Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"

Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"

alignments: alignments used for BEAST ("bayes") and PopArt ("popart"). The "popart" folder also has a traits file per each species.

bayesian_plots: TSVs ("tsv") and PDF files ("ogs") generated by BEAST. The "tsv" folder also has the scripts for plotting the results in R.

easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS.

fineRADstructure: fineRADstructure input files and output PDF plots ("plots") for C. formosanus ipyrad and Stacks ("stacks") data. 

logs: logs for ipyrad, ModelTest, PGDspider, PopArt ("popart") and Stacks ("stacks"). The "popart" folder also have the generated networks in a TXT file. The "stacks" folder also has ODS files for calculating the amount of loci per each M/n fixed value.

snapclust: STR files used with R for snapclust. Scripts included.

stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The C. formosanus folder ("chordodes") also has scripts for R plotting.

vcfs: VCF and HDF5 files used in this study. Also scripts for filtering/converting data and plotting the PCA with ipyrad (activate python first!) for C. formosanus.

"acutogordius" = A. taiwanensis
"chordodes" = C. formosanus
"gordius" = G. chiashanus