-
1
-
-
0032783604
-
Phylogenetic relationships of scenedesmus and scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons
-
An SS, Friedl T, Hegewald E (1999) Phylogenetic relationships of scenedesmus and scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons. Plant Biology, 1, 418-428.
-
(1999)
Plant Biology
, vol.1
, pp. 418-428
-
-
An, S.S.1
Friedl, T.2
Hegewald, E.3
-
2
-
-
79951837282
-
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life
-
Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M (2011) Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One, 6.2, e16931.
-
(2011)
PLoS One
, vol.62
-
-
Buchheim, M.A.1
Keller, A.2
Koetschan, C.3
Förster, F.4
Merget, B.5
Wolf, M.6
-
3
-
-
0036276111
-
Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast
-
Côté CA, Greer CL, Peculis BA (2002) Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA, 8, 786-797.
-
(2002)
RNA
, vol.8
, pp. 786-797
-
-
Côté, C.A.1
Greer, C.L.2
Peculis, B.A.3
-
4
-
-
67650727366
-
VARNA: interactive drawing and editing of the RNA secondary structure
-
Darty K, Denise A, Ponty Y (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
-
(2009)
Bioinformatics
, vol.25
, pp. 1974-1975
-
-
Darty, K.1
Denise, A.2
Ponty, Y.3
-
5
-
-
77952722448
-
Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore
-
Eliáš M, Němcová Y, Škaloud P, Neustupa J, Kaufnerová V, Šejnohová L (2010) Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore. International Journal of Systematic and Evolutionary Microbiology, 60, 1224-1235.
-
(2010)
International Journal of Systematic and Evolutionary Microbiology
, vol.60
, pp. 1224-1235
-
-
Eliáš, M.1
Němcová, Y.2
Škaloud, P.3
Neustupa, J.4
Kaufnerová, V.5
Šejnohová, L.6
-
6
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
7
-
-
0000122573
-
PHYLIP - phylogeny inference package (Version 3.2)
-
Felsenstein J (1989) PHYLIP - phylogeny inference package (Version 3.2). Cladistics, 5, 164-165.
-
(1989)
Cladistics
, vol.5
, pp. 164-165
-
-
Felsenstein, J.1
-
8
-
-
18744401646
-
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances
-
Friedrich J, Dandekar T, Wolf M, Müller T (2005) ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics, 21, 2108-2109.
-
(2005)
Bioinformatics
, vol.21
, pp. 2108-2109
-
-
Friedrich, J.1
Dandekar, T.2
Wolf, M.3
Müller, T.4
-
9
-
-
84856743112
-
Intersection of Chlorella, Muriella and Bracteacoccus: resurrecting the genus Chromochloris KOL et CHODAT (Chlorophyceae, Chlorophyta)
-
Fučíková K, Lewis LA (2012) Intersection of Chlorella, Muriella and Bracteacoccus: resurrecting the genus Chromochloris KOL et CHODAT (Chlorophyceae, Chlorophyta). Fottea, 12, 83-93.
-
(2012)
Fottea
, vol.12
, pp. 83-93
-
-
Fučíková, K.1
Lewis, L.A.2
-
10
-
-
0033062151
-
RNA Movies: visualizing RNA secondary structure spaces
-
Giegerich R, Evers DJ (1999) RNA Movies: visualizing RNA secondary structure spaces. Bioinformatics, 15, 32-37.
-
(1999)
Bioinformatics
, vol.15
, pp. 32-37
-
-
Giegerich, R.1
Evers, D.J.2
-
11
-
-
0036105572
-
A revised secondary structure model for the internal transcribed spacer 2 of the green algae Scenedesmus and Desmodesmus and its implication for the phylogeny of these algae
-
van Hannen E, Fink P, Lurling M (2002) A revised secondary structure model for the internal transcribed spacer 2 of the green algae Scenedesmus and Desmodesmus and its implication for the phylogeny of these algae. European Journal of Phycology, 37, 203-208.
-
(2002)
European Journal of Phycology
, vol.37
, pp. 203-208
-
-
van Hannen, E.1
Fink, P.2
Lurling, M.3
-
12
-
-
0004598107
-
Phylogenetic studies on Scenedesmaceae (Chlorophyta)
-
Hegewald E, Hanagata N (2000) Phylogenetic studies on Scenedesmaceae (Chlorophyta). Algological Studies, 136, 29-49.
