Recombination is a pervasive process generating diversity in most viruses. It joins variants
that arise independently within the same molecule, creating new opportunities for viruses to …

Molecular phylogenetics has revolutionized the study of not only evolution but also disparate
fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular …

Over the past two decades, comparative sequence analysis using codon-substitution
models has been honed into a powerful and popular approach for detecting signatures of …

RDP3 is a new version of the RDP program for characterizing recombination events in DNA-
sequence alignments. Among other novelties, this version includes four new recombination …

Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in
evolutionary biology. Since the original release in 2005, we have expanded the analysis …

Background Likelihood-based phylogenetic inference is generally considered to be the most
reliable classification method for unknown sequences. However, traditional likelihood-based …

Viral sequence classification has wide applications in clinical, epidemiological, structural
and functional categorization studies. Most existing approaches rely on an initial alignment …

Although antiretroviral therapy (ART) is highly effective at suppressing HIV-1 replication, the
virus persists as a latent reservoir in resting CD4+ T cells during therapy. This reservoir …

Background To investigate differences in pathogenesis, diagnosis and resistance pathways
between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed …

Background Sexually transmitted infections spread across contact networks. Partner
elicitation and notification are commonly used public health tools to identify, notify, and offer …