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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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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

Download


download.png
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Versioning


No version available

Documentation


Maintainer


  • person_outline David Posada

Publications for ProtTest

ProtTest citations

 (1329)
library_books

Phylogenetic analyses and in seedling expression of ammonium and nitrate transporters in wheat

2018
Sci Rep
PMCID: 5935732
PMID: 29728590
DOI: 10.1038/s41598-018-25430-8

[…] AMTs 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 al […]

library_books

Genes for de novo biosynthesis of omega 3 polyunsaturated fatty acids are widespread in animals

2018
Sci Adv
PMCID: 5931762
PMID: 29732410
DOI: 10.1126/sciadv.aar6849

[…] mn, 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 wa […]

call_split

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2
call_split See protocol

[…] 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 (https://github.com/widdo […]

library_books

Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages

2018
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 […]

call_split

Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase

2018
PLoS One
PMCID: 5919513
PMID: 29698456
DOI: 10.1371/journal.pone.0196474
call_split See protocol

[…] genes 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 dis […]

library_books

A Predicted Mannoprotein Participates in Cryptococcus gattii Capsular Structure

2018
PMCID: 5917426
DOI: 10.1128/mSphere.00023-18

[…] xal oxidases described by Yin and colleagues (). The sequence alignment was performed in MAFFT v7 server with default parameters. The evolutionary model for amino acid substitutions was determined by ProtTest v3.4.2. The tree was constructed with MEGA 6.0 and maximum likelihood method with a bootstrap of 1,000 replicates. […]

Citations

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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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