-
1
-
-
11144353587
-
Complete genome sequence of the apicomplexan, cryptosporidium parvum
-
Abrahamsen, M.S. et al. (2004) Complete genome sequence of the apicomplexan, cryptosporidium parvum. Science, 304, 441-445.
-
(2004)
Science
, vol.304
, pp. 441-445
-
-
Abrahamsen, M.S.1
-
2
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
Ané, C. et al. (2007) Bayesian estimation of concordance among gene trees. Mol. Biol. Evol., 24, 412-426.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 412-426
-
-
Ané, C.1
-
3
-
-
0037246674
-
Plasmodb: The plasmodium genome resource. A database integrating experimental and computational data
-
Bahl, A. et al. (2003) Plasmodb: the plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res., 31, 212-215.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 212-215
-
-
Bahl, A.1
-
4
-
-
0035520029
-
Geometry of the space of phylogenetic trees
-
Billera, L. et al. (2001) Geometry of the space of phylogenetic trees. Adv. Appl. Math., 27, 733-767.
-
(2001)
Adv. Appl. Math
, vol.27
, pp. 733-767
-
-
Billera, L.1
-
5
-
-
36048987965
-
Genome sequence of babesia bovis and comparative analysis of apicomplexan hemoprotozoa
-
Brayton, K.A. et al. (2007) Genome sequence of babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog., 3, e148.
-
(2007)
PLoS Pathog
, vol.3
-
-
Brayton, K.A.1
-
6
-
-
65449133181
-
Multilocus phylogeography and phylogenetics using sequence-based markers
-
Brito, P. and Edwards, S. (2009)Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica, 135, 439-455.
-
(2009)
Genetica
, vol.135
, pp. 439-455
-
-
Brito, P.1
Edwards, S.2
-
7
-
-
0002074731
-
The recovery of trees from measures of similarity
-
Hodson, F. et al. (ed.), Edinburgh University Press, Edinburgh
-
Buneman, P. (1971) The recovery of trees from measures of similarity. In: Hodson, F. et al. (ed.) Mathematics of the Archaeological and Historical Sciences. Edinburgh University Press, Edinburgh, pp. 387-395.
-
(1971)
Mathematics of the Archaeological and Historical Sciences
, pp. 387-395
-
-
Buneman, P.1
-
8
-
-
18144401294
-
A novel kernel method for clustering
-
Camastra, F. and Verri, A. (2005) A novel kernel method for clustering. IEEE Trans. Pattern Anal., 27, 801-804.
-
(2005)
IEEE Trans. Pattern Anal
, vol.27
, pp. 801-804
-
-
Camastra, F.1
Verri, A.2
-
9
-
-
40849120246
-
Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in passerina buntings
-
Carling, M. and Brumfield, R. (2008) Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in passerina buntings. Genetics, 178, 363-377.
-
(2008)
Genetics
, vol.178
, pp. 363-377
-
-
Carling, M.1
Brumfield, R.2
-
10
-
-
34249700809
-
Estimating species phylogeny from genetree probabilities despite incomplete lineage sorting: An example from melanoplus grasshoppers
-
Carstens, B.C. and Knowles, L.L. (2007) Estimating species phylogeny from genetree probabilities despite incomplete lineage sorting: an example from melanoplus grasshoppers. Syst. Biol., 56, 400-411.
-
(2007)
Syst. Biol
, vol.56
, pp. 400-411
-
-
Carstens, B.C.1
Knowles, L.L.2
-
12
-
-
84861368644
-
PHYLO-mcoa: A fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis
-
de Vienne, D.M. et al. (2012) PHYLO-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol. Biol. Evol., 29, 1587-1598.
