-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
3
-
-
41149095079
-
Novel methodology for construction and pruning of quasi-median networks
-
Ayling SC, Brown TA. 2008. Novel methodology for construction and pruning of quasi-median networks. BMC Bioinformatics 9:115.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 115
-
-
Ayling, S.C.1
Brown, T.A.2
-
4
-
-
0033936421
-
When one is not enough: Introgression of mitochondrial DNA in Drosophila
-
Ballard JWO. 2000. When one is not enough: introgression of mitochondrial DNA in Drosophila. Mol Biol Evol. 17:1126-1130.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 1126-1130
-
-
Ballard, J.W.O.1
-
6
-
-
33645750438
-
Exploring reticulate patterns in DNA sequence data
-
Bakker FT, Chatrou LW, Gravendeel B, Pelser PB, editors Königstein (Germany): Koeltz
-
Bandelt H-J. 2005. Exploring reticulate patterns in DNA sequence data. In: Bakker FT, Chatrou LW, Gravendeel B, Pelser PB, editors. Plant species-level systematics: new perspectives on pattern and process. Königstein (Germany): Koeltz. p. 245-269.
-
(2005)
Plant Species-level Systematics: New Perspectives on Pattern and Process
, pp. 245-269
-
-
Bandelt, H.-J.1
-
7
-
-
0026911267
-
Split decomposition: A new and useful approach to phylogenetic analysis of distance data
-
Bandelt H-J, Dress AWM. 1992. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol. 1:242-252.
-
(1992)
Mol Phylogenet Evol.
, vol.1
, pp. 242-252
-
-
Bandelt, H.-J.1
Dress, A.W.M.2
-
8
-
-
0003100899
-
A relational approach to split decomposition
-
Opitz O, Lausen B, Klar R, editors Berlin (Germany): Springer
-
Bandelt H-J, Dress AWM. 1993. A relational approach to split decomposition. In: Opitz O, Lausen B, Klar R, editors. Information and classification. Berlin (Germany): Springer. p. 123-131.
-
(1993)
Information and Classification
, pp. 123-131
-
-
Bandelt, H.-J.1
Dress, A.W.M.2
-
9
-
-
0033928911
-
Median networks: Speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA
-
Bandelt H-J, Macauley V, Richards M. 2000. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol. 16:8-28.
-
(2000)
Mol Phylogenet Evol.
, vol.16
, pp. 8-28
-
-
Bandelt, H.-J.1
MacAuley, V.2
Richards, M.3
-
10
-
-
18844371267
-
Exploratory data analysis
-
Schinka JA, Velicer WF, editors Hoboken (NJ): John Wiley & Sons
-
Behrens JT, Yu CH. 2003. Exploratory data analysis. In: Schinka JA, Velicer WF, editors. Handbook of psychology, vol.2: research methods in psychology. Hoboken (NJ): John Wiley & Sons. p. 33-64.
-
(2003)
Handbook of Psychology, Vol 2: Research Methods in Psychology
, pp. 33-64
-
-
Behrens, J.T.1
Yu, C.H.2
-
11
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten J. 2005. A review of long-branch attraction. Cladistics. 21:163-193.
-
(2005)
Cladistics.
, vol.21
, pp. 163-193
-
-
Bergsten, J.1
-
12
-
-
84957000934
-
NeighborNet: An agglomerative method for the construction of planar phylogenetic networks
-
Bryant D, Moulton V. 2002. NeighborNet: an agglomerative method for the construction of planar phylogenetic networks. Lect Notes Comput Sci. 2452:375-391.
-
(2002)
Lect Notes Comput Sci.
, vol.2452
, pp. 375-391
-
-
Bryant, D.1
Moulton, V.2
-
13
-
-
1542347067
-
Neighbor-Net: An agglomerative method for the construction of phylogenetic networks
-
Bryant D, Moulton V. 2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 21:255-265.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 255-265
-
-
Bryant, D.1
Moulton, V.2
-
14
-
-
0035543309
-
Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae)
-
Comes HP, Abbott RJ. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55:1943-1962.
-
(2001)
Evolution
, vol.55
, pp. 1943-1962
-
-
Comes, H.P.1
Abbott, R.J.2
-
15
-
-
0035825652
-
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution
-
Cooper AS, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. 2001. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409: 704-707.
