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).