-
1
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
-
(1970)
Syst. Zool.
, vol.19
, pp. 99-113
-
-
Fitch, W.1
-
2
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin, E. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 309-338
-
-
Koonin, E.1
-
3
-
-
0036889686
-
Orthology, paralogy and proposed classification for paralog subtypes
-
Sonnhammer, E. and Koonin, E. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet., 18, 619-620.
-
(2002)
Trends Genet.
, vol.18
, pp. 619-620
-
-
Sonnhammer, E.1
Koonin, E.2
-
4
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R., Fedorova, N., Jackson, J., Jacobs, A., Kiryutin, B., Koonin, E., Krylov, D., Mazumder, R., Mekhedov, S., Nikolskaya, A. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform., 4, 41.
-
(2003)
BMC Bioinform.
, vol.4
, pp. 41
-
-
Tatusov, R.1
Fedorova, N.2
Jackson, J.3
Jacobs, A.4
Kiryutin, B.5
Koonin, E.6
Krylov, D.7
Mazumder, R.8
Mekhedov, S.9
Nikolskaya, A.10
-
5
-
-
33644787447
-
OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
-
Chen, F., Mackey, A., Stoeckert, C.J. and Roos, D. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363-D368.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Chen, F.1
Mackey, A.2
Stoeckert, C.J.3
Roos, D.4
-
6
-
-
84857847281
-
Roundup 2.0: Enabling comparative genomics for over 1800 genomes
-
DeLuca, T.F., Cui, J., Jung, J.Y., St Gabriel, K.C. and Wall, D.P. (2012) Roundup 2.0: enabling comparative genomics for over 1800 genomes. Bioinformatics, 28, 715-716.
-
(2012)
Bioinformatics
, vol.28
, pp. 715-716
-
-
DeLuca, T.F.1
Cui, J.2
Jung, J.Y.3
St. Gabriel, K.C.4
Wall, D.P.5
-
7
-
-
78651316211
-
OMA 2011: Orthology inference among 1000 complete genomes
-
Altenhoff, A.M., Schneider, A., Gonnet, G.H. and Dessimoz, C. (2011) OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res., 39, D289-D294.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Altenhoff, A.M.1
Schneider, A.2
Gonnet, G.H.3
Dessimoz, C.4
-
8
-
-
84861203603
-
EggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
-
Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T. et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res., 40, D284-D289.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Powell, S.1
Szklarczyk, D.2
Trachana, K.3
Roth, A.4
Kuhn, M.5
Muller, J.6
Arnold, R.7
Rattei, T.8
Letunic, I.9
Doerks, T.10
-
9
-
-
75549086594
-
InParanoid 7: New algorithms and tools for eukaryotic orthology analysis
-
Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D., Roopra, S., Frings, O. and Sonnhammer, E. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res., 38, D196-D203.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Kostler, T.4
Messina, D.5
Roopra, S.6
Frings, O.7
Sonnhammer, E.8
-
10
-
-
84862578796
-
QuartetS-DB: A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence
-
Yu, C., Desai, V., Cheng, L. and Reifman, J. (2012) QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. BMC Bioinform., 13, 143.
-
(2012)
BMC Bioinform.
, vol.13
, pp. 143
-
-
Yu, C.1
Desai, V.2
Cheng, L.3
Reifman, J.4
-
11
-
-
78651305141
-
OrthoDB: The hierarchical catalog of eukaryotic orthologs in 2011
-
Waterhouse, R.M., Zdobnov, E.M., Tegenfeldt, F., Li, J. and Kriventseva, E.V. (2011) OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res., 39, D283-D288.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Waterhouse, R.M.1
Zdobnov, E.M.2
Tegenfeldt, F.3
Li, J.4
Kriventseva, E.V.5
-
12
-
-
78650991450
-
OrthoInspector: Comprehensive orthology analysis and visual exploration
-
Article 11
-
Linard, B., Thompson, J.D., Poch, O. and Lecompte, O. (2011) OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinform., 12, Article 11.
-
(2011)
BMC Bioinform.
, vol.12
-
-
Linard, B.1
Thompson, J.D.2
Poch, O.3
Lecompte, O.4
-
13
-
-
67649115335
-
Databases of homologous gene families for comparative genomics
-
Penel, S., Arigon, A.M., Dufayard, J.F., Sertier, A.S., Daubin, V., Duret, L., Gouy, M. and Perriere, G. (2009) Databases of homologous gene families for comparative genomics. BMC Bioinform., 10(Suppl. 6), S3.
