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


Versioning


Add your version

Documentation


Maintainer


  • person_outline David Posada <>

ProtTest articles

ProtTest citations

 (32)
2018
PMCID: 5845897

[…] 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: 5932025

[…] each of those orthologue groups. their amino-acid sequences were aligned using mafft and curated using trimal as described above. the best substitution model of each alignment was selected by using prottest3. the alignments of 155 eggnog orthologue groups were concatenated and subjected to phylogenetic tree reconstruction using raxml with the best substitution model for each protein column […]

2017
PMCID: 5646239

[…] sequence alignment [15–17], which was then translated and used to infer phylogenetic relationships, using maximum likelihood (ml) as implemented in raxml, and an evolutionary model selected using prottest [18, 19]. as shown in fig. 2(a), all six novel parvovirus sequences robustly group with previously characterized chapparvoviruses in bootstrapped ml trees. furthermore, within […]

2017
PMCID: 5510158

[…] a partitioned maximum likelihood analysis was performed to construct the phylogenetic tree with raxml (version 8.1.22) [23] using the best-fit evolutionary models predicted for each alignment by prottest [24]. the number of bootstrap replicates was set at 1,000. all the species were well separated with high bootstrap support values. the most closely related species of l. parakefiri is l. […]

2017
PMCID: 5295241

[…] using mafft 7 [49]. alignments were refined to select reliably-aligned positions by using gblocks version 0.91b [50]. the substitution model lg (+i +g +f) used in this study was selected using prottest 3.4.2 [51]. the maximum likelihood phylogenetic tree was constructed using phyml 3.0 [52], and tree robustness was assessed with 100 bootstrap replications. tree visualization was performed […]

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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