Computational protocol: Diversity of Microsporidia, Cryptosporidium and Giardia in Mountain Gorillas (Gorilla beringei beringei) in Volcanoes National Park, Rwanda

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Protocol publication

[…] The nucleotide sequences of each gene obtained in this study were edited using the software ChromasPro 1.5 (Technelysium, Pty, Ltd., Brisbane, Australia) and were aligned with each other and with reference sequences from GenBank using ClustalX 2.0.6. Alignment adjustments were made manually to remove artificial gaps using BioEdit. Phylogenetic analyses were performed using the software MEGA5 . Neighbour joining (NJ) trees were constructed. All ambiguous positions were removed for each sequence pair. The reliability of branches in trees was assessed using the bootstrap analysis with 1000 pseudo-replicates, with values above 50% reported. Phylograms were drawn using the MEGA5 and were manually adjusted using CorelDrawX5 (Ottawa, Canada). ITS and SSU sequences have been deposited in GenBank under the accession numbers KJ469967–KJ469979, respectively. […]

Pipeline specifications

Software tools ChromasPro, Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Cryptosporidium muris, Gorilla gorilla, Homo sapiens, Enterocytozoon bieneusi, Encephalitozoon cuniculi
Diseases Altitude Sickness, Communicable Diseases, Infection, Substance-Related Disorders