Lep-MAP2

Linkage map construction suite

Brought to you by: fedster9, lep-map, mattb23

Downloads: 0 This Week

Last Update: 2017-04-10

Get an email when there's a new version of Lep-MAP2

Note: Lep-MAP3 is now available https://sourceforge.net/projects/lep-map3/. Expect 20x-1000x speedup over LM2 and more accurate maps.

Lep-MAP2 is a novel linkage map construction software suite. Please refer to the wiki for its documentation.

For further information, please contact Pasi Rastas, pasi.rastas@gmail.com.

If you use Lep-MAP2, please cite
Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example
P. Rastas, F.C.F. Calboli, B. Guo, T. Shikano & J. Merilä
Genome Biology and Evolution, in press.

Project Activity

See All Activity >

Follow Lep-MAP2

Lep-MAP2 Web Site

Other Useful Business Software

AI-powered service management for IT and enterprise teams Icon

AI-powered service management for IT and enterprise teams

Enterprise-grade ITSM, for every business

Give your IT, operations, and business teams the ability to deliver exceptional services—without the complexity. Maximize operational efficiency with refreshingly simple, AI-powered Freshservice.

Try it Free

Rate This Project

Login To Rate This Project

User Reviews

Be the first to post a review of Lep-MAP2!

Additional Project Details

Registered

2015-02-06

Report inappropriate content

Recommended Projects

Lep-MAP3
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
Lep-Anchor
Linkage map guided genome anchoring
LDx
LDx uses approximate ML to estimate linkage from pooled NGS data
CViT
CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.
GeneMiner
GeneMiner2 is based on our previously developed GeneMiner and Easy353 software and integrates excellent tools such as Blast, Minimap2, Fasttree, Muscle5, Mafft, Astral, PPD, PGA, NOVOPlasty, and OrthoFinder. Please cite the literature prompted by the software when using the corresponding functionalities. Our GeneMiner2 manuscript is currently under review: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. GeneMiner2: Accurate and automated recovery of genes from genome-skimming data. Manuscript submitted, 2025. Until that paper is formally published, please cite our earlier work instead: Zhang Z, Xie PL, Guo YL, Zhou WB, Liu EY, Yu Y. 2022. Easy353: A tool to get Angiosperms353 genes for phylogenomic research. Molecular Biology and Evolution 39(12): msac261. Xie PL, Guo YL, Teng Y, Zhou WB, Yu Y. 2024. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Molecular Ecology Resources e139.