Creates a skyline style plot from data on a csv_file. This csv file should be compliant with the one generated by Tracer and is parsed by par

Filters the columns from a structure file based on the subset tuple.

Converts VCF file into Nexus binary format to SNAPP. Ignores non-biallelic SNPs.

Converts a vcf file into treemix format.

Determines the SNPs and chromosome overlap between two vcf storage objects

Parses a VCF file and returns a dict with loci names and a sortd list with taxa names.

Parses a vcf file and returns TODO

Grabs a VCF file and a loci list and matches the SNP order number to that of the VCF. If they match, the "real" SNP name is retrieved.

Parses a VCF file and returns a sorted list with loci names

Parses a VCF file and returns a sorted list with loci names and a list with taxa names.

Parses the Weir and Cockerham FST output file

Write a Baypass inpt file based on the GESTE dict.

Writes the records into a SNP file format

Writes a alignment dictionary {taxon: seq} to a phylip file

Writes the variable sites of the VCF file directly to phylip format

Returns only fully segregated loci: Group1 is 100% AA, Aa or aa, and Group2 is 0% of that allele

Writter function to be used when a loci list is provided.

Standard fasta writter function. To be used when no loci list is provided.

This checks the coverage of each SNP in the VCF file according to the SAM files