List of haplotype estimation and genotype imputation software

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

1. Haplotype estimation
2. Imputation (genetics)
3. Identity by descent
4. Mega2, the Manipulation Environment for Genetic Analysis