-
1
-
-
84865231395
-
Transforming clinical microbiology with bacterial genome sequencing
-
Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13:601–612. http://dx.doi.org/10.1038/nrg3226.
-
(2012)
Nat. Rev. Genet
, vol.13
, pp. 601-612
-
-
Didelot, X.1
Bowden, R.2
Wilson, D.J.3
Peto, T.4
Crook, D.W.5
-
3
-
-
0033793521
-
Consequences of recombination on traditional phylogenetic analysis
-
Schierup MH, Hein J. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879–891.
-
(2000)
Genetics
, vol.156
, pp. 879-891
-
-
Schierup, M.H.1
Hein, J.2
-
4
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
Anisimova M, Nielsen R, Yang Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229–1236.
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
5
-
-
0037986694
-
Potential impact of recombination on sitewise approaches for detecting positive natural selection
-
Shriner D, Nickle DC, Jensen MA, Mullins JI. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81:115–121. http://dx.doi.org/10.1017/S0016672303006128.
-
(2003)
Genet. Res
, vol.81
, pp. 115-121
-
-
Shriner, D.1
Nickle, D.C.2
Jensen, M.A.3
Mullins, J.I.4
-
6
-
-
0036183042
-
The effect of recombination on the accuracy of phylogeny estimation
-
Posada D, Crandall KA. 2002. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54:396–402. http://dx.doi.org/10.1007/s00239-001-0034-9.
-
(2002)
J. Mol. Evol
, vol.54
, pp. 396-402
-
-
Posada, D.1
Crandall, K.A.2
-
7
-
-
52949152371
-
Phylogenetic inference using whole genomes
-
Rannala B, Yang Z. 2008. Phylogenetic inference using whole genomes. Annu. Rev. Genomics Hum. Genet. 9:217–231. http://dx.doi.org/10.1146/annurev.genom.9.081307.164407.
-
(2008)
Annu. Rev. Genomics Hum. Genet
, vol.9
, pp. 217-231
-
-
Rannala, B.1
Yang, Z.2
-
8
-
-
84866928158
-
Insights from genomics into bacterial pathogen populations
-
Wilson DJ. 2012. Insights from genomics into bacterial pathogen populations. PLoS Pathog. 8:e1002874. http://dx.doi.org/10.1371/journal.ppat.1002874.
-
(2012)
Plos Pathog
, vol.8
-
-
Wilson, D.J.1
-
9
-
-
31344468046
-
Approximating the coalescent with recombination
-
McVean GAT, Cardin NJ. 2005. Approximating the coalescent with recombination. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360:1387–1393. http://dx.doi.org/10.1098/rstb.2005.1673.
-
(2005)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.360
, pp. 1387-1393
-
-
McVean, G.1
Cardin, N.J.2
-
10
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254–267. http://dx.doi.org/10.1093/molbev/msj030.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
11
-
-
72049128651
-
Unifying vertical and nonvertical evolution: A stochastic ARG-based framework
-
Bloomquist EW, Suchard MA. 2010. Unifying vertical and nonvertical evolution: a stochastic ARG-based framework. Syst. Biol. 59:27–41. http://dx.doi.org/10.1093/sysbio/syp076.
-
(2010)
Syst. Biol
, vol.59
, pp. 27-41
-
-
Bloomquist, E.W.1
Suchard, M.A.2
-
12
-
-
79251573854
-
Inference of homologous recombination in bacteria using whole-genome sequences
-
Didelot X, Lawson D, Darling A, Falush D. 2010. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 186:1435–1449. http://dx.doi.org/10.1534/genetics.110.120121.
-
(2010)
Genetics
, vol.186
, pp. 1435-1449
-
-
Didelot, X.1
Lawson, D.2
Darling, A.3
Falush, D.4
-
13
-
-
0033756316
-
Maximum likelihood estimation of recombination rates from population data
-
Kuhner MK, Yamato J, Felsenstein J. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393–1401.
-
(2000)
Genetics
, vol.156
, pp. 1393-1401
-
-
Kuhner, M.K.1
Yamato, J.2
Felsenstein, J.3
-
14
-
-
0035675042
-
Estimating recombination rates from population genetic data
-
Fearnhead P, Donnelly P. 2001. Estimating recombination rates from population genetic data. Genetics 159:1299–1318.
