ProtTest: selection of best-fit models of protein evolution

By Federico Abascal, Rafael Zardoya, David Posada. 2005

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Citations in the corpus

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink (2012, methodology): “The LGþG substitution model (Le and Gascuel, 2008) with empirically determined amino-acid frequencies (þF) was used based on results from the Prottest program (Abascal et al., 2005), whereas the binary partition was analyzed using a binary substitution model with a G rate heterogeneity parameter.”
Estimating maximum likelihood phylogenies with PhyML. (2009, methodology): “This pre-analysis can be done using popular software such as Modeltest (29) or ProtTest (30) for instance.”
Molecular evidence for species separation in the water mite Hygrobates nigromaculatus Lebert, 1879 (Acari, Hydrachnidia): evolutionary consequences of the loss of larval parasitism (2010, methodology): “1.4 (Abascal et al. 2005).”
Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction (2010, methodology): “We used ProtTest [75] to assess the best model of substitution to infer the phylogeny.”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “The best-suited evolutionary model was selected using ProtTest (Abascal et al., 2005) and was found to be WAG (Whelan and Goldman, 2001) with gamma distributed rates.”
ALTER: program-oriented conversion of DNA and protein alignments (2010, methodology): “INPUT: multiple sequence alignment programs Clustal (10) ALN, FASTA, GDE, MSF, NEXUS, PHYLIP, PIR MAFFT (11) ALN, FASTA TCoffee (12) ALN, FASTA, MSF, PHYLIP, PIR MUSCLE (13) ALN, FASTA, MSF, PHYLIP PROBCONS (14) ALN, FASTA OUTPUT: alignment Clustal ALN, FASTA, GDE, MSF, PIR MAFFT FASTA MUSCLE FASTA ”
SMS: Smart Model Selection in PhyML (2017, methodology): “This forms the basis of widely used, user-friendly software programs such as ProtTest for proteins (Abascal et al. 2005).”
ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution (2010, methodology): “Because, the use of different models can change the outcome of the analysis [15], different model selection tools for protein alignments have been implemented in the past, like ProtTest [2] or ModelGenerator [9].”
Differential gene transfers and gene duplications in primary and secondary endosymbioses (2006, neutral): “6 [30,31], implementing the Akaike Information criterion (AIC) was used to select the most appropriate amino acid substitution models for tree building analyses.”
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. (2009, methodology): “6 (Abascal et al. 2005) under the same criteria.”
Endogenous Viral Elements in Animal Genomes (2010, methodology): “Maximum likelihood (ML) phylogenies were estimated using amino acid sequence alignments with RAXML [60], implementing in each case the best fitting substitution model as determined by ProtTest [61].”
Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data (2011, methodology): “Software such as MODELTEST (Posada & Crandall 1998), PROTTEST (Abascal et al. 2005), MRMODELTEST , MRAIC , MODELGENERATOR (Keane et al. 2006) and JMODELTEST (Posada 2008) have been developed to compare substitu-tion models, but these programs are not able to simultaneously conduct model selection fo”