-
(2012)
Mol. Biol. Evol
, vol.29
, pp. 1587-1598
-
-
De Vienne, D.M.1
-
13
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan, J.H. and Salter, L.A. (2005) Gene tree distributions under the coalescent process. Evolution, 59, 24-37.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
15
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards, S. (2009) Is a new and general theory of molecular systematics emerging? Evolution, 63, 1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.1
-
16
-
-
34347256397
-
High-resolution species trees without concatenation
-
Edwards, S. et al. (2007) High-resolution species trees without concatenation. Proc. Natl Acad. Sci. USA, 104, 5936-5941.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 5936-5941
-
-
Edwards, S.1
-
17
-
-
33748598232
-
Macronuclear genome sequence of the ciliate tetrahymena thermophila, a model eukaryote
-
Eisen, J.A. et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol., 4, 1620-1642.
-
(2006)
PLoS Biol
, vol.4
, pp. 1620-1642
-
-
Eisen, J.A.1
-
18
-
-
38549128700
-
Toxodb: An integrated toxoplasma gondii database resource
-
Gajria, B. et al. (2008) Toxodb: an integrated toxoplasma gondii database resource. Nucleic Acids Res., 36, D553-D556.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gajria, B.1
-
19
-
-
0037015614
-
Genome sequence of the human malaria parasite plasmodium falciparum
-
Gardner, M.J. et al. (2002) Genome sequence of the human malaria parasite plasmodium falciparum. Nature, 419, 498-511.
-
(2002)
Nature
, vol.419
, pp. 498-511
-
-
Gardner, M.J.1
-
20
-
-
49249109947
-
Calculating spr distances between trees
-
Goloboff, P.A. (2008) Calculating spr distances between trees. Cladistics, 24, 591-597.
-
(2008)
Cladistics
, vol.24
, pp. 591-597
-
-
Goloboff, P.A.1
-
21
-
-
78649527910
-
A survey of multiple tree visualisation
-
Graham, M. and Kennedy, J. (2010) A survey of multiple tree visualisation. Inf. Vis., 9, 235-252.
-
(2010)
Inf. Vis
, vol.9
, pp. 235-252
-
-
Graham, M.1
Kennedy, J.2
-
22
-
-
0003684449
-
-
2nd edn. Springer-Verlag, New York, NY
-
Hastie, T. et al. (2009) The Elements of Statistical Learning: Data Mining, Inference, and Prediction. 2nd edn. Springer-Verlag, New York, NY.
-
(2009)
The Elements of Statistical Learning: Data Mining, Inference, and Prediction
-
-
Hastie, T.1
-
23
-
-
84865100080
-
A support vector machine based test for incongruence between sets of trees in tree space
-
Haws, D. et al. (2012) A support vector machine based test for incongruence between sets of trees in tree space. BMC Bioinformatics, 13, 210.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 210
-
-
Haws, D.1
-
24
-
-
33644875511
-
Cryptodb: A cryptosporidium bioinformatics resource update
-
Heiges, M. et al. (2006) Cryptodb: a cryptosporidium bioinformatics resource update. Nucleic Acids Res., 34, D419-D422.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Heiges, M.1
-
25
-
-
84862556870
-
Improvements to a class of distance matrix methods for inferring species trees from gene trees
-
Helmkamp, L. et al. (2012) Improvements to a class of distance matrix methods for inferring species trees from gene trees. J. Comput. Biol., 19, 632-649.
-
(2012)
J. Comput. Biol
, vol.19
, pp. 632-649
-
-
Helmkamp, L.1
-
26
-
-
9144264843
-
Genedb: A resource for prokaryotic and eukaryotic organisms
-
Hertz-Fowler, C. et al. (2004) Genedb: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res., 32, D339-D343.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Hertz-Fowler, C.1
-
27
-
-
22844442543
-
Analysis and visualization of tree space
-
Hillis, D.M. et al. (2005) Analysis and visualization of tree space. Syst. Biol., 54, 471-482.
-
(2005)
Syst. Biol
, vol.54
, pp. 471-482
-
-
Hillis, D.M.1
-
28
-
-
30744478457
-
Statistical approach to tests involving phylogenies
-
Gascuel, O. (ed.), chapter 4. Oxford University Press, New York
-
Holmes, S. (2005) Statistical approach to tests involving phylogenies. In: Gascuel, O. (ed.) Mathematics of Phylogeny and Evolution. chapter 4. Oxford University Press, New York, pp. 91-117.
