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AlphaPhase specifications


Unique identifier OMICS_33128
Name AlphaPhase
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes




No version available



  • person_outline John Hickey
  • person_outline AlphaPhase Team

Publications for AlphaPhase

AlphaPhase citations


A method for allocating low coverage sequencing resources by targeting haplotypes rather than individuals

PMCID: 5655873
PMID: 29070022
DOI: 10.1186/s12711-017-0353-y
call_split See protocol

[…] ales were used as parents.All individuals were assumed to be genotyped with a panel of 10,000 SNPs distributed equally across the 10 chromosomes. Marker genotypes of all individuals were phased using AlphaPhase [–] as input for AlphaSeqOpt. The parameters used for determining the population haplotype libraries were: (1) population haplotype libraries were created using individuals and SNPs with at […]


Genomic evaluation for a three way crossbreeding system considering breed of origin of alleles

PMCID: 5653471
PMID: 29061123
DOI: 10.1186/s12711-017-0350-1

[…] the breed-of-origin of the alleles in CB pigs, we used the BOA approach that was developed by Vandenplas et al. []. It consists of three steps: (1) phasing the haplotypes of both PB and CB pigs with AlphaPhase1.1 software [], (2) determining the unique haplotypes among the PB, and (3) assigning the breed-of-origin for each allele carried on the haplotypes of CB. This approach was applied to the s […]


A method for the allocation of sequencing resources in genotyped livestock populations

PMCID: 5437657
PMID: 28521728
DOI: 10.1186/s12711-017-0322-5
call_split See protocol

[…] dividuals had genotypes for 10,000 single nucleotide polymorphisms (SNPs) distributed equally across the ten chromosomes, i.e. 1000 SNPs per chromosome. Genotypes of all individuals were phased using AlphaPhase [–] as input. We also performed the same analysis with a pedigree from a real livestock breeding program. Since the results showed the same trends as the simulated data and in the interests […]


A strategy to improve phasing of whole genome sequenced individuals through integration of familial information from dense genotype panels

PMCID: 5434521
PMID: 28511677
DOI: 10.1186/s12711-017-0321-6

[…] programs that are primarily designed for human genetics studies. Popular rule-based phasing and imputation methods that are commonly used in animal breeding genetics such as FImpute [], findhap [] or AlphaPhase [] use information from relatives genotyped at lower marker density to phase animals in the reference panel. A recent study [] compared haplotypes that were obtained from genotyping array d […]


A hybrid method for the imputation of genomic data in livestock populations

PMCID: 5439152
PMID: 28253858
DOI: 10.1186/s12711-017-0300-y

[…] individuals genotyped at low-density. The hybrid method creates a reference set of extremely accurate haplotypes by applying a long-range phasing and haplotype library heuristic imputation algorithm, AlphaPhase []. The advantage of AlphaPhase is that the phasing algorithm can use the genotype information of surrogate parents (i.e., individuals that share a haplotype with the proband and that do no […]


Assigning breed origin to alleles in crossbred animals

PMCID: 4994281
PMID: 27549177
DOI: 10.1186/s12711-016-0240-y

[…] ween breeds because long-range haplotypes are longer than one LD block but are still shared between purebreds and their close crossbred relatives. Also, LRP does not require knowledge of pedigree []. AlphaPhase1.1 (version 1) software [] that implements LRPHLI without pedigree was therefore chosen for this study.Based on their experience, Hickey et al. [] recommended the use of core and tail lengt […]


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AlphaPhase institution(s)
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
AlphaPhase funding source(s)
Supported by the BBSRC ISPG to The Roslin Institute BB/J004235/1, from Genus PLC, and from Grant Nos. BB/M009254/1, BB/L020726/1, BB/N004736/1, BB/N004728/1, BB/L020467/1, BB/N006178/1 and Medical Research Council (MRC) Grant No. MR/M000370/1.

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