-
(2001)
Genetics
, vol.159
, pp. 1299-1318
-
-
Fearnhead, P.1
Donnelly, P.2
-
15
-
-
0025133386
-
Molecular evolution of the Escherichia coli chromosome
-
Milkman R, Bridges MM. 1990. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126:-505–527.
-
(1990)
III. Clonal Frames. Genetics
, vol.126
, pp. 505-527
-
-
Milkman, R.1
Bridges, M.M.2
-
16
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17–24. http://dx.doi.org/10.1080/10635150601146041.
-
(2007)
Syst. Biol
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
17
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.
-
(1987)
Mol. Biol. Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
18
-
-
0003608559
-
Numerical taxonomy: The principles and practice of numerical classification
-
W. H. Freeman & Co, San Francisco, CA
-
Sneath PHA, Sokal RR. 1973. Numerical taxonomy: the principles and practice of numerical classification. A series of books in biology. W. H. Freeman & Co, San Francisco, CA.
-
(1973)
A Series of Books in Biology
-
-
Sneath, P.1
Sokal, R.R.2
-
19
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368–376. http://dx.doi.org/10.1007/BF01734359.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
20
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214. http://dx.doi.org/10.1186/1471-2148-7-214.
-
(2007)
BMC Evol. Biol
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
21
-
-
0025951996
-
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations
-
Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562.
-
(1991)
Genetics
, vol.129
, pp. 555-562
-
-
Slatkin, M.1
Hudson, R.R.2
-
22
-
-
78649470145
-
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
-
Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M. 2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat. Genet. 42:1140–1143. http://dx.doi.org/10.1038/ng.705.
-
(2010)
Nat. Genet
, vol.42
, pp. 1140-1143
-
-
Morelli, G.1
Song, Y.2
Mazzoni, C.J.3
Eppinger, M.4
Roumagnac, P.5
Wagner, D.M.6
Feldkamp, M.7
Kusecek, B.8
Vogler, A.J.9
Li, Y.10
Cui, Y.11
Thomson, N.R.12
Jombart, T.13
Leblois, R.14
Lichtner, P.15
Rahalison, L.16
Petersen, J.M.17
Balloux, F.18
Keim, P.19
Wirth, T.20
Ravel, J.21
Yang, R.22
Carniel, E.23
Achtman, M.24
more..
-
23
-
-
47949097485
-
Noisy: Identification of problematic columns in multiple sequence alignments
-
Dress AWM, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF. 2008. Noisy: identification of problematic columns in multiple sequence alignments. Algor. Mol. Biol. 3:7. http://dx.doi.org/10.1186/1748-7188-3-7.
-
(2008)
Algor. Mol. Biol
, vol.3
, pp. 7
-
-
Dress, A.1
Flamm, C.2
Fritzsch, G.3
Grünewald, S.4
Kruspe, M.5
Prohaska, S.J.6
Stadler, P.F.7
-
24
-
-
80355129294
-
Rapid typing of Coxiella burnetii
-
Hornstra HM, Priestley RA, Georgia SM, Kachur S, Birdsell DN, Hilsabeck R, Gates LT, Samuel JE, Heinzen RA, Kersh GJ, Keim P, Massung RF, Pearson T. 2011. Rapid typing of Coxiella burnetii. PLoS One 6:e26201. http://dx.doi.org/10.1371/journal.pone.0026201.
-
(2011)
Plos One
, vol.6
-
-
Hornstra, H.M.1
Priestley, R.A.2
Georgia, S.M.3
Kachur, S.4
Birdsell, D.N.5
Hilsabeck, R.6
Gates, L.T.7
Samuel, J.E.8
Heinzen, R.A.9
Kersh, G.J.10
Keim, P.11
Massung, R.F.12
Pearson, T.13
-
25
-
-
0031897789
-
Detecting recombination from gene trees. Mol
-
Maynard Smith J, Smith NH. 1998. Detecting recombination from gene trees. Mol. Biol. Evol. 15:590–599. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025960.
-
(1998)
Biol. Evol
, vol.15
, pp. 590-599
-
-
Maynard Smith, J.1
Smith, N.H.2
|