Just W:Computational complexity of multiple sequence alignment with SP-score. J Comput Biol. 2001, 8: 615-623.

Article
CAS
PubMed
Google Scholar

Wang L, Jiang T:On the complexity of multiple sequence alignment. J Comput Biol. 1994, 1: 337-348.

Article
CAS
PubMed
Google Scholar

Lunter G, Miklo?s I, Drummond A, Jensen JL, Hein J:Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics. 2005, 6: 83-

Article
PubMed
PubMed Central
Google Scholar

Redelings BD, Suchard MA:Joint bayesian estimation of alignment and phylogeny. Syst Biol. 2005, 54: 401-418.

Article
PubMed
Google Scholar

Farris JS:The retention index and the rescaled consistency index. Cladistics. 1989, 5: 417-419. 10.1111/j.1096-0031.1989.tb00573.x.

Article
Google Scholar

Felsenstein J:Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 1978, 27: 401-410. 10.2307/2412923.

Article
Google Scholar

Telford MJ, Copley RR:Animal phylogeny: fatal attraction. Curr Biol. 2005, 15: 296-299. 10.1016/j.cub.2005.04.001.

Article
Google Scholar

Simões-Pereira JMS:A note on the tree realizability of a distance matrix. J Combin Theory. 1969, 6: 303-310. 10.1016/S0021-9800(69)80092-X.

Article
Google Scholar

Buneman P:A note on the metric property of trees. J Combin Theory Ser B. 1974, 17: 48-50. 10.1016/0095-8956(74)90047-1.

Article
Google Scholar

Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu C-h:Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci. 2009, 128: 109-120.

Article
CAS
PubMed
PubMed Central
Google Scholar

Eigen M, Winkler-Oswatitsch R, Dress AWM:Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Proc Natl Acad Sci USA. 1988, 85: 5913-5917.

Article
CAS
PubMed
PubMed Central
Google Scholar

Nieselt-Struwe K:Graphs in sequence spaces: a review of statistical geometry. Biophys Chem. 1997, 30: 111-131. 10.1016/S0301-4622(97)00064-1.

Article
Google Scholar

Holland BR, Huber KT, Dress AWM, Moulton V:*?*plots: A tool for analyzing phylogenetic distance data. Mol Biol Evol. 2002, 19: 2051-2059.

Article
CAS
PubMed
Google Scholar

Huson D, Steel M:Distances that perfectly mislead. Syst Biol. 2004, 53: 327-332.

Article
PubMed
Google Scholar

Nieselt-Struwe K, von Haeseler A:Quartet-mapping, a generalization of the Likelihood-Mapping procedure. Mol Biol Evol. 2001, 18: 1204-1219.

Article
CAS
PubMed
Google Scholar

Strimmer K, von Haeseler A:Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA. 1997, 94: 6815-6819.

Article
CAS
PubMed
PubMed Central
Google Scholar

Stadler PF, Fried C, Prohaska SJ, Bailey WJ, Misof BY, Ruddle FH, Wagner GP:Evidence for independent Hox gene duplications in the hagfish lineage: A PCR-based gene inventory of*Eptatretus stoutii*. Mol Phylog Evol. 2004, 32: 686-692. 10.1016/j.ympev.2004.03.015.

Article
CAS
Google Scholar

Raincrow JD, Dewar K, Stocsits C, Prohaska SJ, Amemiya CT, Stadler PF, Chiu C-h:Hox clusters of the bichir (Actinopterygii,*Polypterus senegalus*), highlight unique patterns of sequence evolution in gnathostome phylogeny. J Exp Zool. 2011, 316: 451-464. 10.1002/jez.b.21420.

Article
CAS
Google Scholar

Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP:Visualization of the phylogenetic content of five genomes using dekapentagonal maps. Genome Biol. 2004, 5: 20-10.1186/gb-2004-5-3-r20.

Article
Google Scholar

Hamel L, Zhaxybayeva O, Gogarten JP:PentaPlotPentaPlot: A software tool for the illustration of genome mosaicism. BMC Bioinformatics. 2005, 6: 139-

Article
PubMed
PubMed Central
Google Scholar

Hendy M, Penny D:A framework for the quantitative study of evolutionary trees. Syst Zool. 1989, 38: 297-309. 10.2307/2992396.

