File conversion scripts for DNA sequence data
All the scripts require Python 3
Help Menus:
./<script> -h
loci2fasta - converts a .loci file from pyRAD to a separate FASTA file for each locus
loci2phylip - does the same, except it creates a PHYLIP file for each locus
phylip2fasta - converts a PHYLIP file to a single FASTA file
phylip2svdq - converts PHYLIP file to NEXUS format with a taxpartition for use with SVDquartets
multifasta2clades - converts directory of FASTA files to CLADES format
phylip2onehotsnps - converts PHYLIP file to one-hot SNP format for input to VAE machine learning species delimitation.
vcf2bgc - converts ipyrad VCF file to BGC (Bayesian Genomic Cline) genotype uncertainty format. Currently only works with 3 populations. Also writes locinames to $prefix_loci.txt