A conserved bacterial genetic basis for commensal-host specificity

Alignments and all the trees used to construct all the figures are available in this public repository. For further information related to the code and programs used to generate the figures, please visit: Gutierrez-Garcia, K., Aumiller, K., Dodge, R., Obadia, B., Deng, A., Agrawal, S., Yuan, X., Wolfe, R., Garud, N., & Ludington, W. B. (2024). A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics. Zenodo. https://doi.org/10.5281/zenodo.13115916(opens in new window) Or https://github.com/K-Gutierrez/LpColonizationIsland/(opens in new window)) Files related to Figure 3: Fig3-SpeciesTree-36Org-rooted.tree Fig3-SpeciesTree-36Org.fasta Files related to aSec tree: aSec-phylogeny-based-on-the-core-genes-aln-gb.fasta aSec-phylogeny-based-on-the-core-genes-MappingFile.txt aSec-phylogeny-based-on-the-core-genes-rooted.tree Files related to dN/dS analysis: Cluster1-pal2nal.fasta Cluster1-aBSREL.json Cluster2-pal2nal.fasta Cluster2-aBSREL.json Cluster3-pal2nal.fasta Cluster3-aBSREL.json Files for the core genome tree: Phylogeny_of_colonization_island-containing_strains-MappingFile.txt Phylogeny_of_colonization_island-containing_strains.fasta Phylogeny_of_colonization_island-containing_strains.tree Files to perform the Co-phylogenetic analysis aSecTree1-rooted.tree aSecTree1.fasta SpeciesTree1-rooted.tree SpeciesTree1.fasta aSecTree2-rooted.tree aSecTree2.fasta SpeciesTree2-rooted.tree SpeciesTree2.fasta aSecTree3-rooted.tree aSecTree3.fasta SpeciesTree3-rooted.tree SpeciesTree3.fasta aSecTree4-rooted.tree aSecTree4.fasta SpeciesTree4-rooted.tree SpeciesTree4.fasta Funding National Science Foundation, Award: IOS 2032985 National Science Foundation, Award: IOS 2144342 National Institutes of Health, Award: R21AI173779 NIH Office of the Director, Award: DP5OD017851 National Institute of Diabetes and Digestive and Kidney Diseases, Award: R01DK128454 Carnegie Institution of Washington