Computational protocol: A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut

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Protocol publication

[…] The evolutionary history of the MINPP protein was inferred using the Maximum Likelihood method in the MEGA5 software tool (). Amino acid sequences were aligned with PRANK and highly variable regions removed from the data set. The model of evolution was used, and initial tree(s) for the heuristic search was obtained automatically as follows. When the number of common sites was <100 or less than one-fourth of the total number of sites, the maximum parsimony method was used; otherwise, BIONJ method with MCL distance matrix was used. To provide statistical support for each node on the tree, a consensus tree was generated from 1,000 bootstrap data sets. […]

Pipeline specifications

Software tools MEGA, PRANK, BIONJ
Application Phylogenetics
Organisms Homo sapiens, Bacteroides thetaiotaomicron