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Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families. Especially, it supports whole genome sequencing data even with low sequencing depth.
If you use Lep-MAP3, please cite
P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494.
Please note Lep-Anchor for anchoring genomes with Lep-MAP3 linkage maps http://sourceforge.net/projects/lep-anchor
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