Author: Niema Moshiri
Title: ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Document date: 2020_4_21
ID: l9a7upui_10
Snippet: Because it uses the positions of the reference genome as anchors with which to merge the individual pairwise alignments, ViralMSA only keeps matches, mismatches, and deletions with respect to the reference genome: it discards all insertions with respect to the reference genome. For closely-related viral strains, insertions with respect to the reference genome are typically unique and thus lack usable phylogenetic or transmission clustering inform.....
Document: Because it uses the positions of the reference genome as anchors with which to merge the individual pairwise alignments, ViralMSA only keeps matches, mismatches, and deletions with respect to the reference genome: it discards all insertions with respect to the reference genome. For closely-related viral strains, insertions with respect to the reference genome are typically unique and thus lack usable phylogenetic or transmission clustering information, so their removal results in little to no impact on downstream analyses (Fig. 1b) .
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