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URL: https://dx.doi.org/DOI:10.17504/protocols.io.q2pdydn

Authors: Elaina Graham, Benjamin Tully

Summary: Making a Phylogenetic TreeIn this procedure we are going to build a phylogenetic tree! Throughout I'll refer to scripts available on my github here. We will be using the 16 ribosomal proteins used in Hug et al. 2016. The HMM models for these are available on my github in a file called `hug_ribosomalmarkers.hmm`. We will be running this tutorial using the genomes and files found in the folder `Example`.As an overview I will be explaining1. How to generate gene predictions using prodigal for genomes of interest2. How to identify ribosomal proteins using an hmm model3. How to align, trim, and concatenate proteins for a phylogenetic tree4. building a phylogenetic treeTo cite this workflow reference this paper:Graham, E. D., J. F. Heidelberg, and B. J. Tully. 'Potential for primary productivity in a globally-distributed bacterial phototroph.' The ISME journal (2018)doi: https://doi.org/10.1038/s41396-018-0091-3

Affiliations: University of Southern California, Center for Dark Energy Biosphere Investigations

Version: 2

Publication Date: 2018

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