In order to explore the feasibility of our method, the whole DNA sequences (including protein-coding and non-coding regions), all protein-coding DNA sequences and all protein sequences from the complete genomes of the following two data sets were obtained from the NCBI genome database http://www.ncbi.nlm.nih.gov/genbank/genomes.
Data set 1 (used in )
We selected 124 large dsDNA viruses. The species in the family Adenoviridae are: Bovine adenovirus D (BAdV_4, NC_002685), Ovine adenovirus D (OAdV_D, NC_004037), Duck adenovirus A (DAdV_A, NC_001813), Fowl adenovirus A (FAdV_A, NC_001720) and Fowl adenovirus D (FAdV_D, NC_000899) in the genus Atadenovirus; Bovine adenovirus B (BAdV_B, NC_001876), Canine adenovirus (CAdV, NC_001734), Human adenovirus A (HAdV_A, NC_001460), Human adenovirus B (HAdV_B, NC_004001), Human adenovirus C (HAdV_C, NC_001405), Human adenovirus D (HAdV_D, NC_002067), Human adenovirus E (HAdV_E, NC_003266), Murine adenovirus A (MAdV_A, NC_000942), Ovine adenovirus A (OAdV_A, NC_002513), Porcine adenovirus C (PAdV_C, NC_002702), Simian adenovirus A (SAdV_3, NC_006144), Bovine adenovirus A (BAdV_A, NC_006324), Human adenovirus F (HAdV_F, NC_001454), Porcine adenovirus A (PAdV_A, NC_005869), Tree shrew adenovirus (TSAdV, NC_004453) and Simian adenovirus 1 (SAdV_1, NC_006879) in the genus Mastadenovirus; Frog adenovirus (FrAdV, NC_002501) and Turkey adenovirus A (TAdV_A, NC_001958) in the genus Siadenovirus. In the family Asfarviridae, we only selected the African swine fever virus (ASFV, NC_001659) in the genus Asfivirus. The viruses in the family Baculoviridae are: Adoxophyes orana granulovirus (AdorGV, NC_005038), Agrotis segetum granulovirus (AsGV, NC_005839), Cryptophlebia leucotreta granulovirus (CrleGV, NC_005068), Cydia pomonella granulovirus (CpGV, NC_002816), Phthorimaea operculella granulovirus (PhopGV, NC_004062), Plutella xylostella granulovirus (PlxyGV, NC_002593) and Xestia c-nigrum granulovirus (XecnGV, NC_002331) in genus Granulovirus; Autographa californica nucleopolyhedrovirus (AcMNPV, NC_001623), Bombyx mori nucleopolyhedrovirus (BmNPV, NC_001962), Choristoneura fumiferana defective nucleopolyhedrovirus (CfDeFNPV, NC_005137), Choristoneura fumiferana MNPV (CfMNPV, NC_004778), Epiphyas postvittana nucleopolyhedrovirus (EppoNPV, NC_003083), Helicoverpa armigera nuclear polyhedrosis virus (HearNPV, NC_003094), Helicoverpa armigera nucleopolyhedrovirus G4 (HearNPVG4, NC_002654), Helicoverpa zea single nucleocapsid nucleopolyhedrovirus (HzSNPV, NC_003349), Lymantria dispar nucleopolyhedrovirus (LdMNPV, NC_001973), Mamestra configurata nucleopolyhedrovirus A (MacoNPV_A, NC_003529), Mamestra configurata nucleopolyhedrovirus B (MacoNPV_B, NC_004117), Neodiprion sertifer nucleopolyhedrovirus (NeseNPV, NC_005905), Orgyia pseudotsugata multicapsid nucleopolyhedrovirus (OpMNPV, NC_001875), Rachiplusia ou multiple nucleopolyhedrovirus (RoMNPV, NC_004323), Spodoptera exigua nucleopolyhedrovirus (SeMNPV, NC_002169) and Spodoptera litura nucleopolyhedrovirus (SpltNPV, NC_003102) in genus Nucleopolyhedrovirus; and two unclassified viruses Culex nigripalpus baculovirus (CuniNPV, NC_003084), Neodiprion lecontei nucleopolyhedrovirus (NeleNPV, NC_005906). The species in the family