BEAST xml file for divergence time analysis

This is the BEAST xml file used to run the divergence time analysis

Supermatrix alignment

Supermatrix alignment of 7 genes as used for phylogenetic and divergence time analysis. Please see readme file for details of gene partitions

Per individual read depth for all RAD markers with greater than or equal to 20x coverage

RAW reads for each individual were mapped back to the catalogue of RAD marker consensus sequences using Stampy. SAMtools was then used to generate a pileup from which read depth was extracted. RAD markers with less than 20x coverage were considered absent

Per individual haplotypes for all RAD markers

Haplotypes produced by Stacks for all assembled RAD markers

All_loci_aligned_SM

7 gene supermatrix alignment used for phylogenetic analysis in fasta format. See readme file for partition information

Consensus sequences for all RAD markers

Fasta file containing consensus sequences for all RAD markers de novo assembled by stacks