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» An Investigation of Phylogenetic Likelihood Methods
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BMCBI
2007
131views more  BMCBI 2007»
13 years 6 months ago
An improved method for identifying functionally linked proteins using phylogenetic profiles
Background: Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein c...
Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
SAC
2006
ACM
14 years 25 days ago
Protein classification using transductive learning on phylogenetic profiles
Phylogenetic profiles of proteins − strings of ones and zeros encoding respectively the presence and absence of proteins in a group of genomes − have recently been used to iden...
Roger A. Craig, Li Liao
IJDMB
2007
110views more  IJDMB 2007»
13 years 6 months ago
Transductive learning with EM algorithm to classify proteins based on phylogenetic profiles
: Phylogenetic profiles of proteins  strings of ones and zeros encoding respectively the presence and absence of proteins in a group of genomes  have recently been used to id...
Roger A. Craig, Li Liao
IPPS
2006
IEEE
14 years 27 days ago
Phylogenetic models of rate heterogeneity: a high performance computing perspective
Inference of phylogenetic trees using the maximum likelihood (ML) method is NP-hard. Furthermore, the computation of the likelihood function for huge trees of more than 1,000 orga...
Alexandros Stamatakis
IJCBDD
2008
113views more  IJCBDD 2008»
13 years 6 months ago
Parsimony accelerated Maximum Likelihood searches
: Phylogenetic search is a key tool used in a variety of biological research endeavors. However, this search problem is known to be computationally difficult, due to the astronomic...
Kenneth Sundberg, Timothy O'Connor, Hyrum Carroll,...