. 2013 Feb 23;30(6):1270–1280. doi: 10.1093/molbev/mst034

Table 2.

Real Data Sets Used for Testing CodonPhyML.

ID	Protein-Coding Sequence	Organism Range	No. Taxa	Sequence Length (Nucleotides)	Phylog. Signal^a	Average Branch Length	RF Distance^b			Best-Fitting Model^c
							Codon vs. AA	Codon vs. NT	AA vs. NT
R1	Caudal-like protein activation region (PF04731)	Metazoa	8	567	0.42	0.38	0.00	0.15	0.15	LG + F + Γ
R2	PetM family of cytochrome b6f complex subunit 7 (PF08041)	Bacteria and Eukaryota	12	135	0.26	0.39	0.10	0.67	0.67	WAG + F + Γ,
R2	PetM family of cytochrome b6f complex subunit 7 (PF08041)	Bacteria and Eukaryota	12	135	0.26	0.39	0.10	0.67	0.67	LG + F + Γ
R3	DKCLD (NUC011) domain (PF08068)	Archaea and Eukaryota	18	177	0.24	0.24	0.42	0.67	0.67	LG + F + Γ
R4	6-phosphofructo-2-kinase (PF01591)	Eukaryota	11	726	0.17	0.57	0.00	0.32	0.32	LG + F + Γ
R5	Intermediate filament head (DNA binding) region (PF04732)	Eukaryota	30	315	0.38	0.46	0.42	0.39	0.49	WAG + F + Γ,
R5	Intermediate filament head (DNA binding) region (PF04732)	Eukaryota	30	315	0.38	0.46	0.42	0.39	0.49	LG + F + Γ
R6	Zinc finger, ZZ type (PF00569)	Eukaryota	8	138	0.24	0.62	0.15	0.77	0.77	WAG + F,
R6	Zinc finger, ZZ type (PF00569)	Eukaryota	8	138	0.24	0.62	0.15	0.77	0.77	WAG + F + Γ
R7	Protein of unknown function (PF08004)	Archaea	6	393	0.13	1.29	0.00	0.00	0.00	ECM07 + ω_M0 + κ + Γ
R8	Repeated sequence found in lipoprotein LPP (PF04728)	Bacteria	9	33	0.41	0.32	0.53	0.13	0.53	ECM07 + ω_M0 + κ + Γ, ECM07 + ω_M5 + κ + Γ
R9	Myogenic basic domain (PF01586)	Metazoa	6	345	0.58	0.46	0.00	0.00	0.00	WAG + F + Γ,
R9	Myogenic basic domain (PF01586)	Metazoa	6	345	0.58	0.46	0.00	0.00	0.00	LG + F + Γ
R10	7 transmembrane receptor, rhodopsin family (PF00001)	Metazoa	64	819	0.23	0.61	0.58	0.45	0.64	LG + F + Γ
R11	Homeobox domain (PF00046)	Eukaryota	179	174	0.34	0.24	0.62	0.61	0.73	LG + Γ
R12	Protein of unknown function (PF01973)	Archaea and Bacteria	23	522	0.30	0.47	0.42	0.23	0.42	WAG + F + Γ,
R12	Protein of unknown function (PF01973)	Archaea and Bacteria	23	522	0.30	0.47	0.42	0.23	0.42	LG + F + Γ
R13	EPH receptor A4	Mammalia	21	3,141	0.18	0.09	0.51	0.05	0.56	M0 + Γ
R14	Transcription factor 20	Mammalia	21	6,081	0.21	0.09	0.41	0.10	0.41	M3
R15	WD repeat domain 23	Mammalia	21	1,677	0.20	0.07	0.51	0.31	0.56	M3
R16	Tu translation elongation factor, mitochondrial	Mammalia	21	1,377	0.22	0.11	0.51	0.10	0.46	M3
R17	Zinc finger protein 641	Mammalia	21	1,323	0.21	0.10	0.62	0.10	0.62	M3
R18	Nucleoporin like 2	Mammalia	21	1,380	0.22	0.15	0.26	0.10	0.31	M5
R19	Gm527	Mammalia	21	930	0.16	0.05	0.72	0.31	0.72	M0 + Γ
R20	Integrin β11 binding protein 1	Mammalia	21	600	0.27	0.11	0.87	0.26	0.87	M3
R21	GALA (type III effectors)^d	Bacterium	426	81	0.84	0.16	0.41	0.30	0.39	ECM07 + ω_M5 + κ
R22	Lady bird early (lbe)^e	Drosophila	73	429	0.37	0.005	0.97	0.45	0.97	M0 + Γ
R23	Lady bird early (lbl)^e	Drosophila	72	420	0.31	0.002	0.45	0.38	0.10	M0 + Γ

Note.—Data sets R1–R12 are from PANDIT (Whelan et al. 2006); detailed annotations available from PANDITplus (Dimitrieva and Anisimova 2010); in parentheses shown are their respective Pfam IDs (Punta et al. 2012). Data sets R13–R20 are OMA orthologs (Altenhoff et al. 2011).

^aThe phylogenetic signal is the proportion of the total tree length that is taken up by internal branches (Phillips et al. 2001).

^bPairwise normalized RF distance between phylogenies inferred with best-fitting codon, amino acid (AA), and nucleotide (NT) models.

^cWithin two units to the minimum AICc.

^dData from Kajava et al. (2008).

^eData from Balakirev et al. (2011).