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» A Mechanization of Phylogenetic Trees
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BMCBI
2010
104views more  BMCBI 2010»
15 years 1 months ago
A systematic study of genome context methods: calibration, normalization and combination
Background: Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patter...
Luciana Ferrer, Joseph M. Dale, Peter D. Karp
AB
2008
Springer
15 years 8 months ago
The Geometry of the Neighbor-Joining Algorithm for Small Trees
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstr...
Kord Eickmeyer, Ruriko Yoshida
TCBB
2008
107views more  TCBB 2008»
15 years 6 months ago
Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem
Abstract-- The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-comp...
Adrien Goëffon, Jean-Michel Richer, Jin-Kao H...
UAI
2008
15 years 7 months ago
Bayesian Out-Trees
A Bayesian treatment of latent directed graph structure for non-iid data is provided where each child datum is sampled with a directed conditional dependence on a single unknown p...
Tony Jebara
RECOMB
2004
Springer
16 years 6 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