-
1
-
-
84893511241
-
Towards a taxonomic coherence between average nucleotide identity and 16 S rRNA gene sequence similarity for species demarcation of prokaryotes
-
Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16 S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64: 346-351.
-
(2014)
Int J Syst Evol Microbiol
, vol.64
, pp. 346-351
-
-
Kim, M.1
Oh, H.-S.2
Park, S.-C.3
Chun, J.4
-
2
-
-
84865370448
-
PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses
-
Bao Y, Chetvernin V, Tatusova T (2012) PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses. Viruses 4: 1318-1327.
-
(2012)
Viruses
, vol.4
, pp. 1318-1327
-
-
Bao, Y.1
Chetvernin, V.2
Tatusova, T.3
-
3
-
-
84878598727
-
A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
-
Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, et al. (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158: 1411-1424.
-
(2013)
Arch Virol
, vol.158
, pp. 1411-1424
-
-
Muhire, B.1
Martin, D.P.2
Brown, J.K.3
Navas-Castillo, J.4
Moriones, E.5
-
4
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
5
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
-
6
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772-780.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
7
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
8
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
-
11
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27: 2682-2690.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
12
-
-
34248374330
-
An enhanced RNA alignment benchmark for sequence alignment programs
-
Wilm A, Mainz I, Steger G (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol 1: 19. doi:10.1186/1748-7188-1-19.
-
(2006)
Algorithms Mol Biol
, vol.1
, pp. 19
-
-
Wilm, A.1
Mainz, I.2
Steger, G.3
-
13
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
14
-
-
84876220535
-
Making automated multiple alignments of very large numbers of protein sequences
-
Sievers F, Dineen D, Wilm A, Higgins DG (2013) Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics 29: 989-995.
-
(2013)
Bioinformatics
, vol.29
, pp. 989-995
-
-
Sievers, F.1
Dineen, D.2
Wilm, A.3
Higgins, D.G.4
-
15
-
-
33846197539
-
Settling the intractability of multiple alignment
-
Elias I (2006) Settling the intractability of multiple alignment. J Comput Biol 13: 1323-1339.
-
(2006)
J Comput Biol
, vol.13
, pp. 1323-1339
-
-
Elias, I.1
-
16
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
17
-
-
0003991673
-
-
Sunderland, Massachusetts: Sinauer Associates, Inc.
-
Felsenstein J (2004) Inferring Phylogenies. Sunderland, Massachusetts: Sinauer Associates, Inc.
-
(2004)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
19
-
-
84861323730
-
Partitioning the genetic diversity of a virus family: Approach and evaluation through a case study of picornaviruses
-
Lauber C, Gorbalenya AE (2012) Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol 86: 3890-3904.
-
(2012)
J Virol
, vol.86
, pp. 3890-3904
-
-
Lauber, C.1
Gorbalenya, A.E.2
-
20
-
-
84903612358
-
Complete genome sequence of Jacquemontia yellow mosaic virus, a novel begomovirus from Venezuela related to other New World bipartite begomoviruses infecting Convolvulaceae
-
Fiallo-Olivé E, Chirinos DT, Geraud-Pouey F, Moriones E, Navas-Castillo J (2014) Complete genome sequence of Jacquemontia yellow mosaic virus, a novel begomovirus from Venezuela related to other New World bipartite begomoviruses infecting Convolvulaceae. Arch Virol. 159: 1857-1860.
-
(2014)
Arch Virol
, vol.159
, pp. 1857-1860
-
-
Fiallo-Olivé, E.1
Chirinos, D.T.2
Geraud-Pouey, F.3
Moriones, E.4
Navas-Castillo, J.5
-
21
-
-
41149115557
-
Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains
-
Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, et al. (2008) Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol 82: 3204-3219.
-
(2008)
J Virol
, vol.82
, pp. 3204-3219
-
-
Matthijnssens, J.1
Ciarlet, M.2
Heiman, E.3
Arijs, I.4
Delbeke, T.5
-
22
-
-
84903595327
-
Revisiting the classification of curtoviruses based on genome-wide pairwise identity
-
Varsani A, Martin DP, Navas-Castillo J, Moriones E, Hernández-Zepeda C, et al. (2014) Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Arch Virol.158: 1873-82.