-
(2001)
Nature
, vol.409
, pp. 704-707
-
-
Cooper, A.S.1
Lalueza-Fox, C.2
Anderson, S.3
Rambaut, A.4
Austin, J.5
Ward, R.6
-
16
-
-
0030866388
-
Evolution of the genus Leishmania revealed by comparison of DNA and RNA poly-merase gene sequences
-
Croan DG, Morrison DA, Ellis JT. 1997. Evolution of the genus Leishmania revealed by comparison of DNA and RNA poly-merase gene sequences. Mol Biochem Parasitol. 89:149-159.
-
(1997)
Mol Biochem Parasitol.
, vol.89
, pp. 149-159
-
-
Croan, D.G.1
Morrison, D.A.2
Ellis, J.T.3
-
17
-
-
1342308811
-
Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences
-
Donoghue MJ, Baldwin BG, Li J, Winkworth RC. 2004. Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Syst Bot. 29:188-198.
-
(2004)
Syst Bot.
, vol.29
, pp. 188-198
-
-
Donoghue, M.J.1
Baldwin, B.G.2
Li, J.3
Winkworth, R.C.4
-
18
-
-
1842608023
-
Exploratory data analysis and graphic display
-
Scheiner SM, Gurevitch J, editors 2nd ed. Oxford: Oxford University Press
-
Ellison AM. 2001. Exploratory data analysis and graphic display. In: Scheiner SM, Gurevitch J, editors. Design and analysis of ecological experiments, 2nd ed. Oxford: Oxford University Press. p. 37-62.
-
(2001)
Design and Analysis of Ecological Experiments
, pp. 37-62
-
-
Ellison, A.M.1
-
19
-
-
77951577026
-
Phylogenetic networks
-
Junker BH, Schreiber F, editors Hoboken (NJ): Wiley-Interscience
-
Gemeinholzer B. 2008. Phylogenetic networks. In: Junker BH, Schreiber F, editors. Analysis of biological networks. Hoboken (NJ): Wiley-Interscience. p. 255-282.
-
(2008)
Analysis of Biological Networks
, pp. 255-282
-
-
Gemeinholzer, B.1
-
21
-
-
0038287878
-
Data exploration in phylogenetic inference: Scientific, heuristic, or neither
-
Grant T, Kluge AG. 2003. Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics. 19:379-418.
-
(2003)
Cladistics.
, vol.19
, pp. 379-418
-
-
Grant, T.1
Kluge, A.G.2
-
22
-
-
11144319958
-
Phylogeny of the New World true frogs (Rana)
-
Hillis DM, Wilcox TP. 2005. Phylogeny of the New World true frogs (Rana). Mol Phylogenet Evol. 34:299-314.
-
(2005)
Mol Phylogenet Evol.
, vol.34
, pp. 299-314
-
-
Hillis, D.M.1
Wilcox, T.P.2
-
23
-
-
33745115885
-
Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques
-
Höglund J, Morrison DA, Mattsson JG, Engström A. 2006. Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques. Parasitology 133:89-99.
-
(2006)
Parasitology
, vol.133
, pp. 89-99
-
-
Höglund, J.1
Morrison, D.A.2
Mattsson, J.G.3
Engström, A.4
-
24
-
-
15944415088
-
Visualizing conflicting evolutionary hypotheses in large collections of trees: Using consensus networks to study the origins of placentals and hexapods
-
Holland BR, Delsuc F, Moulton V. 2005. Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Syst Biol. 54:66-76.
-
(2005)
Syst Biol.
, vol.54
, pp. 66-76
-
-
Holland, B.R.1
Delsuc, F.2
Moulton, V.3
-
25
-
-
3042637206
-
Using consensus networks to visualize contradictory evidence for species phylogeny
-
Holland BR, Huber KT, Moulton V, Lockhart PJ. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol. 21:1459-1461.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1459-1461
-
-
Holland, B.R.1
Huber, K.T.2
Moulton, V.3
Lockhart, P.J.4
-
26
-
-
33646584166
-
Improved consensus network techniques for genome-scale phylogeny
-
Holland BR, Jermiin LS, Moulton V. 2006. Improved consensus network techniques for genome-scale phylogeny. Mol Biol Evol. 23:848-855.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 848-855
-
-
Holland, B.R.1
Jermiin, L.S.2
Moulton, V.3
-
27
-
-
21144444309
-
Consensus networks: A method for visualizing incompatibilities in collections of trees
-
Holland B, Moulton V. 2003. Consensus networks: a method for visualizing incompatibilities in collections of trees. Lect Notes Bioinform. 2812:165-176.
-
(2003)
Lect Notes Bioinform.
