Computational protocol: Nodular Worm Infections in Wild Non-human Primates and Humans Living in the Sebitoli Area (Kibale National Park, Uganda): Do High Spatial Proximity Favor Zoonotic Transmission?

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Protocol publication

[…] Sequence alignments were performed on SeaView software by inputting our sequences with the sequences obtained by Ghai et al. [] (accession numbers: KF250585 –KF250660) and by Krief et al. [] (KT592234, KT592235). In addition, we included three Oesophagostomum stephanostomum reference sequences (AF136576, AB821022, AB821031), one O. bifurcum sequence (AF136575) and five outgroups (HQ844232, Y11736, Y11735, Y10790, AJ006149). Phylogenetic trees were established using the maximum likelihood method in MEGA [] and the Hasegawa-Kishino-Yano substitution model with five discrete gamma categories []. To assess the phylogenetic robustness of the tree, 1000 bootstrap replicates were performed. […]

Pipeline specifications

Software tools SeaView, MEGA
Application Phylogenetics
Organisms Papio anubis, Pan troglodytes, Homo sapiens, Caenorhabditis elegans, Colobus guereza, Papio hamadryas