WFES specifications

Information


Unique identifier OMICS_14430
Name WFES
Alternative name Wright-Fisher Exact Solver
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Python
Computer skills Advanced
Stability Beta
Requirements
MKL, cython, numpy
Maintained Yes

Subtool


  • NAP (Network Annotation Propagation)

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Jason de Koning
  • person_outline Nuno Bandeira

Publications for Wright-Fisher Exact Solver

WFES citations

 (2)
library_books

Allele Age Under Non Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach

2017
Sci Rep
PMCID: 5605573
PMID: 28928413
DOI: 10.1038/s41598-017-12239-0

[…] .e. iteratively solving15(I−Q)TMk+1=Mkfor M k+1, where MkT is the p-th row of (I − Q)−k.We have implemented this approach for the first two moments in our software package Wright-Fisher Exact Solver, WFES (available at https://github.com/dekoning-lab/wfes/). In practice it takes only seconds to minutes to calculate the relevant quantities for population sizes under N e = 100,000.As an aside, we no […]

library_books

Wright–Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory

2016
Bioinformatics
PMCID: 5408789
PMID: 28453671
DOI: 10.1093/bioinformatics/btw802

[…] y solving a much simpler linear system. Furthermore, because the transition matrices for most Wright–Fisher models are very sparse, sparsity can be exploited to save both computation time and memory. Wright–Fisher Exact Solver (WFES) is our implementation of these and other ideas. […]

WFES institution(s)
Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; NPPNS, Department of Physic and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil; Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
WFES funding source(s)
Supported by the Collaborative Mass Spectrometry Innovation Center and the Center for Microbiome Innovation, University of California - San Diego, and funding support from the US National Institutes of Health 1R03CA211211-01 and grant P41GM103484-07 from the National Institute of General Medical Sciences; and from the US National Science Foundation IOS-1656481; Bruker and NIH grants GMS10RR029121 and R01 GM107550 and by the São Paulo Research Foundation (Awards FAPESP2015/03348-3, 2014/50265-3 and 14/01884-2).

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