dvstar: dvstar: Construction and comparison of variable-length Markov chains

dvstar is an open-source tool for constructing and applying variable-length Markov chains (VLMCs) as applied to genomes. The VLMCs are computed based on k-mer counts, enabling them to be built on arbitrarily large genomes and sequencing data. Using the computed VLMCs, the similarity between VLMCs can be assessed using either the dvstar comparison method, which compares parameters of the models or with the negative log-likelihood to assess similarity to other genomes. The tool has been used to study the evolution of viruses and can be used to monitor environments for emerging pathogens.

For further information contact Joel Gustafsson (me@joelgustafsson.com). This software is a result of or used in the following projects: GenomicSignatures.

Team

Members: Joel Gustafsson, Alexander Schliep, Joel Gustafsson.