-
(2000)
Algological Studies
, vol.136
, pp. 29-49
-
-
Hegewald, E.1
Hanagata, N.2
-
13
-
-
0344584956
-
Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons
-
Hegewald E, Wolf M (2003) Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons. Plant Systematics and Evolution, 241, 185-191.
-
(2003)
Plant Systematics and Evolution
, vol.241
, pp. 185-191
-
-
Hegewald, E.1
Wolf, M.2
-
14
-
-
78951484458
-
ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus
-
Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L (2010) ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus. Phycologia, 49, 325-335.
-
(2010)
Phycologia
, vol.49
, pp. 325-335
-
-
Hegewald, E.1
Wolf, M.2
Keller, A.3
Friedl, T.4
Krienitz, L.5
-
15
-
-
84876200630
-
-
Inkscape. Inkscape
-
Inkscape (2011) Inkscape. http://www.inkscape.org/.
-
(2011)
-
-
-
16
-
-
33947202062
-
The diversity of Scenedesmus and Desmodesmus (Chlorophyceae) in Itasca State Park, Minnesota, USA
-
Johnson JL, Fawley MW, Fawley KP (2007) The diversity of Scenedesmus and Desmodesmus (Chlorophyceae) in Itasca State Park, Minnesota, USA. Phycologia, 46, 214-229.
-
(2007)
Phycologia
, vol.46
, pp. 214-229
-
-
Johnson, J.L.1
Fawley, M.W.2
Fawley, K.P.3
-
17
-
-
0033485458
-
Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast
-
Joseph N, Krauskopf E, Vera MI, Michot B (1999) Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Research, 27, 4533-4540.
-
(1999)
Nucleic Acids Research
, vol.27
, pp. 4533-4540
-
-
Joseph, N.1
Krauskopf, E.2
Vera, M.I.3
Michot, B.4
-
18
-
-
50249093325
-
ITS 2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)
-
Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M (2008) ITS 2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evolutionary Biology, 8, 218.
-
(2008)
BMC Evolutionary Biology
, vol.8
, pp. 218
-
-
Keller, A.1
Schleicher, T.2
Förster, F.3
Ruderisch, B.4
Dandekar, T.5
Müller, T.6
Wolf, M.7
-
19
-
-
58049115079
-
5.8S-28S rRNA interaction and HMM-based ITS2 annotation
-
Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M (2009) 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene, 430, 50-57.
-
(2009)
Gene
, vol.430
, pp. 50-57
-
-
Keller, A.1
Schleicher, T.2
Schultz, J.3
Müller, T.4
Dandekar, T.5
Wolf, M.6
-
20
-
-
76749097624
-
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
-
Keller A, Förster F, Müller T, Dandekar T, Schultz J, Wolf M (2010) Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct, 5, 4.
-
(2010)
Biology Direct
, vol.5
, pp. 4
-
-
Keller, A.1
Förster, F.2
Müller, T.3
Dandekar, T.4
Schultz, J.5
Wolf, M.6
-
21
-
-
75549088448
-
The ITS2 Database III - sequences and structures for phylogeny
-
Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Müller T, Wolf M, Schultz J (2010) The ITS2 Database III - sequences and structures for phylogeny. Nucleic Acids Research, 38, D275-D279.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Koetschan, C.1
Förster, F.2
Keller, A.3
Schleicher, T.4
Ruderisch, B.5
Schwarz, R.6
Müller, T.7
Wolf, M.8
Schultz, J.9
-
22
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (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
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
23
-
-
0031020581
-
The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants
-
Mai JC, Coleman AW (1997) The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. Journal of Molecular Evolution, 44, 258-271.
-
(1997)
Journal of Molecular Evolution
, vol.44
, pp. 258-271
-
-
Mai, J.C.1
Coleman, A.W.2
-
24
-
-
23144440350
-
DINAMelt web server for nucleic acid melting prediction
-
Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Research, 33, W577-W581.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Markham, N.R.1
Zuker, M.2
-
25
-
-
84934438960
-
UNAFold: software for nucleic acid folding and hybridization
-
Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods in Molecular Biology, 453, 3-31.
-
(2008)
Methods in Molecular Biology
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
26
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology, 288, 911-940.
-
(1999)
Journal of Molecular Biology
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
27
-
-
13444309144
-
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
-
Müller T, Rahmann S, Dandekar T, Wolf M (2004) Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology, 4, 20.
