Computational protocol: Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences

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Protocol publication

[…] A large set of ISAV isolates sequenced on either one or both RNA segments 5 and 6 was used. In order to guarantee the quality of the analyses, the existing sequences were obtained directly from GenBank [], making sure they were unique, correct and current [see Additional file ]. For each RNA segment, all the isolates were used in a multiple alignment by using CLUSTAL X2 with the default settings []. The same reference isolates were then used for phylogenetic analysis. For RNA segment 6, only the first 1,008 nucleotides were used; thus the HPR containing gaps and the remaining 3' end sequences were excluded from the analysis []. Phylogenetic trees were generated. Bootstrapping values (1000 replicates) were calculated. Branches with bootstrapping values ≥ 70% were considered significant, corresponding to a confidence interval ≥ 95% []. For visualization and printing of the trees, the NJPLOT program, Version 2.1 (Written by M. Gouy) was used. […]

Pipeline specifications

Software tools Clustal W, NJplot
Application Phylogenetics
Organisms Salmo salar
Diseases Anemia