Phylogenetic estimation of context-dependent substitution rates by maximum likelihood.

By Adam C. Siepel, David Haussler. Molecular biology and evolution, 2003

408 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/c1c2a1a9a475aaac2a10d14462bb24a08f6c3cf3

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Citations in the corpus

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model (2007, neutral): “Many directions have already been explored to improve phylogenetic models, by accounting for compositional biases [23,24], across site heterogeneities of the rates [25,26], or of the substitution processes [27-32], or by acknowledging the variation of site-specific rates with time [33], non-independ”
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, background): “It was proposed that nucleotide substitutions in both coding and noncoding regions are contextdependent in the sense that substitution rates depend on the identity of neighboring bases by adopting an approach of incorporating gamma distribution [29].”
Distribution and intensity of constraint in mammalian genomic sequence. (2005, background): “In addition, there is comparative evidence suggesting that at least some repetitive element fragments are conserved between human and mouse (Silva et al. 2003).”
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions (2010, methodology): “In each M-step, we update the ECM exchangeability parameters using a spectral approximation method (Arvestad and Bruno, 1997) and the branch lengths by numerical optimization of the expected log-likelihood function (Siepel and Haussler, 2004).”
Phylogenomics and the reconstruction of the tree of life (2005, background): “Research in this area is continuing, with the most recently developed models relaxing the assumption of independence among sites by taking into account the occurrence of context-dependen”
Amino acid coevolution induces an evolutionary Stokes shift (2012, background): “There have been other substitution models including context dependency (34, 35), but most of these include the effect of context on the mutation process.”
Aligning multiple genomic sequences with the threaded blockset aligner. (2004, background): “Extensions of TBA to automatically produce the richer class of blocksets obtained by dropping these requirements remain as future work.”
Predicting effective microRNA target sites in mammalian mRNAs (2015, methodology): “1, utilizing the generalized time-reversible substitution model and a fixed-tree topology provided by UCSC (parameters ‘-i SS–subst-mod REV–tree $tree’, where $tree is the Newick format tree of the placental mammals) ( Siepel and Haussler, 2004 ).”
Efficient approximations for learning phylogenetic HMM models from data (2004, methodology): “The same inconsistency is present and noted in Siepel and Haussler (2003).”
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. (2005, background): “(A high rate of turnover of constrained bases might put this fraction considerably higher; see Smith et al. 2004.)”