This is the Linux app named QSdpR whose latest release can be downloaded as run1.zip. It can be run online in the free hosting provider OnWorks for workstations.
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This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population.
- mRNA virus
- Semidefinite program
- HIV-1 virus
Unix Shell, Python, C
This is an application that can also be fetched from https://sourceforge.net/projects/qsdpr/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.