partis specifications

Information


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
Requirements
ham, ig-sw
Maintained Yes

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Maintainers


  • person_outline Frederick A. Matsen <>
  • person_outline Duncan Ralph <>

Publications for partis

partis in publications

 (14)
PMCID: 5913683
PMID: 29688540
DOI: 10.1093/molbev/msy024

[…] 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, […]

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

[…] 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 […]

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

[…] 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, […]

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

[…] 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 […]

PMCID: 5600260
PMID: 28943648
DOI: 10.1177/0011392117717294

[…] with future directions for theorizing and research., cet article examine trois tendances qui coexistent au sein des travaux de recherche sur la droite radicale et populiste. il se penche sur les partis politiques et la mobilisation extraparlementaire dans les démocraties européennes contemporaines. après avoir passé en revue les questions de définition et sélectionné plusieurs cas d’études, […]


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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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