Data	Source	Identifier
tAI	dos Reis et al., 2004
Ribosome density at A site	Fang et al., 2018;
Ribosome density at A site	Gardin et al., 2014
Ribosome density at A site	Weinberg et al., 2016
tRNA abundance	Tuller et al., 2010
Frequency of optimal codons	CodonW-Saccharomyces Genome Database
Protein abundance	Ho et al., 2018
mRNA abundance	Yassour et al., 2009
Reads per kilobase per million	Heyer and Moore, 2016
Protein abundance	Kulak et al., 2014
Induced stress proteins	Breker et al., 2013
S. cerevisiae CHX-free Riboseq data	Gerashchenko and Gladyshev, 2014	SRR1520311
S. cerevisiae + CHX Riboseq data	Gerashchenko and Gladyshev, 2014	SRR1520315
S. cerevisiae CHX-free Riboseq data	Weinberg et al., 2016	SRR1049521
S. cerevisiae CHX-free Riboseq data	Pop et al., 2014	SRR1688545
Software and algorithms
Codon stabilization coefficient gene (CSCg)	This paper	https://github.com/RodolfoCarneiro/CodonOptmality/tree/master/Sequence_mean_values
Shuffled genome	This paper	https://github.com/RodolfoCarneiro/CodonOptmality/tree/master/Shuffle
Localization of non-optimal/optimal codon stretches	This paper	https://github.com/RodolfoCarneiro/CodonOptmality/tree/master/Distribution