add phylogenetic analysis assay and protocol

assays/PhylogeneticAnalysis/protocols/PhylogeneticAnalysisProtocol.md

+## Phylogenomic analysis of the *Lj*- and *At*-SPHERE culture collections
+
+Genomes from the *Lj*- and *At*-SPHERE culture collections (Bai, Y. et al., 2015) were searched for the presence of a set of 31 conserved, single-copy marker genes, known as AMPHORA (Wu, M. & Eisen, J. A., 2008) genes. Sequences of each gene were aligned using Clustal Omega (Sievers, F. et al., 2011) with default parameters. Using a concatenated alignment of each gene, we inferred a maximum likelihood phylogeny using FastTree (Price, M. N. et al., 2010). We visualized this tree using the Interactive Tree of Life web tool (Letunic, I. & Bork, P., 2019). Genomes from both collections (*Lj*-SPHERE and *At*-SPHERE) were clustered into phylogroups, roughly corresponding to a species designation (Olm, M. R. et al., 2020) using FastANI (Jain, C. et al., 2018) and a threshold of average nucleotide identity at the whole-genome level of at least 97%.
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