Computational protocol: Prevalence and Phylogeny of Coronaviruses in Wild Birds from the Bering Strait Area (Beringia)

Similar protocols

Protocol publication

[…] Sequences were assembled and edited using the BioEdit v.7.0.7. and the DNASTAR 7 (Lasergene, WI, USA) software packages. Identification was performed using the Basic Local Alignment Search Tool (BLAST) to search for sequences available at the National Center for Biotechnology Information in Bethesda, Maryland, USA (http://www.ncbi.nlm.nih.gov). Distance based neighbour-joining and character based maximum parsimony phylogenetic trees were generated using the Molecular Evolutionary Genetics Analysis (MEGA) software v.4.0. . The neighbour-joining algorithm was implemented with the Kimura-2 parameter model using a transition-to-translation ratio of 2.0. Other models were tested that showed similar topologies. The topology of the trees was confirmed by 1,000 bootstrap replicates. Maximum likelihood phylogenetic trees were generated using the PHYLIP version 3.68 software . The sequences were deposited in GenBank under the following accession numbers: GU396668-GU396690. […]

Pipeline specifications

Software tools BioEdit, BLASTN, MEGA, PHYLIP
Application Phylogenetics
Organisms Homo sapiens, Gallus gallus, SARS coronavirus
Diseases Virus Diseases, HIV Infections