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» Fixed-Parameter Algorithms in Phylogenetics
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79
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ALMOB
2008
131views more  ALMOB 2008»
14 years 10 months ago
Fast algorithms for computing sequence distances by exhaustive substring composition
The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reco...
Alberto Apostolico, Olgert Denas
BMCBI
2006
92views more  BMCBI 2006»
14 years 10 months ago
Recrafting the neighbor-joining method
Background: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical (n3)...
Thomas Mailund, Gerth Stølting Brodal, Rolf...
RECOMB
2004
Springer
15 years 10 months ago
Reconstructing reticulate evolution in species: theory and practice
We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of...
Luay Nakhleh, Tandy Warnow, C. Randal Linder
WABI
2009
Springer
128views Bioinformatics» more  WABI 2009»
15 years 4 months ago
Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models
Abstract. Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present e...
Xiuwei Zhang, Bernard M. E. Moret
98
Voted
BMCBI
2005
134views more  BMCBI 2005»
14 years 10 months ago
Ancestral sequence alignment under optimal conditions
Background: Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multipl...
Alexander K. Hudek, Daniel G. Brown 0001