README for WRAP dataset 162247, http://wrap.warwick.ac.uk/162247/

Manuscript Title:
	EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

Authors:
	Achtman, Mark; University of Warwick Warwick Medical School
	Zhou, Zhemin; University of Warwick, Warwick Medical School
	Charlesworth, Jane; University of Warwick Warwick Medical School
	Baxter, Laura; University of Warwick, Bioinformatics Research Technology Platform

Accepted for publication by Phil Trans Roy Soc B, March 2022

The accepted manuscript is deposited on WRAP: http://wrap.warwick.ac.uk/164101/

The full set of deposited files is listed below:

Data Files:
	Cdiff.2021.HC5.cgMLST
	Cdiff.2021.HC5.cgMLST.alleles.fasta.gz
	Cdiff.2021.HC5.wgMLST_detail.presence.gz
	EscherichiaReps.cgMLST.alleles.fasta.gz
	EscherichiaReps.cgMLST
	EscherichiaReps.wgMLST_detail.presence.gz
	Salmonella.2021.HC5_lg4_OR_HC400.cgMLST
	Salmonella.2021.HC5_lg4_OR_HC400.cgMLST.alleles.fasta.gz
	Salmonella.2021.HC5_lg4_OR_HC400.wgMLST_detail.presence.gz
	Streptococcus.2021.HC5_lg4_OR_HC50.cgMLST
	Streptococcus.2021.HC5_lg4_OR_HC50.cgMLST.alleles.fasta.gz
	Streptococcus.2021.HC5_lg4_OR_HC50.wgMLST_detail.presence.gz
	Vibrio.2021.HC5.cgMLST
	Vibrio.2021.HC5.cgMLST.alleles.fasta.gz
	Vibrio.2021.HC5.wgMLST_detail.presence.gz
	Yersinia.2021.HC5.cgMLST
	Yersinia.2021.HC5.cgMLST.alleles.fasta.gz
	Yersinia.2021.HC5.wgMLST_detail.presence.gz


Trees were computed using the data files, as according to materials and methods:
	*.alleles.fasta.gz files contain the nucleotide sequences for all alleles in the cgMLST scheme for that genus
	*.cgMLST is the matrix of cgMLST allelic profiles used to build the Maximum Likelihood super-tree from SNPs among core genes
		rows = Strain ID
		columns = Gene ID
		values = allelic number
	*.wgMLST_detail.presence.gz is the matrix used to build the Maximum Likelihood super-tree from wgMLST sequence presence/absence
		rows = Strain ID
		columns = Gene ID
		values = 1/0 denotes presence/absence 

The cgMLST trees are shown in the following figures:
	Fig 1, Salmonella
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53257
	Fig 2, Escherichia
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=52101
	Fig 3, Clostridioides
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53253
	Fig S1, Yersinia
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53269
	Fig S2, Vibrio
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53265
	Fig S3, Streptococcus
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53261

The wgMLST presence/absence trees are linked in the figure legends as follows:
	Fig 1, Salmonella:
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53258
	Fig 2, Escherichia:
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=71125
	Fig 3, Clostridioides
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53254
	Fig S1, Yersinia
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53270
	Fig S2, Vibrio
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53266
	Fig S3, Streptococcus
		https://enterobase.warwick.ac.uk/ms_tree?tree_id=53262

Supplementary Materials which accompany the accepted manuscript are also included:
	SupplementalMaterialOverview.docx
	SupplementalText.pdf
	Table_S1.xlsx
	Table_S2.xlsx
	Table_S3.xlsx
	Table_S4.pdf
	Table_S5.xlsx
	Table_S6.xlsx
	Table_S7.xlsx
	Table_S8.xlsx
	Table_S9.xlsx
	Table_S10.xlsx
	Fig_S1.pdf
	Fig_S5.pdf
	Fig_S4.pdf
	Fig_S3.pdf
	Fig_S2.pdf