Table 2.

Comparison of the codon permutation, synonymous mutation and combined methods to Synplot2 for the Synplot2 validation data set (table 1 from Firth 2014).

Taxon	RefSeq	Gene overlap	Genomic location (nt)	ORF length (nuc)	Codon perm. P value	Synonymous mut. P value
Picornaviridae, Cardiovirus, Theilovirus	NC_001366.1	L/L*	1081–1551	470	0.0005	0.002
Arteriviridae,	NC_001961.1	GP2/GP3	12696–12843	147	0.87	0.52
Arterivirus, PRRSV		GP3/GP4	13241–13460	219	0.06	0.03
Bromoviridae, Cucumovirus, Cucumber mosaic virus	NC_002035.1	ORF2a/2b	2419–2660	241	0.002	0.0007
Hepeviridae, Hepevirus, HEV	NC_001434.1	CP/ORF3	5123–5453	330	0.15	0.02
Betaflexiviridae, Capillovirus, Apple stem grooving virus	NC_001749.2	replicase-CP/MP	4787–5749	962	< 0.0001	<0.0001
Betaflexiviridae, Trichovirus, Apple chlorotic leaf spot virus	NC_001409.1	MP/CP	6784–7100	316	0.004	<0.0001
Alphaflexiviridae, Potexvirus, Pepino mosaic virus	NC_004067.1	TGB2/TGB3	5340–5488	148	0.19	0.23
Sobemovirus, Rice yellow mottle virus	NC_001575.2	replicase/CP	3447–3607	160	0.57	0.56
Nodaviridae, Betanodavirus, Striped jack nervous necrosis virus	NC_003448.1	replicase/B2	2756–2983	227	0.15	0.007
Tombusviridae, Tombusvirus, Tomato bushy stunt virus	NC_001554.1	MP/p19	3888–4406	518	<0.0001	<0.0001
Birnaviridae, Aquabirnavirus, Infectious pancreatic necrosis virus	NC_001915.1	VP5/VP2	120–514	394	0.002	0.0005
Birnaviridae, Avibirnavirus, Infectious bursal disease virus	NC_004178.1	VP5/VP2	130–533	403	0.002	0.03
Reoviridae, Orthoreovirus, Mammalian orthoreovirus 3	NC_004277.1	σ1/σ1s	71–433	362	0.002	0.001
Totiviridae, Totivirus, Saccharomyces cerevisiae virus L-A	NC_003745.1	gag/pol	1964–2072	108	0.88	0.97
Bunyaviridae, Orthobunyavirus, La Crosse virus	NC_004110.1	N/NSs	101–379	278	0.01	0.03
Paramyxoviridae, Morbillivirus, Measles virus	NC_001498.1	P/C	1829–2389	560	0.0001	<0.0001
		P/V	2499–2705	206	0.18	0.007
Paramyxoviridae, Respirovirus, Human parainfluenza virus 3	NC_001796.2	P/C	1794–2393	599	<0.0001	<0.0001
		P/V	2505–2903	398	0.0001	0.0003
Paramyxoviridae, Rubulavirus, Mumps virus	NC_002200.1	P/V	2442–2653	211	0.02	0.02
Picornaviridae, Cardiovirus, Theilovirus	NC_001366.1	L/L*	1081–1551	470	0.0005	0.002
Arteriviridae, Arterivirus, PRRSV	NC_001961.1	GP2/GP3	12696–12843	147	0.87	0.52
		GP3/GP4	13241–13460	219	0.06	0.03
Bromoviridae, Cucumovirus, Cucumber mosaic virus	NC_002035.1	ORF2a/2b	2419–2660	241	0.002	0.0007
Hepeviridae, Hepevirus, HEV	NC_001434.1	CP/ORF3	5123–5453	330	0.15	0.02