Hühn et al., llddRADseq
Description
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