Computational protocol: Characterization of subgroup J avian Leukosis virus isolated from Chinese indigenous chickens

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Protocol publication

[…] The homologies of the nucleic acid and amino acid sequences were compared between gp85 from each ALV-J strains and the reference sequences. To assess the trends in molecular evolution of the ALV-J strains, gp85 from different ALV reference strains were included for phylogenetic analysis (Table ). Phylogenetic analysis was accomplished by muscle alignment and the neighbor-joining and maximum parsimony methods with 500 bootstrap replicates using software MEGA 5.1. […]

Pipeline specifications

Software tools MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Gallus gallus, Human poliovirus 1 Mahoney
Diseases Avian Leukosis, Neoplasms, HIV Infections
Chemicals Amino Acids