-
(2009)
BMC Bioinform.
, vol.10
, Issue.SUPPL. 6
-
-
Penel, S.1
Arigon, A.M.2
Dufayard, J.F.3
Sertier, A.S.4
Daubin, V.5
Duret, L.6
Gouy, M.7
Perriere, G.8
-
14
-
-
78651300216
-
PhylomeDB v3.0: An expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
-
Huerta-Cepas, J., Capella-Gutierrez, S., Pryszcz, L.P., Denisov, I., Kormes, D., Marcet-Houben, M. and Gabaldon, T. (2011) PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res., 39, D556-D560.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Huerta-Cepas, J.1
Capella-Gutierrez, S.2
Pryszcz, L.P.3
Denisov, I.4
Kormes, D.5
Marcet-Houben, M.6
Gabaldon, T.7
-
15
-
-
38549163152
-
TreeFam: 2008 Update
-
Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L., Guo, Y., Heriche, J., Hu, Y., Kristiansen, K., Li, R. et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res., 36, D735-D740.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Ruan, J.1
Li, H.2
Chen, Z.3
Coghlan, A.4
Coin, L.5
Guo, Y.6
Heriche, J.7
Hu, Y.8
Kristiansen, K.9
Li, R.10
-
16
-
-
67849116905
-
Berkeley PHOG: Phylofacts orthology group prediction web server
-
Datta, R., Meacham, C., Samad, B., Neyer, C. and Sjolander, K. (2009) Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res., 37, W84-W89.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Datta, R.1
Meacham, C.2
Samad, B.3
Neyer, C.4
Sjolander, K.5
-
17
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
Vilella, A., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E. (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
-
(2009)
Genome Res.
, vol.19
, pp. 327-335
-
-
Vilella, A.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
18
-
-
75549084894
-
PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
-
Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S. and Thomas, P. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Mi, H.1
Dong, Q.2
Muruganujan, A.3
Gaudet, P.4
Lewis, S.5
Thomas, P.6
-
19
-
-
80052823795
-
Orthology prediction methods: A quality assessment using curated protein families
-
Trachana, K., Larsson, T.A., Powell, S., Chen, W.-H., Doerks, T., Muller, J. and Bork, P. (2011) Orthology prediction methods: a quality assessment using curated protein families. Bioessays, 33, 769-780.
-
(2011)
Bioessays
, vol.33
, pp. 769-780
-
-
Trachana, K.1
Larsson, T.A.2
Powell, S.3
Chen, W.-H.4
Doerks, T.5
Muller, J.6
Bork, P.7
-
20
-
-
80053190440
-
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees
-
Boeckmann, B., Robinson-Rechavi, M., Xenarios, I. and Dessimoz, C. (2011) Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Brief. Bioinform., 12, 423-435.
-
(2011)
Brief. Bioinform.
, vol.12
, pp. 423-435
-
-
Boeckmann, B.1
Robinson-Rechavi, M.2
Xenarios, I.3
Dessimoz, C.4
-
21
-
-
79953324603
-
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi
-
Waterhouse, R.M., Zdobnov, E.M. and Kriventseva, E.V. (2011) Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol. Evol., 3, 75-86.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 75-86
-
-
Waterhouse, R.M.1
Zdobnov, E.M.2
Kriventseva, E.V.3
-
22
-
-
79551632781
-
The ecoresponsive genome of Daphnia pulex
-
Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K. et al. (2011) The ecoresponsive genome of Daphnia pulex. Science, 331, 555-561.
-
(2011)
Science
, vol.331
, pp. 555-561
-
-
Colbourne, J.K.1
Pfrender, M.E.2
Gilbert, D.3
Thomas, W.K.4
Tucker, A.5
Oakley, T.H.6
Tokishita, S.7
Aerts, A.8
Arnold, G.J.9
Basu, M.K.10
-
23
-
-
74549184089
-
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
-
Werren, J.H., Richards, S., Desjardins, C.A., Niehuis, O., Gadau, J., Colbourne, J.K., Beukeboom, L.W., Desplan, C., Elsik, C.G., Grimmelikhuijzen, C.J.P. et al. (2010) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science, 327, 343-348.