-
(2004)
BMC Evolutionary Biology
, vol.4
, pp. 20
-
-
Müller, T.1
Rahmann, S.2
Dandekar, T.3
Wolf, M.4
-
28
-
-
34548352883
-
Distinguishing species
-
Müller T, Philippi N, Dandekar T, Schultz J, Wolf M (2007) Distinguishing species. RNA, 13, 1469-1472.
-
(2007)
RNA
, vol.13
, pp. 1469-1472
-
-
Müller, T.1
Philippi, N.2
Dandekar, T.3
Schultz, J.4
Wolf, M.5
-
29
-
-
0031773680
-
Modeltest: testing the model of DNA substitution
-
Posada D, Crandall K (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.2
-
31
-
-
84900226404
-
Efficient and robust analysis of large phylogenetic datasets
-
Hui-Huang H (Ed), Idea Group Inc, USA
-
Rahmann S, Müller T, Dandekar T, Wolf M (2006) Efficient and robust analysis of large phylogenetic datasets. In: Hui-Huang H (Ed), Advanced Data Mining Technologies in Bioinformatics. Idea Group Inc, USA, pp 104-117.
-
(2006)
Advanced Data Mining Technologies in Bioinformatics
, pp. 104-117
-
-
Rahmann, S.1
Müller, T.2
Dandekar, T.3
Wolf, M.4
-
32
-
-
79951548848
-
phangorn: phylogenetic analysis in R
-
Schliep KP (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.
-
(2011)
Bioinformatics
, vol.27
, pp. 592-593
-
-
Schliep, K.P.1
-
33
-
-
15444361843
-
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota
-
Schultz J, Maisel S, Gerlach D, Müller T, Wolf M (2005) A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA, 11, 361-364.
-
(2005)
RNA
, vol.11
, pp. 361-364
-
-
Schultz, J.1
Maisel, S.2
Gerlach, D.3
Müller, T.4
Wolf, M.5
-
34
-
-
33747844305
-
The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses
-
Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, Wolf M (2006) The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research, 34, W704-W707.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Schultz, J.1
Müller, T.2
Achtziger, M.3
Seibel, P.N.4
Dandekar, T.5
Wolf, M.6
-
35
-
-
33751213606
-
4 SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing
-
Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M (2006) 4 SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics, 7, 498.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 498
-
-
Seibel, P.N.1
Müller, T.2
Dandekar, T.3
Schultz, J.4
Wolf, M.5
-
36
-
-
58049121167
-
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4 SALE
-
Seibel PN, Müller T, Dandekar T, Wolf M (2008) Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4 SALE. BMC Research Notes, 1, 91.
-
(2008)
BMC Research Notes
, vol.1
, pp. 91
-
-
Seibel, P.N.1
Müller, T.2
Dandekar, T.3
Wolf, M.4
-
37
-
-
38549087890
-
The ITS2 Database II: homology modelling RNA structure for molecular systematics
-
Selig C, Wolf M, Müller T, Dandekar T, Schultz J (2008) The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research, 36, D377-D380.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Selig, C.1
Wolf, M.2
Müller, T.3
Dandekar, T.4
Schultz, J.5
-
38
-
-
33947649070
-
The systematics of a small spineless Desmodesmus species, D. costatogranulatus (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses and cell wall morphology
-
Vanormelingen P, Hegewald E, Braband A, Kitschke M, Friedl T, Sabbe K, Vyverman W (2007) The systematics of a small spineless Desmodesmus species, D. costatogranulatus (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses and cell wall morphology. Journal of Phycology, 43, 378-396.
-
(2007)
Journal of Phycology
, vol.43
, pp. 378-396
-
-
Vanormelingen, P.1
Hegewald, E.2
Braband, A.3
Kitschke, M.4
Friedl, T.5
Sabbe, K.6
Vyverman, W.7
-
39
-
-
27144461969
-
Homology modelling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures
-
Wolf M, Achtziger M, Schultz J, Dandekar T, Müller T (2005) Homology modelling revealed more than 20, 000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA, 11, 1616-1623.
-
(2005)
RNA
, vol.11
, pp. 1616-1623
-
-
Wolf, M.1
Achtziger, M.2
Schultz, J.3
Dandekar, T.4
Müller, T.5
-
40
-
-
53849098418
-
ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments
-
Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T (2008) ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics, 24, 2401.
-
(2008)
Bioinformatics
, vol.24
, pp. 2401
-
-
Wolf, M.1
Ruderisch, B.2
Dandekar, T.3
Schultz, J.4
Müller, T.5
-
41
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
|