Author: Maddamsetti, Rohan; Johnson, Daniel T.; Spielman, Stephanie J.; Petrie, Katherine L.; Marks, Debora S.; Meyer, Justin R.
Title: Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature Document date: 2018_9_11
ID: z7alrc7s_12
Snippet: We carried out a complete phylogenetic analysis of recombination in the λ genome in order to compare to J. We made alignments of all 66 proteins in the reference proteome for phage λ in UniProt by using phmmer on the HMMER webserver (Finn et al. 2015) accessible through the EMBL-EBI portal (Chojnacki et al. 2017) (Katoh et al. 2017) to align the homologs, and FastTree to make phylogenies. We calculated normalized geodesic and Robinson-Foulds di.....
Document: We carried out a complete phylogenetic analysis of recombination in the λ genome in order to compare to J. We made alignments of all 66 proteins in the reference proteome for phage λ in UniProt by using phmmer on the HMMER webserver (Finn et al. 2015) accessible through the EMBL-EBI portal (Chojnacki et al. 2017) (Katoh et al. 2017) to align the homologs, and FastTree to make phylogenies. We calculated normalized geodesic and Robinson-Foulds distances between the phylogenies for J, its specificity region, and the rest of the proteins in the λ genome using TreeCl (Gori et al. 2016) . We visualized the distances between trees using metric multidimensional scaling in TreeCl. We visualized individual phylogenies using the ETE Toolkit (Huerta-Cepas et al. 2016).
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