Computational protocol: Rediscovering the genus Lyticum, multiflagellated symbionts of the order Rickettsiales

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Protocol publication

[…] Non-identical 16S rRNA gene sequences obtained were aligned with 42 homologous sequences of Rickettsiales bacteria and 16 of non-Rickettsiales alphaproteobacteria (as outgroup) using the ARB software package. Sequence lengths were reduced to that of the shortest one, then multiple character matrices were produced according to Boscaro and colleagues; unless otherwise stated, similarity values were calculated on the unmodified dataset. Maximum likelihood (ML) phylogenetic analyses were performed with PhyML, employing bootstrap analysis (1,000 pseudoreplicates) to evaluate the reliability of nodes. Bayesian inference (BI) analyses were performed with MrBayes, using three different runs with three heated and one cold chain each, iterating for 1,000,000 generations. The evolutionary model was selected according to the Akaike information criterion calculated by jModelTest. […]

Pipeline specifications

Software tools ARB, PhyML, MrBayes, jModelTest
Application Phylogenetics