-
(2014)
Arch Virol
, vol.158
, pp. 1873-1882
-
-
Varsani, A.1
Martin, D.P.2
Navas-Castillo, J.3
Moriones, E.4
Hernández-Zepeda, C.5
-
23
-
-
84899935904
-
A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease
-
Manzoor MT, Ilyas M, Shafiq M, Haider MS, Shahid AA, et al. (2014) A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease. Arch Virol. 159: 1217-1221.
-
(2014)
Arch Virol
, vol.159
, pp. 1217-1221
-
-
Manzoor, M.T.1
Ilyas, M.2
Shafiq, M.3
Haider, M.S.4
Shahid, A.A.5
-
24
-
-
84885947518
-
Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source
-
Kanakala S, Verma HN, Vijay P, Saxena DR, Malathi VG (2013) Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source. Appl Microbiol Biotechnol 97: 9491-9501.
-
(2013)
Appl Microbiol Biotechnol
, vol.97
, pp. 9491-9501
-
-
Kanakala, S.1
Verma, H.N.2
Vijay, P.3
Saxena, D.R.4
Malathi, V.G.5
-
25
-
-
84905246363
-
Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato
-
Paz-Carrasco LC, Castillo-Urquiza GP, Lima ATM, Xavier CAD, Vivas-Vivas LM, et al. (2014) Begomovirus diversity in tomato crops and weeds in Ecuador and the detection of a recombinant isolate of rhynchosia golden mosaic Yucatan virus infecting tomato. Arch Virol. doi:10.1007/s00705-014-2046-y.
-
(2014)
Arch Virol
-
-
Paz-Carrasco, L.C.1
Castillo-Urquiza, G.P.2
Lima, A.T.M.3
Xavier, C.A.D.4
Vivas-Vivas, L.M.5
-
26
-
-
84907448448
-
Isolation and molecular characterization of a distinct begomovirus and its associated betasatellite infecting Hedyotis uncinella (Hook. et Arn.) in Vietnam
-
Du Z, Chen M, Wang Z, Liu Y, Zhang S, et al. (2014) Isolation and molecular characterization of a distinct begomovirus and its associated betasatellite infecting Hedyotis uncinella (Hook. et Arn.) in Vietnam. Virus Genes 80: 246-250.
-
(2014)
Virus Genes
, vol.80
, pp. 246-250
-
-
Du, Z.1
Chen, M.2
Wang, Z.3
Liu, Y.4
Zhang, S.5
-
27
-
-
84905226337
-
Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus
-
Varsani A, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A, et al. (2014) Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol. doi:10.1007/s00705-014-2050-2.
-
(2014)
Arch Virol
-
-
Varsani, A.1
Navas-Castillo, J.2
Moriones, E.3
Hernández-Zepeda, C.4
Idris, A.5
-
28
-
-
84878631350
-
Diversity of beet curly top Iran virus isolated from different hosts in Iran
-
Gharouni Kardani S, Heydarnejad J, Zakiaghl M, Mehrvar M, Kraberger S, et al. (2013) Diversity of beet curly top Iran virus isolated from different hosts in Iran. Virus Genes 46: 571-575.
-
(2013)
Virus Genes
, vol.46
, pp. 571-575
-
-
Gharouni Kardani, S.1
Heydarnejad, J.2
Zakiaghl, M.3
Mehrvar, M.4
Kraberger, S.5
-
29
-
-
84879684864
-
Genetic diversity and host range studies of turnip curly top virus
-
Razavinejad S, Heydarnejad J, Kamali M, Massumi H, Kraberger S, et al. (2013) Genetic diversity and host range studies of turnip curly top virus. Virus Genes 46: 345-353.
