Table 1.

Publications that use six-state amino acid recoding

Citation	Recoding in main figure	Organismal scope or featured taxon
(Benavides et al., 2021)	Yes	Gonyleptoidea
(Luo et al., 2014)	Yes	Bivalves
(Neumann et al., 2020)	Yes	Metazoa
(Pandey et al., 2020)	Yes	Metazoa
Tikhonenkov et al. (2020)	Yes	Tunicaraptor unikontum
(Weinheimer et al., 2020)	Yes	Caudovirales
(Yan et al., 2020)	Yes	Flesh flies
Cunha and Giribet (2019)	Yes	Gastropods
Laumer et al. (2019)	Yes	Animals
Lawrence et al. (2019)	Yes*	Plastids
Lemer et al. (2019)	Yes	Bivalves
Lozano-Fernandez et al. (2019)	Yes	Chelicerates
Marlétaz et al. (2019)	Yes	Spiralia
Philippe et al. (2019)	Yes	Bilateria
Ballesteros et al. (2019)	No	Palpigradi
Benavides et al. (2019)	No	Pseudoscorpiones
Cheng et al. (2019)	No	Zygnematophyceae
Klinges et al. (2019)	No	Candidatus Aquarickettsia
Moore et al. (2019)	No	Plastids
Narayanan et al. (2019)	No	Calyptratae
Uribe et al. (2019)	No	Gastropods
Wolfe et al. (2019)	No	Decapod crustaceans
Zverkov et al. (2019)	No	Dicyemida and Orthonectida
Aouad et al. (2018)	Yes	Archaea
Laumer et al. (2018)	Yes	Placozoa
Otero-Bravo et al. (2018)	Yes	Pantoea
Puttick et al. (2018)	Yes	Land plants
Schwentner et al. (2018)	Yes	Pancrustacea
Sousa et al. (2018)	Yes	Land plants
Bennett and Mao (2018)	No	Fulgoroidea symbionts
Eitel et al. (2018)	No	Placozoa
Manzano-Marín et al. (2018)	No	Cinara strobi symbionts
Feuda et al. (2017)	Yes	Animals
Szabó et al. (2017)	Yes	Pseudococcidae symbionts
Williams et al. (2017)	Yes	Archaea
Schwentner et al. (2017)	No	Pancrustacea
Shin et al. (2017)	No	Curculionoidea
Simion et al. (2017)	No	Animals
Yoshida et al. (2017)	No	Tardigrades
Leliaert et al. (2016)	Yes	Viridiplantae
Zhang et al. (2016)	Yes	Roseobacter CHAB-I-5 lineage
He et al. (2016)	No	Rhizaria
Song et al. (2016)	No	Holometabola
Domman et al. (2015)	Yes	Plastids
Luo (2015)	Yes	SAR11
Petitjean et al. (2015)	Yes	Archaea
Borowiec et al. (2015)	No	Animals
Derelle et al. (2015)	No	Eukaryotes
Wang and Wu (2015)	No	Mitochondria
(Luo et al., 2014)	Yes	Roseobacter
Fu et al. (2014)	No	Discoba
Lemieux et al. (2014)	No	Trebouxiophyceae
Raymann et al. (2014)	No	Archaea
Luo et al. (2013)	Yes	Marine Alphaproteobacteria
Morgan et al. (2013)	Yes	Placental mammals
Rota-Stabelli et al. (2013)	Yes	Pancrustacea
Hill et al. (2013)	No	Demospongiae
Kayal et al. (2013)	No	Cnidaria
Lasek-Nesselquist and Gogarten (2013)	No	3 domains (eukaryotes, archaea, bacteria)
Ometto et al. (2013)	No	Drosophila suzukii
Lasek-Nesselquist (2012)	Yes	Syndermata
Rodríguez-Ezpeleta and Embley (2012)	Yes	SAR11
Burki et al. (2012)	No	Plastids
Derelle and Lang (2012)	No	Eukaryotes
Heinz et al. (2012)	No	Trachipleistophora hominis
Nishimura et al. (2012)	No	Mitochondria
Brochier-Armanet et al. (2011)	Yes	Archaea
Williams et al. (2011)	Yes	Nucleocytoplasmic large DNA virus
Matsumoto et al. (2011)	No	Plastids
Phillips et al. (2001)	No	Xenacoelomorpha
Wodniok et al. (2011)	No	Streptophyte algae and land plants
Torruella et al. (2011)	No	Opisthokonta
Parfrey et al. (2010)	No	Eukaryotes
Pons et al. (2010)	No	Coleoptera
Deschamps and Moreira (2009)	Yes	Archaeplastida
Foster et al. (2009)	Yes	Eukaryotes
Masta et al. (2009)	Yes	Arachnida
Cox et al. (2008)	Yes	Eukaryotes
Haen et al. (2007)	No	Hexactinellida
Andersson et al. (2006)	Yes	Eukaryotes
Fitzpatrick et al. (2006a)	Yes	Mitochondria
Fitzpatrick et al. (2006b)	Yes	Fungi
O’Halloran et al. (2006)	Yes	Caenorhabditis elegans
Delsuc et al. (2006)	No	Chordates
Wang and Lavrov (2006)	No	Homoscleromorpha
Martin et al. (2005)	Yes	Land plants
Philip et al. (2005)	No	Eukaryotes
Hrdy et al. (2004)	Yes	Hydrogenosomes
Embley et al. (2003a)	Yes	Hydrogenosomes
Embley et al. (2003b)	Yes	Hydrogenosomes
Davidson et al. (2002)	Yes	Hydrogenosomes

Note: Asterisk indicates the publication included recoding approaches in a main figure to test if this strategy was appropriate.