Supplementary data for the article: Lightella neohaematopini: A new lineage of highly reduced endosymbionts coevolving with chipmunk lice of the genus Neohaematopinus
Description
Alignments: 1. Phylogenetic matrix - concatenated matrix of 14 ortholog sequences (AA) extracted from representative set of available proteomes for each major lineage of Enterobacteriales (analyzed by PhyML, MrBayes and PhyloBayes) in a fasta format 2. Coevolutionary matrix (5 proteins) - concatenated matrix of 5 ortholog sequences (AA) extracted from 12 assemblies of L. neohaematopini (analyzed by PhyML and MrBayes) in a fasta format 3. Coevolutionary matrix (50 proteins) - concatenated matrix of 50 ortholog sequences (AA) extracted from 11 assemblies of L. neohaematopini (analyzed by PhyML) in a fasta format 4. Neisseriales matrix - concatenated matrix of 30 ortholog sequences (AA) extracted from representative set of available proteomes for Neisseriales (analyzed by PhyML and MrBayes) in a fasta format 5. Host matrices - individual matrices for 1,107 nuclear loci from Bell et al. 2021 (analyzed by IQ-TREE) in a fasta format Phylogenetic trees folder: Phylogenetic trees generated by PhyML, MrBayes and PhyloBayes in a newick format. KO numbers folder: KO numbers generated by BLAST KOALA server for corresponding genomes. Annotations folder: Annotations of the genome drafts for the five best assemblies in gbk format. Detailed description of used methods can be found in the Materials and Methods section.
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Steps to reproduce
Alignments: 1. Phylogenetic matrix - concatenated matrix of 14 ortholog sequences (AA) extracted from representative set of available proteomes for each major lineage of Enterobacteriales (analyzed by PhyML, MrBayes and PhyloBayes) in a fasta format 2. Coevolutionary matrix (5 proteins) - concatenated matrix of 5 ortholog sequences (AA) extracted from 12 assemblies of L. neohaematopini (analyzed by PhyML and MrBayes) in a fasta format 3. Coevolutionary matrix (50 proteins) - concatenated matrix of 50 ortholog sequences (AA) extracted from 11 assemblies of L. neohaematopini (analyzed by PhyML) in a fasta format 4. Neisseriales matrix - concatenated matrix of 30 ortholog sequences (AA) extracted from representative set of available proteomes for Neisseriales (analyzed by PhyML and MrBayes) in a fasta format 5. Host matrices - individual matrices for 1,107 nuclear loci from Bell et al. 2021 (analyzed by IQ-TREE) in a fasta format Phylogenetic trees folder: Phylogenetic trees generated by PhyML, MrBayes and PhyloBayes in a newick format. KO numbers folder: KO numbers generated by BLAST KOALA server for corresponding genomes. Annotations folder: Annotations of the genome drafts for the five best assemblies in gbk format. Detailed description of used methods can be found in the Materials and Methods section.