PHLAT statistics

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Citations per year

Citations chart

Popular tool citations

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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

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


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  • person_outline Yu Bai <>

Publication for PHLAT

PHLAT in publications

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

[…] molecules. several tools have been developed to obtain hla allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and rna sequencing data), including optitype, polysolver, phlat, hlareporter, hlaforest, hlaminer, and seq2hla. we have tested 961 whole‐exome data from the 1000 genomes project to evaluate the accuracy of these programs. among these algorithms, optitype […]

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 (), […]

PMCID: 5808925
PMID: 28329770
DOI: 10.1038/nature21433

[…] database., coding variants were annotated to provide the corresponding mutated protein sequences using annovar. patient hla alleles were extracted from sequencing of autologous normal cells using phlat . neoantigen predictions were performed with netmhc 3.4 or else when the hla allele was not included in the netmhc model then netmhcpan2.8 was utilized. unless otherwise specified, peptides […]

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

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