-
(2010)
Science
, vol.327
, pp. 343-348
-
-
Werren, J.H.1
Richards, S.2
Desjardins, C.A.3
Niehuis, O.4
Gadau, J.5
Colbourne, J.K.6
Beukeboom, L.W.7
Desplan, C.8
Elsik, C.G.9
Grimmelikhuijzen, C.J.P.10
-
24
-
-
77955459130
-
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
-
Kirkness, E.F., Haas, B.J., Sun, W., Braig, H.R., Perotti, M.A., Clark, J.M., Lee, S.H., Robertson, H.M., Kennedy, R.C., Elhaik, E. et al. (2010) Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc. Natl Acad. Sci. USA, 107, 12168-12173.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 12168-12173
-
-
Kirkness, E.F.1
Haas, B.J.2
Sun, W.3
Braig, H.R.4
Perotti, M.A.5
Clark, J.M.6
Lee, S.H.7
Robertson, H.M.8
Kennedy, R.C.9
Elhaik, E.10
-
25
-
-
77957370433
-
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics
-
Arensburger, P., Megy, K., Waterhouse, R.M., Abrudan, J., Amedeo, P., Antelo, B., Bartholomay, L., Bidwell, S., Caler, E., Camara, F. et al. (2010) Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science, 330, 86-88.
-
(2010)
Science
, vol.330
, pp. 86-88
-
-
Arensburger, P.1
Megy, K.2
Waterhouse, R.M.3
Abrudan, J.4
Amedeo, P.5
Antelo, B.6
Bartholomay, L.7
Bidwell, S.8
Caler, E.9
Camara, F.10
-
26
-
-
77957361060
-
Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens
-
Bartholomay, L.C., Waterhouse, R.M., Mayhew, G.F., Campbell, C.L., Michel, K., Zou, Z., Ramirez, J.L., Das, S., Alvarez, K., Arensburger, P. et al. (2010) Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens. Science, 330, 88-90.
-
(2010)
Science
, vol.330
, pp. 88-90
-
-
Bartholomay, L.C.1
Waterhouse, R.M.2
Mayhew, G.F.3
Campbell, C.L.4
Michel, K.5
Zou, Z.6
Ramirez, J.L.7
Das, S.8
Alvarez, K.9
Arensburger, P.10
-
27
-
-
84858221706
-
Ensembl 2012
-
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
28
-
-
77954226464
-
AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome
-
Legeai, F., Shigenobu, S., Gauthier, J., Colbourne, J., Rispe, C., Collin, O., Richards, S., Wilson, A., Murphy, T. and Tagu, D. (2010) AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. Insect Mol. Biol., 19(Suppl. 2), 5-12.
-
(2010)
Insect Mol. Biol.
, vol.19
, Issue.SUPPL. 2
, pp. 5-12
-
-
Legeai, F.1
Shigenobu, S.2
Gauthier, J.3
Colbourne, J.4
Rispe, C.5
Collin, O.6
Richards, S.7
Wilson, A.8
Murphy, T.9
Tagu, D.10
-
29
-
-
75549087151
-
BeetleBase in 2010: Revisions to provide comprehensive genomic information for Tribolium castaneum
-
Kim, H., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R., Lorenzen, M., Butcher, S., Manak, J. and Brown, S. (2010) BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Res., 38, D437-D442.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Kim, H.1
Murphy, T.2
Xia, J.3
Caragea, D.4
Park, Y.5
Beeman, R.6
Lorenzen, M.7
Butcher, S.8
Manak, J.9
Brown, S.10
-
30
-
-
84860332776
-
FlyBase 101 - The basics of navigating FlyBase
-
McQuilton, P., St Pierre, S.E., Thurmond, J. and Consortium, F. (2012) FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Res., 40, D706-D714.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
McQuilton, P.1
St. Pierre, S.E.2
Thurmond, J.3
Consortium, F.4
-
31
-
-
78651276632
-
Hymenoptera Genome Database: Integrated community resources for insect species of the order Hymenoptera
-
Munoz-Torres, M.C., Reese, J.T., Childers, C.P., Bennett, A.K., Sundaram, J.P., Childs, K.L., Anzola, J.M., Milshina, N. and Elsik, C.G. (2011) Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Res., 39, D658-D662.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Munoz-Torres, M.C.1
Reese, J.T.2
Childers, C.P.3
Bennett, A.K.4
Sundaram, J.P.5
Childs, K.L.6
Anzola, J.M.7
Milshina, N.8
Elsik, C.G.9
-
32
-
-
75549089913
-
SilkDB v2.0: A platform for silkworm (Bombyx mori) genome biology
-
Duan, J., Li, R., Cheng, D., Fan, W., Zha, X., Cheng, T., Wu, Y., Wang, J., Mita, K., Xiang, Z. et al. (2010) SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology. Nucleic Acids Res., 38, D453-D456.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Duan, J.1
