Phylogenetic placement of Pseudoneobacillus sp. JJ-79 within Bacillaceae family

This repository contains phylogenetic trees (and associated sequence data) inferred to assess the phylogenetic placement of <em>Pseudoneobacillus</em> sp. JJ-79 (tax id: 2880968) within 512 type strains representative of the <em>Bacillaceae</em> family. Three phylogenetic trees were inferred, each from a multi-gene dataset (as described at http://giphy.pasteur.fr/PhyloM/Bacillaceae): <strong>BM1</strong>: 87 conserved genes (Wu et al. 2013, Gupta et al. 2020, Patel and Gupta 2020), <strong>BM2</strong>: major subunits of the DNA Gyrase (<em>GyrA</em> and <em>GyrB</em>) and RNA polymerase (<em>RpoB</em> and <em>RpoC</em>; Patel and Gupta 2020), <strong>BM3</strong>: DNA helicase II and DNA polymerase I (<em>UvrD</em> and <em>PolA</em>; Patel and Gupta 2020). For each dataset <strong>BM<em>i</em></strong> (<em>i</em> = 1, 2, 3), four files are available: <code>BM<em>i</em>.faa </code> the concatenation of the filtered multiple sequence alignments (FASTA format); <code>BM<em>i</em>.nwk </code> a maximum likelihood phylogenetic tree inferred from <code>BM<em>i</em>.faa</code> (NEWICK format); <code>BM<em>i</em>.pdf </code> a graphical representation of the phylogenetic tree (PDF format); <code>BM<em>i</em>.seq.tar.gz </code> for each gene name, three FASTA files are available in this tar.gz archive: initial sequences (*.faa), multiple sequence alignment (*.afa), filtered multiple sequence alignment (*.ffa). In complement, the multiple sequence alignments of 11 loci are available in the archive <code>CSI.tar.gz</code>. Each of these loci shares a conservative signature indel (CSI) that is indicative of the closely related <em>Neobacillus</em> genus (see Table 4 —Niacini clade— in Patel and Gupta 2020): <em>fliF</em>, flagellar M-ring protein FliF; <em>rplX</em>, 50S ribosomal protein L24; <em>prmA</em>, 50S ribosomal protein L11 methyltransferase; <em>hisH</em>, imidazole glycerol phosphate synthase subunit HisH; <em>hisZ</em>, ATP phosphoribosyltransferase regulatory subunit; <em>mdoB</em>, LTA synthase family protein; <em>topA</em>, type I DNA topoisomerase; <em>pncB</em>, nicotinate phosphoribosyltransferase; <em>thiD</em>, phosphomethylpyrimidine kinase; <em>recJ</em>, single-stranded-DNA-specific exonuclease RecJ; <em>dxs</em>, 1-deoxy-D-xylulose-5-phosphate synthase.