Article
Google Scholar

Bryant D:Hadamard phylogenetic methods and the*n*-taxon process. Bull Math Biol. 2009, 71: 339-351.

Article
PubMed
Google Scholar

Lento GM, Hickson RE, Chambers GK, Penny D:Use of spectral analysis to test hypotheses on the origin of pinnipeds. J Mol Biol Evol. 1995, 12: 28-52. 10.1093/oxfordjournals.molbev.a040189.

Article
CAS
Google Scholar

Huber KT, Langton M, Penny V, Moulton D, Hendy M:Spectronet: a package for computing spectra and median networks. Appl Bioinform. 2002, 1: 2041-2059.

Google Scholar

White T, Hills SF, Gaddam R, Holland BR, Penny D:Treeness triangles: Visualizing the loss of phylogenetic signal. Mol Biol Evol. 2007, 24: 2029-2039.

Article
CAS
PubMed
Google Scholar

Ogden TH, Rosenberg M:Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol. 2006, 55: 314-328.

Article
PubMed
Google Scholar

Landan G, Graur D:Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol. 2007, 24: 1380-1383.

Article
CAS
PubMed
Google Scholar

Yang Z:On the best evolutionary rate for phylogenetic analysis. Syst Biol. 1998, 47: 125-133.

Article
CAS
PubMed
Google Scholar

Wägele J-W: Foundations of Phylogenetic Systematics. 2005, Verlag Dr Friedrich Pfeil, Munich, Germany

Google Scholar

Kück P, Mayer C, Wägele J-W, Misof B:Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS ONE. 2012, 7: 36593-10.1371/journal.pone.0036593.

Article
Google Scholar

Björklund M:Are third positions really that bad? a test using vertebrate cytochrome b. Cladistics. 1999, 15: 91-97.

Google Scholar

Castresana J:Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552.

Article
CAS
PubMed
Google Scholar

Talavera G, Castresana J:Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007, 56: 564-577.

Article
CAS
PubMed
Google Scholar

Hartmann S, Vision TJ:Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment. BMC Evol Biol. 2008, 8: 95-

Article
PubMed
PubMed Central
Google Scholar

Roure B, Baurain D, Philippe H:Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 2013, 30: 197-214.

Article
CAS
PubMed
Google Scholar

Dress AWM, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF:Identification of homoplastic characters in multiple sequence alignments. Alg Mol Biol. 2008, 3: 7-10.1186/1748-7188-3-7.

Article
Google Scholar

Bandelt HJ, Dress AWM:A canonical decomposition theory for metrics on a finite set. Adv Math. 1992, 92: 47-105. 10.1016/0001-8708(92)90061-O.

Article
Google Scholar

Huson DH:SplitsTreeSplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 1998, 14: 68-73.

Article
CAS
PubMed
Google Scholar

Semple C, Steel M:Cyclic permutations and evolutionary trees. Adv Appl Math. 2004, 32: 669-680. 10.1016/S0196-8858(03)00098-8.

Article
Google Scholar

Bryant D, Moulton V:Neighbor-net: An agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 2004, 21: 255-265.

Article
CAS
PubMed
Google Scholar

Grünewald S, Forslund K, Dress AWM, Moulton V:QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol. 2007, 24: 532-538.

Article
PubMed
Google Scholar

Dress AWM, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF: noisySoftware2011. [], http://www.bioinf.uni-leipzig.de/Software/noisy/

Misof B, Misof K:A Monte Carlo approach successfully identifies randomness of multiple sequence alignments: A more objective approach of data exclusion. Syst Biol. 2009, 58: 21-34.

Article
CAS
PubMed
Google Scholar

Kück P, Meusemann K, Raupach M, von Reumont B, Wägele W, Misof B:Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Frontiers Zool. 2010, 7: 10-10.1186/1742-9994-7-10.

Article
Google Scholar

von Reumont BM, Meusemann K, Szucsich NU, Dell'Ampio E, Bartel D, Simon S, Letsch HO, Stocsits RR, Luan Y, Wägele JW, Pass G, Hadrys H, Misof B:Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? a case study on major arthropod relationships. BMC Evol Biol. 2009, 9: 119-

Article
PubMed
PubMed Central
Google Scholar

Wägele J-W, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H:Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny). Frontiers Zool. 2009, 6: 12-10.1186/1742-9994-6-12.