Li, R.2
Cheng, D.3
Fan, W.4
Zha, X.5
Cheng, T.6
Wu, Y.7
Wang, J.8
Mita, K.9
Xiang, Z.10
-
33
-
-
84858286227
-
VectorBase: Improvements to a bioinformatics resource for invertebrate vector genomics
-
Megy, K., Emrich, S.J., Lawson, D., Campbell, D., Dialynas, E., Hughes, D.S., Koscielny, G., Louis, C., Maccallum, R.M., Redmond, S.N. et al. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res., 40, D729-D734.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Megy, K.1
Emrich, S.J.2
Lawson, D.3
Campbell, D.4
Dialynas, E.5
Hughes, D.S.6
Koscielny, G.7
Louis, C.8
Maccallum, R.M.9
Redmond, S.N.10
-
34
-
-
25444443634
-
WFleaBase: The Daphnia genome database
-
Colbourne, J., Singan, V. and Gilbert, D. (2005) wFleaBase: the Daphnia genome database. BMC Bioinform., 6, 45.
-
(2005)
BMC Bioinform.
, vol.6
, pp. 45
-
-
Colbourne, J.1
Singan, V.2
Gilbert, D.3
-
35
-
-
84862234514
-
Ensembl Genomes: An integrative resource for genome-scale data from non-vertebrate species
-
Kersey, P.J., Staines, D.M., Lawson, D., Kulesha, E., Derwent, P., Humphrey, J.C., Hughes, D.S., Keenan, S., Kerhornou, A., Koscielny, G. et al. (2012) Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res., 40, D91-D97.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kersey, P.J.1
Staines, D.M.2
Lawson, D.3
Kulesha, E.4
Derwent, P.5
Humphrey, J.C.6
Hughes, D.S.7
Keenan, S.8
Kerhornou, A.9
Koscielny, G.10
-
36
-
-
84862174834
-
The genome portal of the Department of Energy Joint Genome Institute
-
Grigoriev, I.V., Nordberg, H., Shabalov, I., Aerts, A., Cantor, M., Goodstein, D., Kuo, A., Minovitsky, S., Nikitin, R., Ohm, R.A. et al. (2012) The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res., 40, D26-D32.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Grigoriev, I.V.1
Nordberg, H.2
Shabalov, I.3
Aerts, A.4
Cantor, M.5
Goodstein, D.6
Kuo, A.7
Minovitsky, S.8
Nikitin, R.9
Ohm, R.A.10
-
37
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
UniProt-Consortium
-
UniProt-Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
-
38
-
-
84857745267
-
Database resources of the National Center for Biotechnology Information
-
Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 40, D13-D25.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
Canese, K.6
Chetvernin, V.7
Church, D.M.8
Dicuccio, M.9
Federhen, S.10
-
39
-
-
79957630864
-
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
-
Rognes, T. (2011) Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinform., 12, 221.
-
(2011)
BMC Bioinform.
, vol.12
, pp. 221
-
-
Rognes, T.1
-
40
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
41
-
-
38549105500
-
OrthoDB: The hierarchical catalog of eukaryotic orthologs
-
Kriventseva, E., Rahman, N., Espinosa, O. and Zdobnov, E. (2008) OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res., 36, D271-D275.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Kriventseva, E.1
Rahman, N.2
Espinosa, O.3
Zdobnov, E.4
-
42
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
43
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh, K. and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
44
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez, S., Silla-Martínez, J.M. and Gabaldón, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
45
-
-
84859699831
-
The gene ontology: Enhancements for 2011
-
GO-Consortium
-
GO-Consortium. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res., 40, D559-D564.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
-
46
-
-
84858602406
-
InterPro in 2011: New developments in the family and domain prediction database
-
Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Hunter, S.1
Jones, P.2
Mitchell, A.3
Apweiler, R.4
Attwood, T.K.5
Bateman, A.6
Bernard, T.7
Binns, D.8
Bork, P.9
Burge, S.10
-
47
-
-
84859727275
-
The Mouse Genome Database (MGD): Comprehensive resource for genetics and genomics of the laboratory mouse
-
Group, M.G.D.
