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» Maximum likelihood of phylogenetic networks
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IPPS
2003
IEEE
15 years 5 months ago
Phylogenetic Tree Inference on PC Architectures with AxML/PAxML
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the maximum likelihood method is computationally extremely expensive. In previous work,...
Alexandros Stamatakis, Thomas Ludwig 0002
ISAAC
2005
Springer
113views Algorithms» more  ISAAC 2005»
15 years 5 months ago
Fast Algorithms for Computing the Tripartition-Based Distance Between Phylogenetic Networks
Consider two phylogenetic networks N and N′ of size n. The tripartition-based distance finds the proportion of tripartitions which are not shared by N and N′ . This distance i...
Nguyen Bao Nguyen, C. Thach Nguyen, Wing-Kin Sung
BMCBI
2005
134views more  BMCBI 2005»
14 years 11 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
GCB
2000
Springer
137views Biometrics» more  GCB 2000»
15 years 3 months ago
Detecting Sporadic Recombination in DNA Alignments with Hidden Markov Models
Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets fro...
Dirk Husmeier, Frank Wright
BMCBI
2007
131views more  BMCBI 2007»
14 years 11 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