### Conversion of variants from vcf file into fasta alignment and plotting a tree


### Conversion of vcf to fasta

writeVcfToFasta.py
'''
This script reads vcf with SNPs, and a file with population info,
converts genotypes to fasta alignment and filters positions with any missing data.
'''

USAGE:
    
python writeVcfToFasta.py

requirements:
SNP_samtools_mtDNA_variants_filter2_miss.recode.vcf
Species_distinction_PCA.txt
output:
SNP_samtools_mtDNA_noMD.phy




### Plotting tree from newick format

USAGE:

python drawTree.py

requirements:
RAxML_bipartitions_50coll.mtDNA		# tree in newick format
Species_distinction_PCA.txt		# Population info

output:
mtDNATree.pdf