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

<p>Supplementary data for &quot;Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)&quot;</p> <p>alignments: alignments used for BEAST (&quot;bayes&quot;) and PopArt (&quot;popart&quot;). The &quot;popart&quot; folder also has a traits file per each species.</p> <p>bayesian_plots: TSVs (&quot;tsv&quot;) and PDF files (&quot;ogs&quot;) generated by BEAST. The &quot;tsv&quot; folder also has the scripts for plotting the results in R.</p> <p>easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS.</p> <p>fineRADstructure: fineRADstructure input files and output PDF plots (&quot;plots&quot;) for <em>C. formosanus</em> ipyrad and Stacks (&quot;stacks&quot;) data.&nbsp;</p> <p>logs: logs for ipyrad, ModelTest, PGDspider, PopArt (&quot;popart&quot;) and Stacks (&quot;stacks&quot;). The &quot;popart&quot; folder also have the generated networks in a TXT file. The &quot;stacks&quot; folder also has ODS files for calculating the amount of loci per each M/n fixed value.</p> <p>snapclust: STR files used with R for snapclust. Scripts included.</p> <p>stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The <em>C. formosanus</em> folder (&quot;chordodes&quot;) also has scripts for R plotting.</p> <p>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 <em>C. formosanus</em>.</p> <p>&quot;acutogordius&quot; = <em>A. taiwanensis</em><br> &quot;chordodes&quot; = <em>C. formosanus</em><br> &quot;gordius&quot; = <em>G. chiashanus</em></p>