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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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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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Documentation


Maintainer


  • person_outline David Posada <>

Publications for ProtTest

ProtTest in pipelines

 (183)
2018
PMCID: 5862453
PMID: 29561852
DOI: 10.1371/journal.pone.0193739

[…] used in the analysis of peptides were detailed on supplementary material ., we selected the mature protein sequences of the putative metalloproteinases without the signal peptide to be used in prottest 2.4 []. prottest selected the model of protein evolution that best fit in the sequence alignment; wag with site heterogeneity model gamma plus invariant sites (g+i). the bayesian analyses […]

2018
PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] conserved blocks was done using “relaxed” conditions in gblocks []. the final concatenated alignment contained 47 726 amino acids. the selection of best amino acid substitution model was done using prottest 3 [] based on bic criterion. the bayesian analysis was performed using mrbayes v3.2.5 [, ], 1 million generations and the dayhoff i+g+f amino acid substitution model []. two simultaneous, […]

2018
PMCID: 5786227
PMID: 29329439
DOI: 10.1093/gbe/evy002

[…] and divergent or ambiguous positions were removed using bioedit v. 7. for each protein, the best evolutionary models with the lowest akaike information criterion (aic) were determined using prottest 3 () and the selected model for each phylogeny were noted with each phylogenetic tree. the phylogenetic trees were inferred by phyml v. 3.0 (), using the best model with 1,000 bootstrap […]

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

[…] performed on protein sequences aligned with mafft v.7.215 []. after estimating the best protein evolution model and alpha parameter of the gamma distribution of substitution rate categories with prottest v.3.4.2 [], the phylogenetic trees were generated with the phyml v.3.3 software [] 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 prottest 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 tree., divergence time between 14 […]


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ProtTest in publications

 (1002)
PMCID: 5935732
PMID: 29728590
DOI: 10.1038/s41598-018-25430-8

[…] and wnrts were aligned separately in muscle 3.8.31 using 100,000 iterations. to identify the most appropriate evolutionary model, the multiple protein alignment generated by muscle was passed to prottest3 3.4.2. prottest3 results showed that the best model for wamt alignment was the jtt (johns-taylor-thornton) model with gamma-distributed rate variation (g); whereas the best model for wnrt […]

PMCID: 5931762
PMID: 29732410
DOI: 10.1126/sciadv.aar6849

[…] and site masking cutoff threshold <0.5. the resultant msa was then filtered to remove columns with gaps in 95% or more of the sequences. the best-fit model of protein evolution was selected using prottest v.3.3 () based on the bayesian information criterion. the ml phylogenetic inference was performed using raxml with 100 rapid bootstrap replicates and 20 ml searches. the bayesian inference […]

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] residues) was generated by concatenating individual gene alignments using a customised python script. protein evolution model selection was performed for each gene of the supermatrix alignment using prottest v3.4 []. the supermatrix tree was inferred with raxml v8.2.4 as previously described [, ]. average nucleotide identity comparisons were calculated using pyani v0.2.3 […]

PMCID: 5924435
PMID: 29719716
DOI: 10.1186/s13227-018-0099-9

[…]  hoxa11 affiliation was confirmed with the program hoxpred (url: http://cege.vub.ac.be/hoxpred) []. the best fitting amino acid substitution models for the hox and meis alignments were selected using prottest 3 [], using the “fast” option and under a full coverage of the amino acidic substitution matrices and of the specific corrections therein proposed. the akaike information criterion (aic), the […]

PMCID: 5919513
PMID: 29698456
DOI: 10.1371/journal.pone.0196474

[…] of dcp () obtained by a blast search were aligned using muscle 3.8.425 software (default parameters) [] and trimmed with bmge 1.12 (-b 5 -m blosum30) []. protein evolution model was selected by prottest 3.2 [] to reconstruct phylogenetic tree by phyml 3.1 (topology search: best of nnis and sprs, initial tree: bionj, substitution model: lg, proportion of invariable sites: fixed (0), gamma […]


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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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