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1. vcf_ref_extraction vcf_ref_extraction Public

   Extracts reference allele for each site SNP substitution site, concatenates the SNP ref alleles to new FASTA

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2. ascb-fels-RAxML ascb-fels-RAxML Public

   bash script for executing ascertainment bias correction and RAxML (ML trees, bootstrapping) for SNP PHYLIP files

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3. cophylogenetic cophylogenetic Public

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   ParaFit and PACo analyses

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4. transpose_DF transpose_DF Public

   Read file as pandas.DataFrame, transpose it, output result to new text file

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5. vcf_SNPgenotypes vcf_SNPgenotypes Public

   Get genotypes of SNP calls from a VCF file using bcftools, adjust formatting using sed/awk/grep

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6. genotypes2genind genotypes2genind Public

   R script for reading file of biallelic genotypes, formatting, and converting to genind object

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