SAMFIRE: multi-locus variant calling for time-resolved sequence data

Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus

(2015) Christopher J.R. Illingworth   MOLECULAR BIOLOGY AND EVOLUTION

High-Definition Reconstruction of Clonal Composition in Cancer

(2014) Andrej Fischer et al.   Cell Reports

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

(2014) Christopher J. R. Illingworth et al.   PLoS Computational Biology

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

(2014) Matthieu Foll et al.   PLoS Genetics

Probabilistic Inference of Viral Quasispecies Subject to Recombination

(2013) Armin Töpfer et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Viral population analysis and minority-variant detection using short read next-generation sequencing

(2013) S. J. Watson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters

(2013) Astrid Gall et al.   Retrovirology