-
(2005)
Mathematics of Phylogeny and Evolution
, pp. 91-117
-
-
Holmes, S.1
-
29
-
-
2542467690
-
Phylogenetic analyses: A brief introduction to methods and their application
-
Horner, D.S. and Pesole, G. (2004) Phylogenetic analyses: a brief introduction to methods and their application. Expert Rev. Mol. Diagn., 4, 339-350.
-
(2004)
Expert Rev. Mol. Diagn
, vol.4
, pp. 339-350
-
-
Horner, D.S.1
Pesole, G.2
-
31
-
-
0001089823
-
Support vector clustering
-
Hur, A.B. et al. (2001) Support vector clustering. JMLR, 2, 125-137.
-
(2001)
JMLR
, vol.2
, pp. 125-137
-
-
Hur, A.B.1
-
32
-
-
33645320249
-
Coco-cl: Hierarchical clustering of homology relations based on evolutionary correlations
-
Jothi, R.E. et al. (2006a) Coco-cl: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics, 22, 779-788.
-
(2006)
Bioinformatics
, vol.22
, pp. 779-788
-
-
Jothi, R.E.1
-
33
-
-
33645320249
-
Coco-cl: Hierarchical clustering of homology relations based on evolutionary correlations
-
doi: 10.1093/bioinformatics/ btl009
-
Jothi, R. et al. (2006b) Coco-cl: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics, 22, 779-788. doi: 10.1093/bioinformatics/ btl009.
-
(2006)
Bioinformatics
, vol.22
, pp. 779-788
-
-
Jothi, R.1
-
34
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from dna sequence data
-
Kishino, H. and Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from dna sequence data. J. Mol. Evol., 29, 170-179.
-
(1989)
J. Mol. Evol
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
35
-
-
84906239230
-
Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite plasmodium falciparum and other apicomplexans
-
Kishore, S.P. et al. (2013) Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite plasmodium falciparum and other apicomplexans. Evol. Biol., 13-37.
-
(2013)
Evol. Biol
, pp. 13-37
-
-
Kishore, S.P.1
-
36
-
-
56449101000
-
The apicomplexan whole-genome phylogeny: An analysis of incongruence among gene trees
-
Kuo, C. et al. (2008) The apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol. Biol. Evol., 25, 2689-2698.
-
(2008)
Mol. Biol. Evol
, vol.25
, pp. 2689-2698
-
-
Kuo, C.1
-
37
-
-
0037291466
-
Partitioned likelihood support and the evaluation of data set conflict
-
Lee, M.S.Y. and Hugall, A.F. (2003) Partitioned likelihood support and the evaluation of data set conflict. Syst. Biol., 52, 15-22.
-
(2003)
Syst. Biol
, vol.52
, pp. 15-22
-
-
Lee, M.S.Y.1
Hugall, A.F.2
-
38
-
-
0023734723
-
Progress in taxonomy of the apicomplexan protozoa
-
Levine, N. (1988) Progress in taxonomy of the apicomplexan protozoa. J. Eukaryot. Microbiol., 35, 518-520.
-
(1988)
J. Eukaryot. Microbiol
, vol.35
, pp. 518-520
-
-
Levine, N.1
-
39
-
-
0141519279
-
Orthomcl: Identification of ortholog groups for eukaryotic genomes
-
Li, L. et al. (2003) Orthomcl: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
-
40
-
-
0028820834
-
Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis
-
Lockhart, P.J. et al. (1995) Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis. J. Mol. Evol., 41, 666-674.
-
(1995)
J. Mol. Evol
, vol.41
, pp. 666-674
-
-
Lockhart, P.J.1
-
41
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W.P. (1997) Gene trees in species trees. Syst. Biol., 46, 523-536.
-
(1997)
Syst. Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
42
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
Maddison, W.P. and Knowles, L.L. (2006) Inferring phylogeny despite incomplete lineage sorting. Syst. Biol., 55, 21-30.
