Computational protocol: Characterization of Farmington virus, a novel virus from birds that is distantly related to members of the family Rhabdoviridae

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Protocol publication

[…] The L protein sequence of FARV was compared with those of 38 other rhabdoviruses downloaded from GenBank. All protein sequences were aligned using MUSCLE [] under default settings. Because these sequences were highly divergent, which could negatively impact phylogenetic analysis, all ambiguously aligned regions were removed using the G-blocks program []. This resulted in a final sequence alignment of 433 amino acid residues. The phylogenetic relationships among these sequences were determined using the maximum likelihood (ML) method available in PhyML 3.0 [] employing the WAG-G model of amino acid substitution and subtree pruning and regrafting (SPR) branch-swapping. The robustness of each node was evaluated using the SH and ChiSq minimum statistic. In addition, trees were determined using the neighbor-joining (NJ) and maximum parsimony (MP) methods using the default settings available in PAUP* v. b10, bootstraps were run for both methods. […]

Pipeline specifications

Software tools MUSCLE, PhyML, PAUP*
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Farmington virus
Diseases Encephalitis, HIV Infections