, vol.2812
, pp. 165-176
-
-
Holland, B.1
Moulton, V.2
-
28
-
-
0031678692
-
SplitsTree: Analyzing and visualizing evolutionary data
-
Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68-73.
-
(1998)
Bioinformatics
, vol.14
, pp. 68-73
-
-
Huson, D.H.1
-
29
-
-
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.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
30
-
-
14744273424
-
Phylogenetic super-networks from partial trees
-
DOI 10.1109/TCBB.2004.44
-
Huson DH, Dezulian T, Klöpper T, Steel MA. 2004. Phylogenetic super-networks from partial trees. IEEE/ACM Trans Computat Biol Bioinform. 1:151-158. (Pubitemid 40325592)
-
(2004)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.1
, Issue.4
, pp. 151-158
-
-
Huson, D.H.1
Dezulian, T.2
Klopper, T.3
Steel, M.A.4
-
31
-
-
27544510614
-
Computing recombination networks from binary sequences
-
Huson DH, Kloepper TH. 2005. Computing recombination networks from binary sequences. Bioinformatics 21:ii159-ii165.
-
(2005)
Bioinformatics
, vol.21
-
-
Huson, D.H.1
Kloepper, T.H.2
-
32
-
-
34547405689
-
Beyond galled trees\decomposition and computation of galled networks
-
Huson DH, Klöpper TH. 2007. Beyond galled trees\decomposition and computation of galled networks. Lect Notes Bioinform. 4453:211-225.
-
(2007)
Lect Notes Bioinform.
, vol.4453
, pp. 211-225
-
-
Huson, D.H.1
Klöpper, T.H.2
-
34
-
-
66349108852
-
Computing galled networks from real data
-
Huson DH, Rupp R, Berry V, Gambette P, Paul C. 2009. Computing galled networks from real data. Bioinformatics 25:i85-i93.
-
(2009)
Bioinformatics
, vol.25
-
-
Huson, D.H.1
Rupp, R.2
Berry, V.3
Gambette, P.4
Paul, C.5
-
36
-
-
4644299089
-
The biasing effect of compositional heterogeneity on phy-logenetic estimates may be underestimated
-
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD. 2004. The biasing effect of compositional heterogeneity on phy-logenetic estimates may be underestimated. Syst Biol. 53: 638-643.
-
(2004)
Syst Biol.
, vol.53
, pp. 638-643
-
-
Jermiin, L.S.1
Ho, S.Y.W.2
Ababneh, F.3
Robinson, J.4
Larkum, A.W.D.5
-
37
-
-
25144453704
-
Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
-
Kennedy M, Holland BR, Gray RD, Spencer HG. 2005. Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst Biol. 54:620-633.
-
(2005)
Syst Biol.
, vol.54
, pp. 620-633
-
-
Kennedy, M.1
Holland, B.R.2
Gray, R.D.3
Spencer, H.G.4
-
38
-
-
77951581653
-
Phylogenetic network construction approaches
-
Arora DK, Berka RM, Singh GB, editors Amsterdam: Elsevier
-
Makarenkov V, Kevorkov D, Legendre P. 2006. Phylogenetic network construction approaches. In: Arora DK, Berka RM, Singh GB, editors. Applied mycology and biotechnology, vol.6: bioinfor-matics. Amsterdam: Elsevier. p. 61-97.
-
(2006)
Applied Mycology and Biotechnology, Vol. 6: Bioinfor-matics
, pp. 61-97
-
-
Makarenkov, V.1
Kevorkov, D.2
Legendre, P.3
-
39
-
-
33746278627
-
Reconstructing reticulate evolutionary histories of plants
-
McBreen K, Lockhart PJ. 2006. Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci. 11:398-404.
-
(2006)
Trends Plant Sci.
, vol.11
, pp. 398-404
-
-
McBreen, K.1
Lockhart, P.J.2
-
40
-
-
0030153359
-
Phylogenetic tree-building
-
Morrison DA. 1996. Phylogenetic tree-building. Int J Parasitol. 26:589-617.
-
(1996)
Int J Parasitol.
, vol.26
, pp. 589-617
-
-
Morrison, D.A.1
-
41
-
-
17044401319
-
Networks in phylogenetic analysis: New tools for population biology
-
Morrison DA. 2005. Networks in phylogenetic analysis: new tools for population biology. Int J Parasitol. 35:567-582.
-
(2005)
Int J Parasitol.
