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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

    Python

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

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

    Shell

  3. cophylogenetic cophylogenetic Public

    Forked from alixmatthews/cophylogenetic

    ParaFit and PACo analyses

    R

  4. transpose_DF transpose_DF Public

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

    Python

  5. vcf_SNPgenotypes vcf_SNPgenotypes Public

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

    Shell 1

  6. genotypes2genind genotypes2genind Public

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

    R