Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.
Jean P ZukurovSieberth do Nascimento-BritoAngela C VolpiniGuilherme C OliveiraLuiz Mario R JaniniFernando AntoneliPublished in: Algorithms for molecular biology : AMB (2016)
The methods described in this paper have been implemented as an integrated tool called Tanden (Tool for Analysis of Diversity in Viral Populations) and successfully tested on samples obtained from HIV-1 strain NL4-3 (group M, subtype B) cultivations on primary human cell cultures in many distinct viral propagation conditions. Tanden is written in C# (Microsoft), runs on the Windows operating system, and can be downloaded from: http://tanden.url.ph/.