-
(2006)
Syst. Biol
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
43
-
-
0036699004
-
Perils of paralogy: Using hsp70 genes for inferring organismal phylogenies
-
Martin, A.P. and Burg, T.M. (2002) Perils of paralogy: using hsp70 genes for inferring organismal phylogenies. Syst. Biol., 51, 570-587.
-
(2002)
Syst. Biol
, vol.51
, pp. 570-587
-
-
Martin, A.P.1
Burg, T.M.2
-
44
-
-
84988122232
-
Asymptotic behaviour of the mean integrated squared error of kernel density estimators for dependent observations
-
Meloche, J. (1990) Asymptotic behaviour of the mean integrated squared error of kernel density estimators for dependent observations. Can. J. Stat., 18, 205-211.
-
(1990)
Can. J. Stat
, vol.18
, pp. 205-211
-
-
Meloche, J.1
-
45
-
-
76849102326
-
Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci
-
Mossel, E. and Roch, S. (2010) Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACMTrans. Comput. Biol. Bioinf., 7, 166-171.
-
(2010)
IEEE/ACMTrans. Comput. Biol. Bioinf
, vol.7
, pp. 166-171
-
-
Mossel, E.1
Roch, S.2
-
46
-
-
77950430912
-
Scps: A fast implementation of a spectral method for detecting protein families on a genome-wide scale
-
Nepusz, T. et al. (2010) Scps: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. BMC Bioinformatics, 11, 120.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 120
-
-
Nepusz, T.1
-
47
-
-
47249109137
-
Trees of trees: An approach to comparing multiple alternative phylogenies
-
Nye, T.M. (2008) Trees of trees: an approach to comparing multiple alternative phylogenies. Syst. Biol., 57, 785-794.
-
(2008)
Syst. Biol
, vol.57
, pp. 785-794
-
-
Nye, T.M.1
-
48
-
-
78449288503
-
A fast algorithm for computing geodesic distances in tree space
-
Owen, M. and Provan, J.S. (2011) A fast algorithm for computing geodesic distances in tree space. IEEE ACM Trans. Comput. Biol., 8, 2-13.
-
(2011)
IEEE ACM Trans. Comput. Biol
, vol.8
, pp. 2-13
-
-
Owen, M.1
Provan, J.S.2
-
49
-
-
21644452778
-
Genome of the host-cell transforming parasite theileria annulata compared with T. Parva
-
Pain, A. et al. (2005) Genome of the host-cell transforming parasite theileria annulata compared with t. parva. Science, 309, 131-133.
-
(2005)
Science
, vol.309
, pp. 131-133
-
-
Pain, A.1
-
50
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo, P. and Nei, M. (1988) Relationships between gene trees and species trees. Mol. Biol. Evol., 5, 568-583.
-
(1988)
Mol. Biol. Evol
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
51
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in r language
-
Paradis, E. et al. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
-
53
-
-
65549165915
-
Testing phylogenetic methods to identify horizontal gene transfer
-
Gogarten, M.B. et al. (ed.), Humana Press, New York, NY
-
Poptsova, M. (2009) Testing phylogenetic methods to identify horizontal gene transfer. In: Gogarten, M.B. et al. (ed.) Horizontal Gene Transfer, Volume 532 of Methods in Molecular Biology. Humana Press, New York, NY, pp. 227-240.
-
(2009)
Horizontal Gene Transfer, Volume 532 of Methods in Molecular Biology
, pp. 227-240
-
-
Poptsova, M.1
-
54
-
-
0036183042
-
The effect of recombination on the accuracy of phylogeny reconstruction
-
Posada, D. and Crandall, K. (2002) The effect of recombination on the accuracy of phylogeny reconstruction. J. Mol. Evol., 54, 396-402.
