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partis specifications


Unique identifier OMICS_13532
Name partis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data B-cell receptor sequences, parameters particular to the input sequence file
Input format FASTA
Output data The germline genes used to make the BCR, the amount of junctional exonuclease deletion for each gene, the size of junctional insertions (N-regions) between the trimmed germline genes, the joint probability of sequence and annotation
Output format CSV
Operating system Unix/Linux
Programming languages C, C++, Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.13.0
Stability Stable
ham, ig-sw
Maintained Yes




No version available



  • person_outline Frederick A. Matsen
  • person_outline Duncan Ralph

Publications for partis

partis citations


Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long Lived Anti HIV B Cell Lineages

Mol Biol Evol
PMCID: 5913683
PMID: 29688540
DOI: 10.1093/molbev/msy024

[…] om a third HIV patient for 15 years starting from ∼5 years after the date of infection. VRC01 is a large lineage that possibly consists of multiple independent B-cell lineages (; ). We therefore used PARTIS, a recently developed hidden-Markov-model-based method () to partition the heavy-chain VRC01 data set into sets of sequences likely to have descended from the same naive B cell, and to identify […]


A PCR Method That Can Be Further Developed into PCR RFLP Assay for Eight Animal Species Identification

PMCID: 5832126
PMID: 29629212
DOI: 10.1155/2018/5890140

[…] assays, the same length fragments were amplified from two or more animals in the PCR procedure, then PCR products were digested using one or more restriction enzymes to yield different patterns [, ]. Partis et al. [] developed a PCR-RFLP method for the detection of 22 animal species, but this method was unsuitable for analyzing meat mixtures. Several similar multiplex species identification assays […]


Evidence of auditory insensitivity to vocalization frequencies in two frogs

Sci Rep
PMCID: 5608807
PMID: 28935936
DOI: 10.1038/s41598-017-12145-5

[…] s) of the basilar papilla lie in the wall of an endolymphatic diverticulum called the basilar recess (Fig. ). The end of the basilar recess typically meets a perilymphatic channel called the recessus partis basilaris (RPB), the two being separated by a very thin ‘contact membrane’ (Fig. ). It is thought that the contact membrane and the RPB together provide a low-impedance outlet pathway, the pres […]


Inbreeding depression is high in a self‐incompatible perennial herb population but absent in a self‐compatible population showing mixed mating

Ecol Evol
PMCID: 5648656
PMID: 29075469
DOI: 10.1002/ece3.3354

[…] negative ID (Collinsia heterophylla, δ = −0.37). Even if some of these species are in a state of evolutionary transition toward higher selfing rates (e.g., Dart & Eckert, ; Goodwillie, ; Goodwillie, Partis, & West, ), it is still not clear what might stabilize others.Several hypotheses are suggested to explain how mixed mating could be stable. Holsinger () showed that pollen discounting might mai […]


Gene Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

Front Immunol
PMCID: 5424261
PMID: 28539926
DOI: 10.3389/fimmu.2017.00537

[…] of the germline sequence. Undocumented polymorphisms can appear as donor-specific, high-frequency mutations, skewing the resulting GSSPs and exaggerating differences between donors. We therefore used partis () to infer novel germline alleles from each non-redundant dataset. (Allele finding is considered a beta feature, available from We used commit 610ae46 fr […]


BRILIA: Integrated Tool for High Throughput Annotation and Lineage Tree Assembly of B Cell Repertoires

Front Immunol
PMCID: 5239784
PMID: 28144239
DOI: 10.3389/fimmu.2016.00681

[…] thm can annotate sequences that have undergone extensive SHM. For the simulated human BCR sequences, BRILIA achieved 83% D gene degenerate matching accuracy, compared to 65% by VQUEST + JA and 76% by partis (Table , “Clonally Expanded” rows). For the simulated mouse BCR sequences, BRILIA achieved 82% degenerate D gene matching accuracy, compared to 65% by VQUEST + JA (Table , “Clonally Expanded” r […]

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partis institution(s)
Fred Hutch, Seattle, Washington, USA
partis funding source(s)
Supported by NIH grants U19- AI117891, R01-GM113246, and R01-AI12096 and, in part, by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation.

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