Author: Mordecai, Gideon J; Miller, Kristina M; Di Cicco, Emiliano; Schulze, Angela D; Kaukinen, Karia H; Ming, Tobi J; Li, Shaorong; Tabata, Amy; Teffer, Amy; Patterson, David A; Ferguson, Hugh W; Suttle, Curtis A
Title: Endangered wild salmon infected by newly discovered viruses Document date: 2019_9_3
ID: 010xj69x_29
Snippet: The phylogeny of each virus was resolved based on the predicted replicase (CAV and SPAV) and ORF1ab (PsNV) amino acid sequences, as nucleotide sequences were too dissimilar to reliably align. Alignments were generated with MAFTT (v7.42) (Katoh and Standley, 2013) employing the E-INS-i algorithm. This alignment algorithm is suited for evolutionarily distinct sequences with conserved motifs (such as viral RNA polymerase) that are embedded within lo.....
Document: The phylogeny of each virus was resolved based on the predicted replicase (CAV and SPAV) and ORF1ab (PsNV) amino acid sequences, as nucleotide sequences were too dissimilar to reliably align. Alignments were generated with MAFTT (v7.42) (Katoh and Standley, 2013) employing the E-INS-i algorithm. This alignment algorithm is suited for evolutionarily distinct sequences with conserved motifs (such as viral RNA polymerase) that are embedded within long unalignable residues. The novel salmon viruses were aligned with other viral genomes with shared amino acid similarity as detected by DIAMOND (Buchfink et al., 2015) . In addition, viral genomes which are known to be evolutionarily related to these were included. The multiple protein alignments were then used as to build phylogenies using PhyML 3.0 (Guindon et al., 2010) plugin within Geneious with 100 bootstraps to generate branch support values. Trees are mid-point rooted for clarity only, and do not necessarily represent the ancestral relationship of the viruses.
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