Herpesviridae are: Gallid herpesvirus 1 (GaHV_1, NC_006623) in genus Iltovirus; Gallid herpesvirus 2 (GaHV_2, NC_002229), Gallid herpesvirus 3 (GaHV_3, NC_002577) and Meleagrid herpesvirus 1 (MeHV_1, NC_002641) in genus Mardivirus; Meleagrid herpesvirus 1 (MeHV_1, NC_002641), Cercopithecine herpesvirus 1 (CeHV_1, NC_004812), Human herpesvirus 1 (HHV_1, NC_001806), Human herpesvirus 2 (HHV_2, NC_001798) and Cercopithecine herpesvirus 2 (CeHV_2, NC_006560) in genus Simplexvirus; Bovine herpesvirus 1 (BoHV_1, NC_001847), Bovine herpesvirus 5 (BoHV_5, NC_005261), Cercopithecine herpesvirus 9 (CHV_7, NC_002686), Equid herpesvirus 1 (EHV_1, NC_001491), Equid herpesvirus 4 (EHV_4, NC_001844), Suid herpesvirus 1 (SuHV_1, NC_006151) and Human herpesvirus 3 (strain Dumas) (HHV_3, NC_001348) in genus Varicellovirus; Human herpesvirus 5 strain AD169 (HHV5L, NC_001347), Human herpesvirus 5 strain Merlin (HHV5w, NC_006273), Pongine herpesvirus 4 (PoHV_4, NC_003521) and Cercopithecine herpesvirus 8 (CeHV_8, NC_006150) in genus Cytomegalovirus; Murid herpesvirus 1 (MuHV_1, NC_004065) and Murid herpesvirus 2 (MuHV_2, NC_002512) in genus Muromegalovirus; Human herpesvirus 6 (HHV_6, NC_001664), Human herpesvirus 6B (HHV_6B, NC_000898) and Human herpesvirus 7 (HHV_7, NC_001716) in genus Roseolovirus; Callitrichine herpesvirus 3 (CalHV_3, NC_004367), Human herpesvirus 4 (HHV_4, NC_009334) and Cercopithecine herpesvirus 15 (CeHV_15, NC_006146) in genus Lymphocryptovirus; Cercopithecine herpesvirus 17 (CeHV_17, NC_003401), Alcelaphine herpesvirus 1 (AIHV_1, NC_002531), Bovine herpesvirus 4 (BoHV_4, NC_002665), Equid herpesvirus 2 (EHV_2, NC_001650), Human herpesvirus 8 (HHV_8, NC_003409), Murid herpesvirus 4 (MuHV_4, NC_001826) and Saimiriine herpesvirus 2 (SaHV_2, NC_001350) in genus Rhadinovirus; Ictalurid herpesvirus 1 (IcHV_1, NC_001493) in genus Ictalurivirus; and 4 unassigned species Tupaiid herpesvirus 1 (TuHV_1, NC_002794), Ostreid herpesvirus 1 (OsHV_1, NC_005881), Psittacid herpesvirus 1 (PsHV_1, NC_005264) and Ateline herpesvirus 3 (AtHV_3, NC_001987). The species in the family Iridoviridae are: Invertebrate iridescent virus 6 (IIV_6, NC_003038) in genus Iridovirus; Lymphocystis disease virus - isolate China (LCDV_IC, NC_005902) and Lymphocystis disease virus 1 (LCDV_1, NC_001824) in genus Lymphocystivirus; Infectious spleen and kidney necrosis virus (ISaKNV, NC_003494) in genus Megalocytivirus; Frog virus 3 (FV_3, NC_005946), Regina ranavirus (ATV, NC_005832) and Singapore grouper iridovirus (SiGV, NC_006549) in genus Ranavirus. In the family Nimaviridae, we only selected Shrimp white spot syndrome virus (WSSV, NC_003225) in genus Whispovirus. The two species in the family Phycodnaviridae are Paramecium bursaria Chlorella virus 1 (PBCV_1, NC_000852) in genus Chlorovirus and Ectocarpus siliculosus virus (EsV_1, NC_002687) in genus Phaeovirus. The two species in the family Polydnaviridae are Cotesia congregata virus (CcBV, NC_006633-62) and Microplitis demolitor bracovirus (MdBV, NC_007028-41) in genus Bracovirus. The species in family Poxviridae are: Canarypox virus (CNPV, NC_005309) and Fowlpox virus (FWPV, NC_002188) in genus Avipoxvirus; Lumpy skin disease virus (LSDV, NC_003027) and Sheeppox virus (SPPV, NC_004002) in