A new method for calculating evolutionary substitution rates

By C. Lanave, G. Preparata, Cecilia Sacone, G. Serio. Journal of Molecular Evolution, 2005

1,309 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f45d00735e69eca3f58caaedfdbb7dc8ce8c5520

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Citations in the corpus

Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates (2010, methodology): “4 (Stamatakis 2006) using the general time-reversible (GTR) substitution model (Lanave et al. 1984; Rodriguez et al. 1990) with rate heterogeneity parameters modeled by the Gamma (C) distribution and four rate categories (Yang 1994).”
One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera (2007, methodology): “b10 software (SwoVord 2002), identiWed the general time reversible (GTR) model (Lanave et al. 1984) as the best model for the analyses, taking into account a proportion of invariant sites (I) and a gamma distribution shape parameter ( ).”
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments (2010, methodology): “…character supermatrix the same methods and software as Phillips, Delsuc and Penny (2004; see [25] for more details), we retrieved the same phylogenetic tree (left-hand tree in Figure 9) by minimizing the Minimum Evolution (ME) criterion with both GTR [79-81] and LogDet [82-84] distance estimates.”
Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps) (2010, methodology): “We used the general time-reversible (GTR) + I + C model of nucleotide substitution (Lanave et al., 1984), applied the Bayesian skyline plot tree prior (Drummond et al.”
Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae) (2010, methodology): “On the other hand, the GTR (Lanave et al., 1984) + I + G were selected as the best-fitting model for nucleotide sequences to be utilized in BI and ML analyses.”
Estimating maximum likelihood phylogenies with PhyML. (2009, neutral): “‘010020’ and ‘012345’ correspond to TN93 and GTR models respectively.”
Bayesian phylogenetic analysis of combined data. (2004, methodology): “For single DNA data partitions, we used standard substitution models: Jukes–Cantor (JC; Jukes and Cantor, 1969), Hasegawa–Kishino–Yano (HKY; Hasegawa et al., 1985), and general time reversible (GTR; Lanave et al., 1984; Tavaré, 1986; Rodríguez et al., 1990).”
A molecular phylogeny of antarctic chironomidae and its implications for biogeographical history (2006, background): “MODELTEST indicated the general time reversible model with among-site rate heterogeneity and the proportion of invariant sites (GTR+I+c; Lanave et al. 1984; Yang 1994; Gu et al. 1995) as the best fit for the combined data set.”
Not so different after all: a comparison of methods for detecting amino acid sites under selection. (2005, methodology): “We consider all models which form a particular case of the general reversible nucleotide model Methods for Detection of Selection 1209 (Lanave et al. 1984; Tavare´ 1986; Rodriguez et al. 1990), whose instantaneous substitution rate matrix is deﬁned by where p A , p C , p G , and p T denote the…”
Molecular phylogeny of the genus Tribonema (Xanthophyceae) using rbcL gene sequence data: monophyly of morphologically simple algal species (2005, methodology): “The GTR model with gamma distribution was used.”
Phylogeny in cryptic weevils: molecules, morphology and new genera of western Palaearctic Cryptorhynchinae (Coleoptera : Curculionidae) (2008, methodology): “…(TVM) + proportion of invariable sites (I) + gamma distribution (G) model of nucleotide substitution (a submodel of general time reversible (GTR; Lanave et al. 1984)) as the best-fit model for CO1, the Hasegawa– Kishino–Yano (HKY) + I +G model (Hasegawa et al. 1985) for 16S and the Kimura…”
Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea) (2003, methodology): “According to this, we used both GTR (General Time Reversible model, Lavane et al., 1984; Rodríguez et al., 1990) and HKY (Hasegawa, Kishino & Yano, 1985) distances.”
Biogeographic partitioning and host specialization among foraminiferan dinoflagellate symbionts (Symbiodinium; Dinophyta) (2004, methodology): “First, the MODELTEST program (Posada and Crandall 1998) identified the general time-reversible (GTR) model (Lanave et al. 1984) as the best model for our ML analyses, taking into Fig.”
A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries (2007, methodology): “The Akaike information criterion selected the general time reversible (GTR) model including the proportion of invariable sites and the gamma distribution of rate variation among sites (GTR + I + C: Lanave et al. 1984; Yang 1994; Gu et al. 1995) as the best-fit evolutionary model.”
Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, methodology): “The best-fit model for each gene resulting from MRMODELTEST was the general time-reversible model (Lanave et al. 1984) with invariant sites and gammadistributed rate variation across sites (GTR + I + Γ).”