Modeling Amino Acid Replacement

By Tobias Müller, Martin Vingron. J. Comput. Biol., 2000

320 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/bbaba929ec6348fa4e249d22666fcccc67e3fbed

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Citations in the corpus

Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria (2005, methodology): “This alignment was used to infer amino acid substitution distances with maximum 6 likelihood (ML) using TREEPUZZLE 5.2 (Strimmer and vonHaeseler 1996; Schmidt et al. 7 2002) with the VT model of evolution (Muller and Vingron 2000).”
Protein database searches using compositionally adjusted substitution matrices (2005, unknown): “This has been true as well of other approaches to constructing substitution matrices [14–17].”
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002, methodology): “, 1992), mtREV24 (Adachi and Hasegawa, 1996), BLOSUM 62 (Henikoff and Henikoff, 1992), VT (Müller and Vingron, 2000), WAG (Whelan and Goldman, 2001).”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, unknown): “VT Nuclear proteins Müller and Vingron (2000)”
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.”
ProtTest: selection of best-fit models of protein evolution (2005, background): “The most common matrices, which are the ones included in ProtTest, are the Dayhoff (Dayhoff et al. 1978), JTT (Jones et al. 1992), WAG (Whelan and Goldman 2001) , mtREV (Adachi and Hasegawa 1996), MtMam (Cao et al. 1998), VT ( Muller and Vingron 2000 ), CpREV (Adachi et al. 2000), RtREV (Dimmic et a”
Bayesian Analysis of Molecular Evolution Using MrBayes (2005, unknown): “, 2000), Blossum (Henikoff and Henikoff, 1992), and Vt (Muller and Vingron. 2000).”
An improved general amino acid replacement matrix. (2008, methodology): “This limitation was alleviated by the resolvent method of Mu¨ller and Vingron (2000), which can exploit more diverging sequence pairs than simple counting methods.”
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing (2006, methodology): “There are several substitution models for this kind of scoring matrices discussed [23,24], we used a model as described by [25,26].”
The human phylome (2007, methodology): “To avoid such pitfalls, we tested using the ML approach several models that are complementary in their scope, namely: JTT [26], a general model for globular, nuclear-encoded proteins; BLOSUM62 [27], inferred from protein blocks of 62% sequence identity; WAG, derived from a database of globular prote”