, vol.35
, pp. 567-582
-
-
Morrison, D.A.1
-
42
-
-
77951561548
-
Phylogenetic networks in systematic biology (and elsewhere)
-
Mohan RM, editor Trivandrum (India): Global Research Network
-
Morrison DA. 2010. Phylogenetic networks in systematic biology (and elsewhere). In: Mohan RM, editor. Research advances in systematic biology. Trivandrum (India): Global Research Network.
-
(2010)
Research Advances in Systematic Biology
-
-
Morrison, D.A.1
-
44
-
-
0042629743
-
Towards the development of computational tools for evaluating phylogenetic network reconstruction methods
-
Nakhleh L, Sun J, Warnow T, Linder CR, Moret BME, Tholse A. 2003. Towards the development of computational tools for evaluating phylogenetic network reconstruction methods. Pac Symp Biocomp. 8:315-326.
-
(2003)
Pac Symp Biocomp.
, vol.8
, pp. 315-326
-
-
Nakhleh, L.1
Sun, J.2
Warnow, T.3
Linder, C.R.4
Moret, B.M.E.5
Tholse, A.6
-
45
-
-
1942473145
-
Identification of a second rRNA gene unit in the Perkinsus andrewsi genome
-
Pecher WT, Robledo JAF, Vasta GR. 2004. Identification of a second rRNA gene unit in the Perkinsus andrewsi genome. J Eukaryot Microbiol. 51:234-245.
-
(2004)
J Eukaryot Microbiol.
, vol.51
, pp. 234-245
-
-
Pecher, W.T.1
Robledo, J.A.F.2
Vasta, G.R.3
-
46
-
-
17744379783
-
The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi, and stronger support for the Coelomata than Ecdysozoa
-
Philip GK, Creevey CJ, McInerney JO. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi, and stronger support for the Coelomata than Ecdysozoa. Mol Biol Evol. 22:1175-1184.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1175-1184
-
-
Philip, G.K.1
Creevey, C.J.2
McInerney, J.O.3
-
47
-
-
0242354974
-
Horizontal gene transfer and phylogenetics
-
Philippe H, Douady CJ. 2003. Horizontal gene transfer and phylogenetics. Curr Opin Microbiol. 6:498-505.
-
(2003)
Curr Opin Microbiol.
, vol.6
, pp. 498-505
-
-
Philippe, H.1
Douady, C.J.2
-
48
-
-
0035139147
-
Intraspecific gene genealogies: Trees grafting into networks
-
Posada D, Crandall KA. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol. 16:37-45.
-
(2001)
Trends Ecol Evol.
, vol.16
, pp. 37-45
-
-
Posada, D.1
Crandall, K.A.2
-
49
-
-
34447250096
-
Distinguishing terminal mono-phyletic groups from reticulate taxa: Performance of phenetic, tree-based, and network procedures
-
Reeves PA, Richards CM. 2007. Distinguishing terminal mono-phyletic groups from reticulate taxa: performance of phenetic, tree-based, and network procedures. Syst Biol. 56:302-320.
-
(2007)
Syst Biol.
, vol.56
, pp. 302-320
-
-
Reeves, P.A.1
Richards, C.M.2
-
50
-
-
0034750288
-
Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons
-
Takahashi K, Terai Y, Nishida M, Okada N. 2001. Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol. 18:2057-2066.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 2057-2066
-
-
Takahashi, K.1
Terai, Y.2
Nishida, M.3
Okada, N.4
-
51
-
-
33748442809
-
Global patterns reveal strong population structure in Haemon-chus contortus, a nematode parasite of domesticated ruminants
-
Troell K, Engström A, Morrison DA, Mattsson JG, Höglund J. 2006. Global patterns reveal strong population structure in Haemon-chus contortus, a nematode parasite of domesticated ruminants. Int J Parasitol. 36:1305-1316.
-
(2006)
Int J Parasitol.
, vol.36
, pp. 1305-1316
-
-
Troell, K.1
Engström, A.2
Morrison, D.A.3
Mattsson, J.G.4
Höglund, J.5
-
53
-
-
27144542150
-
Reconstructing patterns of reticulate evolution in angiosperms: What can we do?
-
Vriesendorp B, Bakker FT. 2005. Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon. 54:593-604.
-
(2005)
Taxon
, vol.54
, pp. 593-604
-
-
Vriesendorp, B.1
Bakker, F.T.2
-
54
-
-
35448965597
-
Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
-
Wägele JW, Mayer C. 2007. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol. 7:147.
-
(2007)
BMC Evol Biol.
, vol.7
, pp. 147
-
-
Wägele, J.W.1
Mayer, C.2
|