-
Eppig, J.T., Blake, J.A., Bult, C.J., Kadin, J.A., Richardson, J.E. and Group, M.G.D. (2012) The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res., 40, D881-D886.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Eppig, J.T.1
Blake, J.A.2
Bult, C.J.3
Kadin, J.A.4
Richardson, J.E.5
-
48
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
-
49
-
-
78651364359
-
ZFIN: Enhancements and updates to the Zebrafish Model Organism Database
-
Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A. et al. (2011) ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res., 39, D822-D829.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Bradford, Y.1
Conlin, T.2
Dunn, N.3
Fashena, D.4
Frazer, K.5
Howe, D.G.6
Knight, J.7
Mani, P.8
Martin, R.9
Moxon, S.A.10
-
50
-
-
84861207340
-
WormBase 2012: More genomes, more data, new website
-
Yook, K., Harris, T.W., Bieri, T., Cabunoc, A., Chan, J., Chen, W.J., Davis, P., de la Cruz, N., Duong, A., Fang, R. et al. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res., 40, D735-D741.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Yook, K.1
Harris, T.W.2
Bieri, T.3
Cabunoc, A.4
Chan, J.5
Chen, W.J.6
Davis, P.7
De La Cruz, N.8
Duong, A.9
Fang, R.10
-
51
-
-
0033971754
-
EcoGene: A genome sequence database for Escherichia coli K-12
-
Rudd, K.E. (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 60-64
-
-
Rudd, K.E.1
-
52
-
-
58149197597
-
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
-
Zhang, R. and Lin, Y. (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res., 37, D455-D458.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Zhang, R.1
Lin, Y.2
-
53
-
-
79954986866
-
A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)
-
Amberger, J., Bocchini, C. and Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Hum. Mutat., 32, 564-567.
-
(2011)
Hum. Mutat.
, vol.32
, pp. 564-567
-
-
Amberger, J.1
Bocchini, C.2
Hamosh, A.3
-
54
-
-
77954209892
-
The Newick utilities: High-throughput phylogenetic tree processing in the Unix shell
-
Junier, T. and Zdobnov, E.M. (2010) The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell. Bioinformatics, 26, 1669-1670.
-
(2010)
Bioinformatics
, vol.26
, pp. 1669-1670
-
-
Junier, T.1
Zdobnov, E.M.2
-
55
-
-
47049086792
-
PhyloWidget: Web-based visualizations for the tree of life
-
Jordan, GE. and Piel, W.H. (2008) PhyloWidget: web-based visualizations for the tree of life. Bioinformatics, 24, 1641-1642.
-
(2008)
Bioinformatics
, vol.24
, pp. 1641-1642
-
-
Jordan, G.E.1
Piel, W.H.2
-
56
-
-
81255178677
-
A remarkably stable TipE gene cluster: Evolution of insect Para sodium channel auxiliary subunits
-
Li, J., Waterhouse, R.M. and Zdobnov, E.M. (2011) A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits. BMC Evol. Biol., 11, 337.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 337
-
-
Li, J.1
Waterhouse, R.M.2
Zdobnov, E.M.3
-
57
-
-
33845670418
-
Quantification of insect genome divergence
-
Zdobnov, E.M. and Bork, P. (2007) Quantification of insect genome divergence. Trends Genet., 23, 16-20.
-
(2007)
Trends Genet.
, vol.23
, pp. 16-20
-
-
Zdobnov, E.M.1
Bork, P.2
-
58
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
59
-
-
79952781362
-
Creating a buzz about insect genomes
-
Robinson, G.E., Hackett, K.J., Purcell-Miramontes, M., Brown, S.J., Evans, J.D., Goldsmith, M.R., Lawson, D., Okamuro, J., Robertson, H.M. and Schneider, D.J. (2011) Creating a buzz about insect genomes. Science, 331, 1386.
-
(2011)
Science
, vol.331
, pp. 1386
-
-
Robinson, G.E.1
Hackett, K.J.2
Purcell-Miramontes, M.3
Brown, S.J.4
Evans, J.D.5
Goldsmith, M.R.6
Lawson, D.7
Okamuro, J.8
Robertson, H.M.9
Schneider, D.J.10
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