-
(2013)
Virus Genes
, vol.46
, pp. 345-353
-
-
Razavinejad, S.1
Heydarnejad, J.2
Kamali, M.3
Massumi, H.4
Kraberger, S.5
-
30
-
-
84907691813
-
A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus species from Axonopus compressus
-
Oluwafemi S, Kraberger S, Shepherd D, Martin D, Varsani A (2014) A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus species from Axonopus compressus. Arch Virol. doi:10.1007/s00705-014-2090-7.
-
(2014)
Arch Virol
-
-
Oluwafemi, S.1
Kraberger, S.2
Shepherd, D.3
Martin, D.4
Varsani, A.5
-
31
-
-
84907704499
-
Association of a distinct strain of hollyhock yellow vein mosaic virus and Ludwigia leaf distortion betasatellite with yellow vein mosaic disease of hollyhock (Alcea rosea) in India
-
Srivastava A, S. Kumar S, Raj SK, Pande SS (2014) Association of a distinct strain of hollyhock yellow vein mosaic virus and Ludwigia leaf distortion betasatellite with yellow vein mosaic disease of hollyhock (Alcea rosea) in India. Arch Virol. DOI 10.1007/s00705-014-2108-1.
-
(2014)
Arch Virol
-
-
Srivastava, A.1
Kumar S, S.2
Raj, S.K.3
Pande, S.S.4
-
32
-
-
84900855346
-
Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of Beak and feather disease viruses
-
Stenzel T, Piasecki T, Chrza¸stek K, Julian L, Muhire BM, et al. (2014) Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of Beak and feather disease viruses. J Gen Virol. 95: 1338-1351.
-
(2014)
J Gen Virol
, vol.95
, pp. 1338-1351
-
-
Stenzel, T.1
Piasecki, T.2
Chrza¸stek, K.3
Julian, L.4
Muhire, B.M.5
-
33
-
-
84897869818
-
Genome Diversity and Evidence of Recombination and Reassortment in Nanoviruses from Europe
-
Grigoras I, Del Cueto Ginzo AI, Martin DP, Varsani A, Romero J, et al. (2014) Genome Diversity and Evidence of Recombination and Reassortment in Nanoviruses from Europe. J Gen Virol.95: 1178-1191.
-
(2014)
J Gen Virol
, vol.95
, pp. 1178-1191
-
-
Grigoras, I.1
Del Cueto Ginzo, A.I.2
Martin, D.P.3
Varsani, A.4
Romero, J.5
-
34
-
-
84885306231
-
Novel myco-like DNA viruses discovered in the faecal matter of various animals
-
Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, et al. (2013) Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res 177: 209-216.
-
(2013)
Virus Res
, vol.177
, pp. 209-216
-
-
Sikorski, A.1
Massaro, M.2
Kraberger, S.3
Young, L.M.4
Smalley, D.5
-
35
-
-
84880144820
-
High global diversity of cycloviruses amongst dragonflies
-
Dayaram A, Potter KA, Moline AB, Rosenstein DD, Marinov M, et al. (2013) High global diversity of cycloviruses amongst dragonflies. J Gen Virol 94: 1827-1840.
-
(2013)
J Gen Virol
, vol.94
, pp. 1827-1840
-
-
Dayaram, A.1
Potter, K.A.2
Moline, A.B.3
Rosenstein, D.D.4
Marinov, M.5
-
36
-
-
84896795221
-
Isolation and Molecular Characterization of a Novel Picornavirus from Baitfish in the USA
-
Phelps NBD, Mor SK, Armien AG, Batts W, Goodwin AE, et al. (2014) Isolation and Molecular Characterization of a Novel Picornavirus from Baitfish in the USA. PLoS One 9: e87593.
-
(2014)
PLoS One
, vol.9
, pp. e87593
-
-
Phelps, N.B.D.1
Mor, S.K.2
Armien, A.G.3
Batts, W.4
Goodwin, A.E.5
-
37
-
-
84901980050
-
Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China
-
Liu Q, Zhang Z, Li Z, Qiao Qi, Qin Y, et al (2014) Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China. Arch Virol. DOI 10.1007/s00705-013-1958-2.
