September 2014 | Volume 9 | Issue 9 | e108277 | Brejnev Muhizi Muhire1*, Arvind Varsani1,2,3, Darren Patrick Martin1
The paper introduces the Sequence Demarcation Tool (SDT), a free and user-friendly computer program designed to aid in the objective classification of viral genome sequences based on pairwise genetic identity calculations. SDT addresses the challenges posed by the increasing rate of viral genome sequencing by providing a robust and reproducible method for classifying nucleotide or amino acid sequences according to International Committee on Taxonomy of Viruses (ICTV) guidelines. The tool includes features such as publication-quality pairwise identity plots and color-coded distance matrices, which help in identifying taxonomic demarcation criteria. SDT is available in both graphical and command-line versions, with parallel versions for high-performance computing clusters. The authors compare SDT's performance with other sequence comparison methods, demonstrating its consistency and speed advantages, particularly in handling large datasets. SDT is intended to complement existing tools like PASC and DEmARC, enhancing the efficiency and accuracy of virus classification.The paper introduces the Sequence Demarcation Tool (SDT), a free and user-friendly computer program designed to aid in the objective classification of viral genome sequences based on pairwise genetic identity calculations. SDT addresses the challenges posed by the increasing rate of viral genome sequencing by providing a robust and reproducible method for classifying nucleotide or amino acid sequences according to International Committee on Taxonomy of Viruses (ICTV) guidelines. The tool includes features such as publication-quality pairwise identity plots and color-coded distance matrices, which help in identifying taxonomic demarcation criteria. SDT is available in both graphical and command-line versions, with parallel versions for high-performance computing clusters. The authors compare SDT's performance with other sequence comparison methods, demonstrating its consistency and speed advantages, particularly in handling large datasets. SDT is intended to complement existing tools like PASC and DEmARC, enhancing the efficiency and accuracy of virus classification.