The rapid generation of mutation data matrices from protein sequences

By David T. Jones, William R. Taylor, Janet M. Thornton. 1992

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “For example, in a benchmark using simulated protein sequences (Lo¨ytynoja et al. 2012) generated by INDELiBLE (Fletcher and Yang 2009), when we tested a more stringent scoring matrix, JTT 1PAM (Jones et al. 1992) with weaker gap penalties than the default, the benchmark scores were considerably impr”
The Glycosyltransferase Repertoire of the Spikemoss Selaginella moellendorffii and a Comparative Study of Its Cell Wall (2012, unknown): “68 [112] with 250 bootstraps from seqboot, using Jones-Taylor-Thornton matrix [113], no global rearrangement, rough analysis and one jumble.”
ProtTest: selection of best-fit models of protein evolution (2005, methodology): “In this way, different empirical matrices with ﬁxed relative rates of amino acid replacement have been already proposed, like the Dayhoff matrix (Dayhoff et al ., 1978), the JTT matrix (Jones et al ., 1992), the mtREV matrix (Adachi and Hasegawa, 1996) or the WAG matrix (Whelan and Goldman, 2001).”
Mutational effects on stability are largely conserved during protein evolution (2013, methodology): “5A shows maximum clade credibility trees constructed using datestamped sequences and a strict molecular clock in BEAST (52) using the JTT (32) substitution model.”
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny (2021, methodology): “, a PAM matrix is equivalent to parameters for the JTT model [10].”
The human phylome (2007, methodology): “Among the models tested, JTT was chosen as the best fitting model in a majority of the trees (14,683, 68.0%), followed by WAG (6,388, 29.6%), Blosum62 (461, 2.1”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, unknown): “JTT Nuclear proteins Jones et al. (1992)”
PHAT: a transmembrane-specific substitution matrix (2000, methodology): “In 1992, Jones and colleagues modified the collection of PAM 1 counts ( Jones et al., 1992 ).”
Everything you must know about Azospirillum and its impact on agriculture and beyond (2020, methodology): “Analysis was made by Maximum Likelihood method, Tamura-Nei substitution model, and a Bootstrap testing of 1000 iterations (Jones et al. 1992).”
Allosteric Disulfide Bonds (2006, background): “At the same time, cysteine is the second most conserved amino acid (after tryptophan) in protein evolution (Jones et al. 1992) suggesting that there is clearly strong positive selection for cysteines.”
Phylotranscriptomic analysis of the origin and early diversification of land plants (2014, methodology): “The JTT and JTTF models (116) had the highest likelihood score for 65% of genes.”
Estimating maximum likelihood phylogenies with PhyML. (2009, unknown): “PhyML implements a wide range of substitution models: JC69 (10), K80 (11), F81 (1), F84 (12), HKY85 (13), TN93 (14) GTR (15, 16) and CUSTOM for nucleotides ; WAG (17), Dayhoff (18), JTT (19), Blosum62 (20), mtREV (21), rtREV (22), cpREV (23), DCMut (24), VT (25) and mtMAM (26) for amino acids.”