Author: Niema Moshiri
Title: ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes Document date: 2020_4_21
ID: l9a7upui_12
Snippet: Because ViralMSA's objective is to be utilized in transmission clustering workflows, which typically rely on pairwise distances between samples, we computed pairwise sequence distances between every pair of samples in each MSA (true, MAFFT, and ViralMSA) under the TN93 model of sequence evolution (Tamura & Nei, 1993) using pairwise distance calculator implemented in HIV-TRACE (Pond et al., 2018) . Then, for each estimated MSA, we measured alignme.....
Document: Because ViralMSA's objective is to be utilized in transmission clustering workflows, which typically rely on pairwise distances between samples, we computed pairwise sequence distances between every pair of samples in each MSA (true, MAFFT, and ViralMSA) under the TN93 model of sequence evolution (Tamura & Nei, 1993) using pairwise distance calculator implemented in HIV-TRACE (Pond et al., 2018) . Then, for each estimated MSA, we measured alignment accuracy by computing the Mantel correlation test (using Spearman correlation) between the true and estimated MSAs.
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