genus Capripoxvirus; Myxoma virus (MYXV, NC_001132) and Rabbit fibroma virus (SFV, NC_001266) in genus Leporipoxvirus; Molluscum contagiosum virus (MOCV, NC_001731) in genus Molluscipoxvirus; Camelpox virus (CMLV, NC_003391), Cowpox virus (CPXV, NC_003663), Ectromelia virus (ECTV, NC_004105), Monkeypox virus (MPXV, NC_003310), Vaccinia virus (VACV, NC_006998) and Variola virus (VARV, NC_001611) in genus Orthopoxvirus; Bovine papular stomatitis virus (BPSV, NC_005337) and Orf virus (ORFV, NC_005336) in genus Parapoxvirus; Swinepox virus (SWPV, NC_003389) in genus Suipoxvirus; Yaba monkey tumor virus (YMTV, NC_005179) and Yaba-like disease virus (YDV, NC_002642) in genus Yatapoxvirus; Amsacta moorei entomopoxvirus (AMEV, NC_002520) and Melanoplus sanguinipes entomopoxvirus (MSEV, NC_001993) in genus Betaentomopoxvirus; and unclassified Mule deer poxvirus (DPV, NC_006966). There are another two viruses Acanthamoeba polyphaga mimivirus (APMiV, NC_006450) in genus Mimivirus (unassigned to a family) and Heliothis zea virus 1 (HZV_1, NC_004156) (unclassified).
Data set 2 (selected from Table one in  and Table three in )
We selected 30 parvoviruses. There are 20 species in the subfamily Parvovirinae and 10 species in the subfamily Densovirinae. The species in the subfamily Parvovirinae are: Aleutian mink disease virus (ADMV, NC_001662) in the genus Amdovirus; Minute virus of canines (MVC, NC_004442) in the genus Bocavirus; Adeno-associated virus 1 (AAV1, NC_002077), Adeno-associated virus 2 (AAV2, NC_001401), Adeno-associated virus 3 (AAV3, NC_001729), Adeno-associated virus 4 (AAV4, NC_001829), Adeno-associated virus 5 (AAV5, NC_006152), Adeno-associated virus 7 (AAV7, NC_006260), Adeno-associated virus 8 (AAV8, NC_006261), Avian adeno-associated
virus ATCC VR-865 (AAAVa, NC_004828), Avian adeno-associated virus strain DA-1 (AAAVd, NC_006263), Bovine adeno-associated virus (BAAV, NC_005889), Bovine parvovirus-2 (BPV2, NC_006259), Goose parvovirus (GPV, NC_001701) and Muscovy duck parvovirus (MDPV, NC_006147) in the genus Dependovirus; B19 virus (B19V, NC_000883) in the genus Erythrovirus; Canine parvovirus (CPV, NC_001539), LuIII parvovirus (LuIIIV, NC_004713), Mouse parvovirus 3 (MPV, NC_008185) and Porcine parvovirus (PPV, NC_001718) in the genus Parvovirus. The species in the subfamily Densovirinae are: Aedes albopictus densovirus (AalDNV, NC_004285) in the genus Brevidensovirus; Acheta domesticus densovirus (AdDNV, NC_004290), Diatraea saccharalis densovirus (DsDNV, NC_001899), Galleria mellonella densovirus (GmDNV, NC_004286), Junonia coenia densovirus (JcDNV, NC_004284) and Mythimna loreyi densovirus (MIDNV, NC_005341) in the genus Densovirus; Bombyx mori densovirus 1 (BmDNV1, NC_003346), Bombyx mori densovirus 5 (BmDNV5, NC_004287) and Casphalia extranea densovirus (CeDNV, NC_004288) in the genus Iteravirus; and Periplaneta fuliginosa densovirus (PfDNV, NC_000936) in the genus Pefudensovirus. The genera Amdovirus and Bocavirus, and the genus Pefudensovirus are newly defined genera in the subfamilies Parvoririnae and Densovirinae respectively in the VIIIth Report of ICTV . We also notice that AAV7, AAV8, AAAVa, BPV2, MPV, AdDNV and CeDNV are still unclassified in the VIIIth Report of ICTV.