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ascb-fels-raxml

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

complicated_string_edits

Python scripts for making text edits in non-standardized file formats

convertczi

cophylogenetic

ParaFit and PACo analyses

ecosystem

Experimental simulated ecosystem using Processing (v3.5)

edit_fasta_headers

Python script to find & replace specified strings from FASTA header lines

genotypes2genind

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

msa_concat_genes

A script for concatenating genes in a multiple sequence alignment (MSA)

transpose_df

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

vcf_ref_extraction

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

vcf_snpgenotypes

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

vcfsnpgeno_to_genind

Bash script to make a table of genotypes based on SNPs from a VCF file using bcftools, format in using Bash and Python, and convert to a genind object in R