Author: Niema Moshiri
Title: ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Document date: 2020_4_21
ID: l9a7upui_2
Snippet: The standard tools for performing MSA such as MAFFT, MUSCLE, and Clustal Omega typically utilize progressive-iterative approaches due to their broad applicability (Katoh & Standley, 2013; Edgar, 2004; Sievers & Higgins, 2014) . However, these methods become prohibitively slow for real-time pathogen surveillance as the number of viral genomes grows. For example, during the COVID-19 pandemic, the number of viral genome assemblies available from aro.....
Document: The standard tools for performing MSA such as MAFFT, MUSCLE, and Clustal Omega typically utilize progressive-iterative approaches due to their broad applicability (Katoh & Standley, 2013; Edgar, 2004; Sievers & Higgins, 2014) . However, these methods become prohibitively slow for real-time pathogen surveillance as the number of viral genomes grows. For example, during the COVID-19 pandemic, the number of viral genome assemblies available from around the world grew exponentially in the initial months of the pandemic, but MAFFT, the fastest of the aforementioned MSA tools, scales quadratically with respect to the number of sequences.
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