core-genome tree of 882 assembled genomes

Pantagruel (Lassalle et al., 2019) was used to infer a maximum-likelihood (ML) “core genome tree” from the concatenated alignments of 291 core-genome genes extracted from the 889 assembled V. cholerae genomes using the “-S” option and otherwise default parameters. The ML tree was computed from the resulting 37,170 polymorphic positions using RAxML v8.2.11 (model ASC_GTRGAMMAX using Stamatakis’ ascertainment bias correction; one starting parsimony tree; 200 rapid bootstraps for estimating branch supports). Seven genomes were removed from the tree as they were identified as contaminated genome assemblies based on the Pantagruel pangenome analysis, for a final total of 882 genomes, presented in the trees with the 'nocontam' tag in the file name.Core-genome gene families were selected as those resent in at least 884/889 genomes i.e. absent in maximum ~0.5% of the genomes; locus_tags of representative genes in genome assembly 33224_2#41 are listed with their predicted protein function in file 'pseudo-core-884-unicopy_families.representative_product.tab'. the full concatenated alignment is given in 'pseudo-core-884-unicopy_concat_cds_0-genomes_contextallyemen2019.aln.gz' the same alignment reduced to its SNP positions is given in 'pseudo-core-884-unicopy_concat_cds_0-genomes_contextallyemen2019.snp.aln.gz'