Hühn et al., llddRADseq

Appendix 1: Detailed lab protocol, DNA clean-up and Bioanalyzer electropherograms
Figure S1: Maximum likelihood phylogeny of the RAxML long dataset
Figure S2: Maximum likelihood phylogeny of the RAxML short dataset
Table S1: Detailed material table and flow cytometry
Table S2: Modified barcode and common adapter
Table S3: Pipetting scheme for digest and ligation
Table S4: Sequencing output and FastQC reports
Table S5: Assembly output of the ISC and BSC CT optimization
Table S6: ASTRAL filtering overview
Supplementary data 1: Nexus alignments of the original and trimmed optimized de novo assembly
Supplementary data 2: ipyrad assembly output files of reference-based vs. de novo assembly comparison
Supplementary data 3: Tree files of the RAxML long and short dataset
Supplementary data 4: Original and trimmed locus files of the optimized de novo assembly, ASTRAL tree files containing the species trees of the minimum samples and minimum variability assemblies and RAxML tree files containing locus trees
Supplementary data 5: Nexus alignments and tree files of the SVDquartets datasets