Paper Info
Title
A new algorithm for analysis of within-host HIV-1 evolution.
Abstract
A new algorithm for inferring the evolution of within-host viral sequences is presented. A sequential-linking approach is developed so that a longitudinal phylogenetic tree can be reconstructed from sequential molecular data that are obtained at different time points from the same host. The algorithm employs a codon-based model, which uses a Markov process to describe substitutions between codons, to calculate nonsynonymous and synonymous substitution rates and to distinguish positive selection and neutral evolution. The algorithm is applied to a data set of the V3 region of the HIV-1 envelope genes sequenced at different years after the infection of a single patient. The results suggest that this algorithm may provide a more realistic description of viral evolution than traditional evolutionary models, because it accounts for both neutral and adaptive evolution, and reconstructs a longitudinal phylogenetic tree that describes the dynamic process of viral evolution.
Year
Venue
Keywords
2001
Pacific Symposium on Biocomputing
phylogenetic tree,neutral evolution,markov process,positive selection
Field
DocType
ISSN
Neutral theory of molecular evolution,Phylogenetic tree,Viral evolution,Biology,Molecular evolution,Natural selection,Neutral mutation,Algorithm,Recurrent evolution,Bioinformatics,Genetics,Molecular clock
Conference
2335-6936
Citations 
PageRank 
References 
4
0.81
2
Authors
3
Name
Order
Citations
PageRank
F Ren1212.94
Soichi Ogishima2707.08
H Tanaka3102.34