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).