This is a list of notable software for haplotype estimation and genotype imputation.
Alphabetical order: AlphaImpute Beagle cnF2freq DAGPHASE Eagle fastPHASE FILLIN (part of TASSEL) FImpute findhap FSFHap (part of TASSEL) HAPI-UR IMPUTE2 LDMIP LinkImpute LinkImputeR MACH PHASE PlantImpute SHAPEIT2 SHAPEIT3 SHAPEIT4 SimWalk2 SNPHAP STITCH WhatsHap HapCUT2 Hap10 H-PoP
References