paratyphiA Files

# All folders except the examples/ contain scripts that are described the publication, as well as related manuals and detailed algorithms in the PDF files. Example files for the scripts above are in the examples/ foler. The command line to run the scripts on the examples are shown in the files "test_xxx.command" in each sub-folder. There are probably minor differences between different runs of RecHMM, DHMM and expandTree. 


# structure of the folders
DHMM/
	DHMM.documents.pdf
	DHMM_prepare.pl
	DHMM.R

ExpandTree/
	ExpandTree.documents.pdf
	ExpandTree.R

MUMmer_filter/
	mummer_aln_extract.pl
	MUMmer_filter.documents.pdf
	mummer_strict_filter.pl

RecHMM/
	RecHMM.documents.pdf
	RecHMM.R
	
examples/
# An alignment located between sites 600,001 and 700,000 in the reference genome (ATCC 9150). 
	DHMM_example/
		ParaA.region.fas
		ParaA.region.gg
		ParaA.region.mut
		ParaA.region.site
		ParaA.region.step1.stderr
		test_DHMM.command

# A simple comparison between two publically available genomes of Paratyphi A. 
	MUMmer_filter_example/
		CP000026.fna
		FM200053.example.delta
		FM200053.example.delta2
		FM200053.example.map
		FM200053.example.map.fas
		FM200053.fna
		test_MUMmer_filter.command

# One of the simulations generated by simMLST as described in the supplementary methods, with theta=200, Ru=50. 
	RecHMM_expandTree_example/
		sim.200.50.clonal
		sim.200.50.clonal.branchLabel
		sim.200.50.expandTree
		sim.200.50.local
		sim.200.50.model
		sim.200.50.region
		sim.200.50.snp
		sim.200.50.xmfa
		test_expandTree.command
		test_RecHMM.command