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» Inferring Phylogenetic Trees Using Answer Set Programming
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BMCBI
2010
142views more  BMCBI 2010»
13 years 8 months ago
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-ba...
Frederick A. Matsen III, Robin B. Kodner, E. Virgi...
BMCBI
2010
118views more  BMCBI 2010»
13 years 8 months ago
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Ph...
Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent...
TKDE
2008
153views more  TKDE 2008»
13 years 7 months ago
Discovering Frequent Agreement Subtrees from Phylogenetic Data
We study a new data mining problem concerning the discovery of frequent agreement subtrees (FASTs) from a set of phylogenetic trees. A phylogenetic tree, or phylogeny, is an unorde...
Sen Zhang, Jason Tsong-Li Wang
ICCS
2005
Springer
14 years 1 months ago
Phylogenetic Networks, Trees, and Clusters
Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowled...
Luay Nakhleh, Li-San Wang
FLAIRS
2008
13 years 10 months ago
Answer Set Programming on Expert Feedback to Populate and Extend Dynamic Ontologies
The next generation of online reference works will require structured representations of their contents in order to support scholarly functions such as semantic search, automated ...
Mathias Niepert, Cameron Buckner, Colin Allen