Supplementary dataset for Quinones in Pseudomonadota, Dataset S4: Phylogenies and alignments

ReferenceThis is part of the Supplementary material of the study "A dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota", submitted to <i>The ISME Journal</i>.Authors' list: Sophie-Carole Chobert, Morgane Roger-Margueritat, Laura Flandrin, Safa Berraies, Christopher T. Lefèvre, Ludovic Pelosi, Ivan Junier, Nelle Varoquaux, Fabien Pierrel, Sophie S. AbbyDescriptionThis folder contains the alignments (original and filtered) and the phylogenetic trees.The folder architecture is as follow:<pre><pre>.<br>├── MenA<br>│ ├── MenA.faa-aln<br>│ ├── MenA_filtered.faa<br>│ └── MenA_filtered.treefile<br>├── MenB<br>│ ├── MenB.faa-aln<br>│ └── ...<br>├── ...<br>├── species_tree<br>│ ├── gamma_tree_aln<br>│ │ ├── COG0012.faa-aln<br>│ │ ├── COG0016.faa-aln<br>│ │ └── ...<br>└── UbiV<br> ├── UbiV.faa-aln<br> ├── UbiV_filered.treefile<br> ├── UbiV_filtered.faa<br> └── UbiV_rooted<br> ├── UbiV_U32_outgroup.faa-aln<br> ├── UbiV_U32_outgroup_filtered.faa<br> └── UbiV_U32_outgroup_filtered.treefile<br></pre></pre>Within each sub-folder are presented the filtered (filtered.faa) and unfiltered alignments (.faa-aln), as well as the phylogenetic trees obtained from the filtered alignments.The different files and how they were obtained are described in the Materials &amp; Methods section of the article.