-
(2014)
Arch Virol
-
-
Liu, Q.1
Zhang, Z.2
Li, Z.3
Qiao, Qi.4
Qin, Y.5
-
38
-
-
84905243110
-
Genetic structure and molecular variability of potato virus M populations
-
Tabasinejad F, Jafarpour B, Zakiaghl M, Siampour M, Rouhani H, et al. (2014) Genetic structure and molecular variability of potato virus M populations. Arch Virol. DOI 10.1007/s00705-014-2037-z.
-
(2014)
Arch Virol
-
-
Tabasinejad, F.1
Jafarpour, B.2
Zakiaghl, M.3
Siampour, M.4
Rouhani, H.5
-
39
-
-
84906075844
-
Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China
-
Liu P, Li Z, Song S, Wu Y, (2014) Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China. Arch Virol. DOI 10.1007/s12600-013-0381-2.
-
(2014)
Arch Virol
-
-
Liu, P.1
Li, Z.2
Song, S.3
Wu, Y.4
-
40
-
-
84883775423
-
Identification and characterisation of a highly divergent geminivirus: Evolutionary and taxonomic implications
-
Bernardo P, Golden M, Akram M, Naimuddin, Nadarajan N, et al. (2013) Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 177: 35-45.
-
(2013)
Virus Res
, vol.177
, pp. 35-45
-
-
Bernardo, P.1
Golden, M.2
Akram, M.3
Naimuddin4
Nadarajan, N.5
-
41
-
-
84875233034
-
Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species
-
Piasecki T, Harkins GW, Chrza¸stek K, Julian L, Martin DP, et al. (2013) Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species. Virology 438: 98-105.
-
(2013)
Virology
, vol.438
, pp. 98-105
-
-
Piasecki, T.1
Harkins, G.W.2
Chrza¸stek, K.3
Julian, L.4
Martin, D.P.5
-
42
-
-
84901975965
-
Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1
-
Du Z, Tang Y, Zhang S, She X, Lan G, et al. (2013) Identification and molecular characterization of a single-stranded circular DNA virus with similarities to Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1. Arch Virol. 159: 1527-1531.
-
(2013)
Arch Virol
, vol.159
, pp. 1527-1531
-
-
Du, Z.1
Tang, Y.2
Zhang, S.3
She, X.4
Lan, G.5
-
43
-
-
84893704521
-
Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches
-
Dayaram A, Galatowitsch M, Harding JS, Argüello-Astorga GR, Varsani A (2014) Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches. Infect Genet Evol 22: 134-141.
-
(2014)
Infect Genet Evol
, vol.22
, pp. 134-141
-
-
Dayaram, A.1
Galatowitsch, M.2
Harding, J.S.3
Argüello-Astorga, G.R.4
Varsani, A.5
-
44
-
-
84900844547
-
A novel papillomavirus in Adelie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica
-
Varsani A, Kraberger S, Jennings S, Porzig EL, Julian L, et al. (2014) A novel papillomavirus in Adelie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica. J Gen Virol. 95: 1352-1365.
-
(2014)
J Gen Virol
, vol.95
, pp. 1352-1365
-
-
Varsani, A.1
Kraberger, S.2
Jennings, S.3
Porzig, E.L.4
Julian, L.5
-
45
-
-
84902006019
-
Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica)
-
Zawar-Reza P, Argüello-Astorga GR, Kraberger S, Julian L, Stainton D, et al. (2014) Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infect Genet Evol 26: 132-138.
-
(2014)
Infect Genet Evol
, vol.26
, pp. 132-138
-
-
Zawar-Reza, P.1
Argüello-Astorga, G.R.2
Kraberger, S.3
Julian, L.4
Stainton, D.5
-
46
-
-
84893474747
-
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses
-
Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett J, et al. (2014) Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol 88: 1972-1989.
-
(2014)
J Virol
, vol.88
, pp. 1972-1989
-
-
Muhire, B.M.1
Golden, M.2
Murrell, B.3
Lefeuvre, P.4
Lett, J.5
|