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» An Investigation of Phylogenetic Likelihood Methods
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RECOMB
2003
Springer
14 years 8 months ago
Combining phylogenetic and hidden Markov models in biosequence analysis
A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process c...
Adam C. Siepel, David Haussler
CEC
2003
IEEE
13 years 11 months ago
Phylogenetic trees using evolutionary search: initial progress in extending Gaphyl to work with genetic data
AbstractGaphyl is an application of evolutionary algorithms (EA's) to phylogenetics, an approach used by biologists to investigate evolutionary relationships among organisms. ...
Clare Bates Congdon, Kevin J. Septor
DAGM
2008
Springer
13 years 9 months ago
Approximate Parameter Learning in Conditional Random Fields: An Empirical Investigation
We investigate maximum likelihood parameter learning in Conditional Random Fields (CRF) and present an empirical study of pseudo-likelihood (PL) based approximations of the paramet...
Filip Korc, Wolfgang Förstner
IPPS
2003
IEEE
14 years 27 days 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
GCB
2000
Springer
137views Biometrics» more  GCB 2000»
13 years 11 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