An improved general amino acid replacement matrix.

By Si Quang Le, Olivier Gascuel. Molecular biology and evolution, 2008

3,007 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/68cceeff9e76968850eaaffb74e1d61592f7017d

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Citations in the corpus

IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, positive): “IQ-TREE 2 implemented mixture models (Le et al. 2008), which assume a user-defined number ( k ) of substitution models (or classes), like partition models.”
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree (2010, methodology): “Reference phylogenetic trees were built based on the full-length gene sequences for each of these genes using PHYML [22] and the LG [18] protein substitution model (LG model chosen based on the evidence presented in the corresponding paper).”
Empirical profile mixture models for phylogenetic reconstruction (2008, methodology): “, 1992), or by direct likelihood maximization (Adachi and Hasegawa, 1996; Adachi et al., 2000; Whelan and Goldman, 2001; Le and Gascuel, 2008).”
FastML: a web server for probabilistic reconstruction of ancestral sequences (2012, methodology): “For amino acids, the server implements the Dayhoff (22), JTT (23), WAG (24), LG (25), mtREV (26) and cpREV (27) replacement matrices; for nucleotides, the JC (28) and the HKY (29) substitution matrices are implemented.”
Olfactory responses of Drosophila suzukii females to host plant volatiles (2015, methodology): “…muscle (Edgar, 2004), and the resulting alignment was processed for phylogenetic inference with phyml (Guindon & Gascuel, 2003) using the lg model (Le & Gascuel, 2008) of sequence evolution plus a discrete gamma distribution using four categories (Yang, 1996) and repeating the search on 100…”
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. (2010, background): “This limitation could be problematic with proteins for which substitutions are much more frequent for specific pairs of amino acids compared with others (e.g., Le and Gascuel 2008).”
Multiple Sequence Alignment (2005, methodology): “A single-linkage guide tree is obtained by Kruskal’s algorithm [37], and an MSA is constructed in a standard way.”
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (2016, methodology): “For protein sequences several models were implemented: LG (36), JTT (37), Dayhoff (38), WAG (39), mtREV for mitochondrial proteins (40) and cpREV for chloroplast proteins (41).”
A predicted sex pheromone receptor of codling moth Cydia pomonella detects the plant volatile pear ester (2014, methodology): “Jacquin-Joly, E., and Merlin, C. (2004). Insect olfactory receptors: contributions of molecular biology to chemical ecology.”
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices (2016, methodology): “For all partition models we assumed the GTR+ (Lanave et al. 1984; Yang 1994) and the LG+ (Yang 1994; Le and Gascuel 2008) models for all genes in the DNA and the AA alignments, respectively.”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, neutral): “LG Nuclear proteins Le and Gascuel (2008)”