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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

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 […]


A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

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 (), […]


Antigen Presentation Profiling Reveals Recognition of Lymphoma Immunoglobulin Neoantigens

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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