Computational protocol: Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas

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Protocol publication

[…] The sequences used for the phylogenetic tree were obtained from the GenBank database. All the sequences obtained were validated with their corresponding publications. Sequences were aligned using ClustalW. The genetic distances and phylogenetic analyses were conducted using MEGA 7 (). Intraspecific and interspecies genetic distances were calculated using the Kimura 2-parameter (K2-p) model. Complete deletion treatment and standard error estimated (SE) were determined using a bootstrap procedure (1000 replicates). The phylogenetic tree was constructed using Maximum Livelihood (ML) algorithm with the K2-p model. The bootstrap consensus results inferred from the 1000 replicates were used to represent the evolutionary history of the taxa. Intraspecific and interspecific pairwise distances of A. pennula were calculated using complete deletion in the ML algorithm and K2-p model. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics