Computational protocol: A novel bacterial symbiont in the nematode Spirocerca lupi

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Protocol publication

[…] Nine nearly-full length sequences of the rrs gene of Comamonas sp. were obtained from five adult S. lupi worms. All clones were sequenced from both directions. Sequences were edited using DNAMAN software (Lynnon Corporation, Canada) and a consensus sequence was determined. The Comamonas sp. rrs sequence was aligned, using MUSCLE 3.7, with other published Comamonas spp. sequences, selected based on BLAST results, and based on their invertebrate host origin. The rrs gene sequence of Verminephrobacter eiseniae was used as an out group. A maximum-likelihood tree was constructed using PhyML 3.0 software. Bootstrap analyses with 1000 re-samplings were performed to test branching robustness. The tree was illustrated using TreeDyn 198.3. All software packages are available at […]

Pipeline specifications

Software tools DNAMAN, PhyML, TreeDyn,
Application Phylogenetics
Organisms Canis lupus familiaris, Caenorhabditis elegans, Spirocerca lupi