genetic linkage maps in a full-sib family

Chunfa Tong, Meng Zhou, Po Liu and Jisen Shi (Email: tongchf@njfu.edu.cn)

Key Laboratory of Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, China

FsLinkageMap is a Windows software for constructing genetic linkage maps with molecular markers generated from a full-sib family. The software is written in VC++ 6.0 and works with Microsoft Windows operating systems, including Windows 95/98, Me, NT, 2000, and XP.

FsLinkageMap can perform two-point linakge analysis and predict the linkage phase between any two different segregation markers, such as 1:1, 3:1, 1:2:1 and 1:1:1:1. After two-point linkage analysis, markers are classified into linkage groups according to the threshold of recombination fraction or LOD score. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating a local ordering method, which has much higher power than that of JoinMap. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis. Some files are generated for recording computational results in details. Finally, linkage maps are drawn and can be saved as a Windows metafile(WMF) format.

FsLinkageMap will be benefical to constructing high-quality genetic linakge maps in some species, especially in forest trees, in which imbred lines are almost impossibly obtained due to their high heterozygosity and long generation times. The software and its manual can be freely downloaded from the following links.

+ FsLinkageMap 2.1
+ Manual


Chunfa Tong, Bo Zhang, and Jisen Shi. 2010. A hidden Markov model approach to multilocus linkage analysis in a full-sib family. Tree Genetics and Genomes, 6:651ĘC662