HyPhy protocols

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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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  • person_outline Spencer Muse <>

Publications for Hypothesis testing using Phylogenies

HyPhy in pipelines

 (29)
2017
PMCID: 5266723
PMID: 28184216
DOI: 10.3389/fmicb.2017.00048

[…] (π) were performed with dnasp ver 5.10 (librado and rozas, ). in order to determine if codons in the catalytic domain were subjected to positive or negative selection, several methods within the hyphy analysis suite were used (pond et al., ). a conservative approach was taken for interpreting the results requiring that more than one method detected selection and that p-values or posterior […]

2017
PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] ()., for each analysis, sequences of venom components from the reference genome were codon-aligned using mafft (), and sites under selection were analyzed using the rel algorithm implemented in the hyphy package on the datamonkey server (; )., a consensus sequence of amino acids was formed from the codon alignment and used as input for developing a pla2 model in swiss-model (; ). the suitable […]

2017
PMCID: 5751542
PMID: 29297327
DOI: 10.1186/s12870-017-1190-4

[…] patterns of the genes in the species chosen were taken from the published articles and schematically combined together in fig. ., codon-based maximum likelihood (ml) methods incorporated in the hyphy package [] were applied to determine the ratios of non-synonymous to synonymous substitutions (dn/ds or ω) which provide a measure of the selective pressure at the protein level, where ω < 1 […]

2016
PMCID: 4748293
PMID: 26861415
DOI: 10.1038/srep20783

[…] calculated using bioedit v7.0. test for natural selection pressures on form id rbcl sequences for each dataset were conducted using maximum likelihood-based slac methodology as implemented in the hyphy package and run using web interface at http://www.datamonkey.org. for analyses of natural selection pressure within each ecoregion dataset, automatic nucleotide substitution model selection […]

2016
PMCID: 4756749
PMID: 26893965
DOI: 10.7717/peerj.1678

[…] and between species fixations and calculated πs, πa, and θ = 4neμ across all populations with dnasp v.5.10.1 (). unless stated otherwise, the majority of the remaining analyses were carried out in hyphy v.2.2.1 () or its online server datamonkey (). we selected a nucleotide substitution model (nucmodelcompare.bf) at a model rejection level of 0.0002, the recommended level based on bonferroni […]


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HyPhy in publications

 (637)
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] were estimated with single likelihood ancestor counting (slac), fast unbiased bayes approximation (fubar), mixed effects model of evolution (meme) and fixed effect likelihood (fel) method with hyphy program v2.11 (), assuming a significance level (a) of 0.05. we used a maximum likelihood (ml) phylogenetic tree, inferred with garli v2.01 (https://code.google.com/archive/p/garli/), […]

PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] by both methods were accepted. the cutoff p-value was set to 0.01 in both gard and rdp4. no method detected recombination in any alignment., after running a codon model selection analysis in hyphy (), gene trees were generated by maximum-likelihood using phyml with the approximate likelihood-ratio test (alrt) method ()., to search for positive selection, we applied the site models […]

PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] complex (v) using mega7 (kumar, et al. 2016). no evidence of positive selection (dn > ds) was found using a codon-based z-test of positive selection (p > 0.05). furthermore, we used the hyphy package to estimate selection per codon, based on the difference of non-synonymous (dn) and synonymous (ds) substitutions maximum likelihood []. positive normalized dn-ds values indicate higher […]

PMCID: 5918913
PMID: 29694349
DOI: 10.1371/journal.pgen.1007325

[…] with positive selection and inferred if we can reject m7 in favor of m8 with a p<0.05. rel and fel codon based models were also used to detect sites under positive selection as implemented by the hyphy package using the best substitution models chosen by akaike information criterion (aic) using the phylogenetic tree (newick format):, ((((s. paradoxus, s. cerevisiae), s. mikatae), s. […]

PMCID: 5921268
PMID: 29699483
DOI: 10.1186/s12862-018-1175-4

[…] the denv3/iii was also recovered in oceania region: australia, french polynesia, and samoa.fig. 2, the selection pressure analysis of the complete coding region of denv3/iii was performed using the hyphy package as implemented in datamonkey server []. a combination of codon-based selection pressure analysis (slac, fel, and ifel) with hierarchical bayesian based analysis (fubar) and branch-site […]


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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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