Unbiased estimation of the rates of synonymous and nonsynonymous substitution

By Wen-Hsiung Li. Journal of Molecular Evolution, 2006

680 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5fdbaba01fa343741124101869d88b37d1bc43af

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In Molecular Biology

Citations in the corpus

γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, methodology): “A modified LWL, LPB (Li-Pamilo-Bianchi) method corrects for bias in counting sites by using different formulas for Ka and Ks estimation, which differentiate LPB from LWL method [9,10].”
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences (2021, methodology): “selection [19-21], has been widely adopted for determining the strength and type of selection 80 operated on coding sequences [22-27].”
Identifying earthworms through DNA barcodes (2007, background): “D4 sites do not affect the protein sequence and are less sensitive to transition–transversion bias (Li 1993).”
Not so different after all: a comparison of methods for detecting amino acid sites under selection. (2005, methodology): “This ﬁnding appears to contradict the claims made by Suzuki and Gojobori (1999), who found counting methods to always be conservative.”
SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis (2007, background): “Called without arguments, choosebank() gives the list of available databases: choosebank() [1] "genbank" "embl" "emblwgs" "swissprot" [5] "ensembl" "emglib" "nrsub" "nbrf" [9] "hobacnucl" "hobacprot" "hovernucl" "hoverprot" [13] "hogennucl" "hogenprot" "hoverclnu" "hoverclpr" [17] "HAMAPnucl" "HAMAP”
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment (2004, methodology): “…26 Yes Yes (G+C) Yes Yes Tajima–Nei 27 Yes Yes Yes Tamura–Nei 25 Yes Yes Yes Yes Log-Det For computing synonymous and non-synonymous distances, both the Nei– Gojobori 34 and Li–Wu–Luo 35 methods and their modiﬁcations, 9,36–40 which account for transition/transversion bias, are available in MEGA.”