ProtTest protocols

ProtTest specifications

Information


Unique identifier OMICS_11547
Name ProtTest
Interface Web user interface
Restrictions to use None
License GNU General Public License version 3.0
Computer skills Basic
Version 2.4
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline David Posada <>

Information


Unique identifier OMICS_11547
Name ProtTest
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.4.1
Stability Stable
Maintained Yes

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Versioning


Add your version

Documentation


Maintainer


  • person_outline David Posada <>

Publications for ProtTest

ProtTest IN pipelines

 (95)
2018
PMCID: 5762703
PMID: 29321589
DOI: 10.1038/s41598-017-18695-y

[…] of hprs). phylogenetic analyses, instead, were performed on five randomized subsets of 100 single-copy orthologs with the estimation of the best substitution models for each subset from prottest 3.358 and the calculation of maximum likelihood phylogenetic trees in mega659 using 1000 bootstrap replicates. the consensus phylogeny was then used as a reference to estimate the ancestral […]

2018
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] relationship of the concatenated data was inferred using raxmlv8.2.4 [36] based on the maximum-likelihood (ml) algorithm with the protgammalgf evolutionary model and 1000 bootstrap replicates, after prottest 3.4 [37] was performed to estimate the best-fit substitution model. the genome of shewanella denitrificans os217 was chosen to serve as an outgroup. the phylogenetic network […]

2018
PMCID: 5845897
PMID: 29563916
DOI: 10.3389/fimmu.2018.00456

[…] analyses. the protein sequences were multiply aligned using the accurate mode of t-coffee (57). this method takes into account the 3d structures available for improving the alignment quality. prottest v3.2.2 (58) was applied to find an optimal substitution model for each alignment. wag (whelan and goldman) was the best-fit model. phylogenetic analyses were performed […]

2018
PMCID: 5867864
PMID: 29509668
DOI: 10.3390/genes9030143

[…] performed on protein sequences aligned with mafft v.7.215 [34]. after estimating the best protein evolution model and alpha parameter of the gamma distribution of substitution rate categories with prottest v.3.4.2 [35], the phylogenetic trees were generated with the phyml v.3.3 software [36] with approximate likelihood-ratio test (alrt) implementation for the calculation of branch supports […]

2018
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] were concatenated to a super alignment matrix. the super alignment matrix was used for phylogenetic tree reconstruction through maximum likelihood (ml) methods. before ml reconstruction, we used prottest64 to select the best substitution models. the jtt + i + g + f model was selected as the best-fit model, and raxmlwas used to reconstruct the phylogenetic tree65., divergence time between 14 […]

ProtTest institution(s)
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Department of Electronics and Systems, Computer Architecture Group, University of A Coruña, A Coruña, Spain
ProtTest funding source(s)
This work was financially supported by the European Research Council (ERC-2007-Stg 203161-PHYGENOM); the Spanish Ministry of Science and Education (BFU2009-08611); Xunta de Galicia (Galician Thematic Networks RGB 2010/90 and GHPC2 2010/53).

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