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