vcf_4fold_degenerate_dating_haploid

A script for dating the branching points of different organisms, using the 4fold degenerate dating method, analysing the mutations in the protein-coding sequences.

Mutation Rate

The mutation rate used is the mutation Rate of A.thaliana.
1.3*(10**-8) Substitutions/year

To adapt the parsing of gene-name search "parsing" in the script.
Use option "-h" or "--help" for further information.

MANUAL

vcf_4fold_degenerate_dating.py        
		
	--transcript <maker.fa>        
	--gff <maker.gff>        
	--vcf <vcf_file>        
		
	--cores <int> *specify nr of threads, default=cpu_count-1*        
	--mincov <int> *opt, one integer, multiple can be given for each sample comma separated in sample order of vcf columns* 
	--single *opt, consider only single variants(default!)*        
	--multi *opt, consider only multi variants*        
	--all *opt, consider single and multi variants*        
	--save_filtered_vcfs *opt,safe vcf with valid ffdg snp's for each sample pair*
	--ffdg_pos_output *opt,safe ffdg positions on contigs*        
		
	*search for filtering (default: mindiff >=1 & ratio <=0.05)*        
	*pre-filter vcf with vcftools recommended, only snp's*        
	*for parsing adaptions search'parsing' in script*        
	*in multivariant mode each variant is seen as a own snp*        
	*change mutation rate in script (search 'substitution' in script)*        
	default is A.thaliana 1.3*(10**-8)(mut/(bp*year))        
		
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