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- L-POP
- LAMARC, Likelihood Analysis with Metropolis Algorithm using Random Coalescence
- LAMBDAA
- LAMP, Linkage and Association Modeling in Pedigrees
- LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure
- LCP, Linkage Control Program
- LDA, Linkage Disequilibrium Analyzer
- LDB/LDB+, Location DataBase
- LDGROUP
- LDHAT
- LDHEATMAP
- LDMAP
- LDMET
- LDSELECT
- LDSUPPORT
- LEA, Likelihood-based Estimation of Admixture
- LINKAGE - CEPH, LINKAGE CEPH (three-generation) pedigrees
- LINKAGE - general pedigrees
- LINKAGE-IMPRINT, LINKAGE allowing for IMPRINITING
- LINKBASE
- LIPED, Likelihoods in Pedigrees
- LNKTOCRI
- LOCUSMAP
- LOCUSZOOM
- LOGINSERM_ESTIHAPLO
- LOH-LINKAGE
- LOKI
- LOT, Linkage analysis of Ordinal Traits
- LRP, Linkage Report Program
- LRTAE, Likelihood Ratio Test Allowing for Errors
- LSP, Linkage Setup Program
- LTSOFT