-
(2002)
J. Mol. Evol
, vol.54
, pp. 396-402
-
-
Posada, D.1
Crandall, K.2
-
55
-
-
84863304598
-
-
R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
-
R Development Core Team. (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
-
(2011)
R: A Language and Environment for Statistical Computing
-
-
-
56
-
-
0032568587
-
Genomic evidence for two functionally distinct gene classes
-
Rivera, M.C. et al. (1998) Genomic evidence for two functionally distinct gene classes. Proc. Natl Acad. Sci. USA, 95, 6239-6244.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 6239-6244
-
-
Rivera, M.C.1
-
57
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson, D.F. and Foulds, L.R. (1981) Comparison of phylogenetic trees. Math. Biosci., 53, 131-147.
-
(1981)
Math. Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
58
-
-
0036515730
-
The probability of topological concordance of gene trees and species trees
-
Rosenberg, N. (2002) The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol., 61, 225-247.
-
(2002)
Theor. Popul. Biol
, vol.61
, pp. 225-247
-
-
Rosenberg, N.1
-
59
-
-
0042697667
-
The shapes of neutral gene genealogies in two species: Probabilities of monophyly, paraphyly, and polyphyly in a coalescent model
-
Rosenberg, N.A. (2003) The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution, 57, 1465-1477.
-
(2003)
Evolution
, vol.57
, pp. 1465-1477
-
-
Rosenberg, N.A.1
-
60
-
-
58149357704
-
A two-stage pruning algorithm for likelihood computation for a population tree
-
RoyChoudhury, A. et al. (2008) A two-stage pruning algorithm for likelihood computation for a population tree. Genetics, 180, 1095-1105.
-
(2008)
Genetics
, vol.180
, pp. 1095-1105
-
-
Roychoudhury, A.1
-
61
-
-
84874772540
-
Plant-symbiotic fungi as chemical engineers: Multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci
-
Schardl, C.L. et al. (2013) Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet., 9, e1003323.
-
(2013)
PLoS Genet
, vol.9
-
-
Schardl, C.L.1
-
62
-
-
1642364229
-
-
Oxford University Press, Oxford, UK
-
Semple, C. and Steel, M. (2003) Oxford Lecture Series in Mathematics and its Applications. Vol. 24, Oxford University Press, Oxford, UK, p. xiv+239.
-
(2003)
Oxford Lecture Series in Mathematics and Its Applications
, vol.24
-
-
Semple, C.1
Steel, M.2
-
63
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira, H. (2002) An approximately unbiased test of phylogenetic tree selection. Syst. Biol., 51, 492-508.
-
(2002)
Syst. Biol
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
64
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applcations to phylogenetic inference
-
Shimodaira, H. and Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applcations to phylogenetic inference. Mol. Biol. Evol., 16, 1114-1116.
-
(1999)
Mol. Biol. Evol
, vol.16
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
65
-
-
12044252586
-
Distributions of tree comparison metrics-some new results
-
Steel, M. and Penny, D. (1993) Distributions of tree comparison metrics-some new results. Syst. Biol., 42, 126-141.
-
(1993)
Syst. Biol
, vol.42
, pp. 126-141
-
-
Steel, M.1
Penny, D.2
-
66
-
-
77954202497
-
Dendropy: A python library for phylogenetic computing
-
Sukumaran, J. and Holder, M.T. (2010) Dendropy: a python library for phylogenetic computing. Bioinformatics, 26, 1569-1571.
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
67
-
-
0024713112
-
Gene genealogy in 3 related populations: Consistency probability between gene and population trees
-
Takahata, N. (1989) Gene genealogy in 3 related populations: consistency probability between gene and population trees. Genetics, 122, 957-966.
-
(1989)
Genetics
, vol.122
, pp. 957-966
-
-
Takahata, N.1
-
68
-
-
0025255468
-
Allelic genealogy under overdominant and frequency- dependent selection and polymorphism of major histocompatibility complex loci
-
Takahata, N. and Nei, M. (1990) Allelic genealogy under overdominant and frequency- dependent selection and polymorphism of major histocompatibility complex loci. Genetics, 124, 967-978.
-
(1990)
Genetics
, vol.124
, pp. 967-978
-
-
Takahata, N.1
Nei, M.2
|