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PHLAT specifications


Unique identifier OMICS_08351
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Python, cPickle, Bowtie
Maintained Yes


No version available


  • person_outline Yu Bai

Publication for PHLAT

PHLAT citations


Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

Cancer Sci
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] e the accuracy of these programs. Among these algorithms, OptiType showed the highest accuracy of 97.2% for HLA class I alleles at the second field level, followed by 94.0% in Polysolver and 85.6% in PHLAT. […]


A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

Front Immunol
PMCID: 5797543
PMID: 29441070
DOI: 10.3389/fimmu.2018.00099

[…] at a rate of ~6 h/sample on four Microsoft Azure machines (Supplementary Data S1 in Supplementary Material). MHC haplotypes for MHC class I and MHC class II are called from the sequencing data using PHLAT (). The haplotype for a sample is decided based on a consensus decision of the three input haplotypes. Somatic point mutations were called using a panel of five mutation callers, MuTECT (), MuSE […]


Comparison of exome based HLA class I genotyping tools: identification of platform specific genotyping errors

J Hum Genet
PMCID: 5334549
PMID: 27881843
DOI: 10.1038/jhg.2016.141

[…] HLA typing using whole-exome data: Optitype, Polysolver, PHLAT, HLAreporter, HLAforest, HLAminer and seq2HLA, using 12 clinical samples, and further evaluated three of them, Optitype, Polysolver and PHLAT, which displayed the highest accuracy (>90%) in the preliminary screening, using 961 samples from the 1000 Genomes Project database.One of the common platform-specific miscalls is from HLA-A*25: […]


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PHLAT institution(s)
Regeneron Pharmaceuticals, Inc, Tarrytown, NY, USA

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