A model of evolutionary change in protein

By M. O. Dayhoff. 1978

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Citations in the corpus

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. (2003, methodology): “The Dayhoff (Dayhoff et al., 1978) and JTT (Jones et al., 1992) models for proteins are also available and run quickly, requiring about 3 min to analyze a data set comprising 50 mammalian sequences and 1,729 sites (F. Delsuc, pers. com.).”
MUSCLE: a multiple sequence alignment method with reduced time and space complexity (2004, methodology): “The alphabet used in MAFFT is taken from [20], and is one of the options implemented in MUSCLE.”
A model of substitution trajectories in sequence space and long-term protein evolution. (2015, methodology): “Amino acid sequence divergence models often use a precomputed matrix of amino acid substitution rates, such as BLOSUM or PAM (Dayhoff et al. 1978; Henikoff S and Henikoff JG 1992; Whelan and Goldman 2001).”
Pitfalls in supermatrix phylogenomics (2017, unknown): “More recent alignment fi ltering methods, such as trimAl (Capella-Gutierrez et al. 2009) or BMGE (Criscuolo & Gribaldo 2010), refi ne this measure of site conservation through the use of, e.g., PAM or BLOSUM matrices (Dayhoff et al. 1978; Henikoff & Henikoff 1992).”
Scoring residue conservation (2002, background): “In 1986, Taylor(18) classified amino acid types according to their stereochemical properties and their patterns of conservation in the Dayhoff mutation data matrix.(19) He embodied them in a Venn diagram (Fig.”
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).”
Clustering of database sequences for fast homology search using upper bounds on alignment score. (2004, methodology): “However, our proposed method can be extended for other matrices such as PAM [5] using the inequality (1), which was not obtained by Stojmirovic.”