Article
Google Scholar

Schwarzer J, Misof B, Tautz D, Schliewen UK:The root of the East African cichlid radiations. BMC Evol Biol. 2009, 9: 186-

Article
PubMed
PubMed Central
Google Scholar

Letsch HO, Kück P, Schmidt C, Fleck G, Stocsits RR, Misof B:The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Mol Biol Evol. 2010, 27: 2507-2521.

Article
CAS
PubMed
Google Scholar

Murienne J, Edgecombe GD, Giribet G:Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol Phylog Evol. 2010, 57: 301-313. 10.1016/j.ympev.2010.06.022.

Article
Google Scholar

Meusemann K, von Reumont , Kueck P, Ebersberger I, Strauss S, Walzl M, Pass G, Breuers S, Achter V, Wägele J-W, Hadrys H, Burmester T, von Haeseler A, Misof B:A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol. 2010, 27: 2451-2464.

Article
CAS
PubMed
Google Scholar

Sanderson MJ, Driskell AC:The challenge of constructing large phylogenetic trees. Trends Plant Sci. 2003, 8: 374-379.

Article
CAS
PubMed
Google Scholar

Driskell AC, Anë C, Burleigh JG, McMahon MM, Meara BC, Sanderson MJ:Prospects for building the tree of life from large sequence databases. Science. 2004, 306: 1172-1174.

Article
CAS
PubMed
Google Scholar

Wiens JJ:Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol. 2003, 52: 528-538.

Article
PubMed
Google Scholar

Wiens JJ:Missing data and the design of phylogenetic analyses. J Biomed Inform. 2006, 39: 34-42.

Article
CAS
PubMed
Google Scholar

Alexe G, Alexe S, Crama Y, Foldes S, Hammer PL, Simeone B: Consensus algorithms for the generation of all maximal bicliques. DIMACS Technical Reports 2002-52, Rutgers University, Piscataway, NJ, USA, 2002. [], http://dimacs.rutgers.edu/TechnicalReports/2002.html

Sanderson MJ, Driskell AC, Ree RH, Eulenstein O, Langley S:Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol Biol Evol. 2003, 20: 1036-1042.

Article
CAS
PubMed
Google Scholar

Yan C, Burleigh JG, Eulenstein O:Identifying optimal incomplete phylogenetic data sets from sequence databases. Mol Phylogenet Evol. 2005, 30: 528-535. 10.1016/j.ympev.2005.02.008.

Article
Google Scholar

Liu X, Li J, Wang L:Modeling protein interacting groups by quasi-bicliques: complexity, algorithm, and application. IEEE/ACM Trans Comput Biol Bioinform. 2010, 7: 354-364.

Article
CAS
PubMed
Google Scholar

Yannakakis M:Node deletion problems on bipartite graphs. SIAM J Comput. 1981, 10: 310-327. 10.1137/0210022.

Article
Google Scholar

Peeters R:The maximum edge biclique problem is NP-complete. Discrete Appl Math. 2003, 131: 651-654. 10.1016/S0166-218X(03)00333-0.

Article
Google Scholar

Chang W-C, Vakati S, Krause R, Eulenstein O:Exploring biological interaction networks with tailored weighted quasi-bicliques. BMC Bioinformatics 2012. 2012, 13 (S10): 16-10.1186/1471-2105-13-S10-S16.

Article
Google Scholar

Misof B, Meyer B, von Reumont BM, Kück P, Misof K, Meusemann K: Selecting informative subsets of sparse supermatrices increases the chance to find correct trees BMC Bioinformatics. 2013, 14: 348

Article
PubMed
PubMed Central
Google Scholar

Gribaldo S, Philippe H:Ancient phylogenetic relationships. Theor Popul Biol. 2002, 61: 391-408.

Article
PubMed
Google Scholar

Wake DB, Wake MH, Specht CD:Homoplasy: from detecting pattern to determining process and mechanism of evolution. Science. 2011, 331: 1032-1035.

Article
CAS
PubMed
Google Scholar