HyPhy pipeline

HyPhy specifications

Information


Unique identifier OMICS_04235
Name HyPhy
Alternative name Hypothesis testing using Phylogenies
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
Computer skills Advanced
Version 2.2.7
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Spencer Muse <>

Publications for Hypothesis testing using Phylogenies

HyPhy citations

 (7)
2017
PMCID: 5297179

[…] selection, fast single-likelihood ancestor counting (slac), fixed effects likelihood (fel), random effects likelihood (rel) and mixed effects model of evolution (meme) methods available in the hyphy package [41] and in a free public web implementationon http://www.datamonkey.org (last accessed 15 march 2016; [42]) were applied to our atp6 and nd2 sequences using the best fit nucleotide […]

2016
PMCID: 5181398

[…] ic 13.1 software (statacorp lp, college station, tx, usa)., selection pressure was examined by estimating non-synonymous (dn) and synonymous (ds) substitution rates during darunavir therapy using the hyphy software package available on datamonkey, a web-based interface.15,16 the dn:ds ratio was calculated for amino acid sites 5–99 of the protease gene and positive selection was inferred if dn > […]

2016
PMCID: 5108218

[…] (beb) for models m2a and m8. additionally, we conducted the fixed effects likelihood (fel), random effects likelihood (rel) and the mixed effects model of evolution (meme) tests implemented in the hyphy software (hosted at datamonkey: http://www.datamonkey.org/). we checked for signatures of recombination using the genetic algorithm recombination detection method using the datamonkey website., […]

2016
PMCID: 4973242

[…] counting (slac), fixed-effects likelihood (fel), internal fixed-effects likelihood (ifel), and random effects likelihood (rel) methods3334 available at the datamonkey3536 online version of the hyphy package37. all analyses utilized the hky85 nucleotide substitution model, which was tested as the best fitting model for the data sets, and employed input neighbor joining phylogenetic trees. […]

2015
PMCID: 4598017

[…] procedure (beb) for models m2a and m8 [67]. we also tested for codon based positive selection using the fixed effects likelihood (fel) and mixed effects model of evolution (meme) implemented in the hyphy software (hosted at datamonkey: http://www.datamonkey.org/ [68–70]). we checked for signatures of recombination using the genetic algorithm recombination detection (gard) method using […]

HyPhy institution(s)
Antiviral Research Center, University of California San Diego, San Diego, CA, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
HyPhy funding source(s)
Supported by grants from the NSF (DBI- 0096033 and DEB-9996118), NIH (5 R01 AI47745 and 5 U01 AI43638 Supp), the University of California University wide AIDS Research Program (IS02-SD-701), and by a University of California, San Diego Center for AIDS Research/NIAID Developmental Award (grant no. 2 P30 AI36214).

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